TITLE File : 56a6@CARBO_carbo.mtb Force field : 56A6@CARBO (condensed-phase simulations) Reference : Hansen & Hunenberger. J. Comput. Chem. 2011, 32, 998-1032 File content : Molecular topology building blocks (carbohydrates) Format : GROMOS11 Initial file : HALVOR 56A6@CARBO --- PHH, HSH Zuerich, Oct. 2011 Time stamp : PHH, Sat Jul 28 20:53:32 CEST 2012 Residue names : according to new GROMOS11 nomenclature, based on the residue alphabet defined in DeMarco & Wood, Glycobiology 2008, 18, 426-440 Remark : ***warning*** this file is an auxiliary mtb file - since Nov 2011, these files no longer contain blocks that were redundant with those of the corresponding main mtb file. As a result, make_top must always be called with inclusion of the main mtb file in addition to possible auxiliary ones. Remark : ******************************************************************************** **** topologies must be built using a make_top version of June 2012 or later *** ******************************************************************************** Reason: make_top must recognize negative dihedral-angle type codes in patches, which indicate that, if present, an existing dihedral angle with the given type code must be removed (used in HO2C, HO3C, HO4C, HO6C and C1OH patches for carbohydrates to delete existing T2 or T6/T7 dihedrals assuming a OC instead of a OH) Remark : Change from 53A(B)6 involves a reparametrization of the carbohydrates. There are three new atom types (Or, CH0r, CH1r) and the parameters of an existing atom type (CH2r) are slightly altered. Besides the latter (slight) change, the force field can be used with 53A(B)6 for other biomolecules Remark : This file differs significantly from the 53A6 file (reparametrization of the cabbohydrates) Remark : PHH, Nov 2011 - all isomers & linkages of simple hexopyranoses + some uronates (177 residues, generated by script) - includes *many* comments, including extensive information just below the TITLE block Remark : There is no B force-field version for this set (use 54B7 instead) Remark : Versions beyond 54A(B)7 [including 54C(D)7, 53A(B)6@OXY, 56A(B)6@CARBO] are only available in GROMOS11 format (i.e. all after the release of May 2011) Remark : PHH, Nov 2011 - finalized GROMOS11 files for local usage only (no web distribution yet) Modifications : [list below changes after Nov 2011 - with initials, location and date - and update time stamp] PHH, 09.11.2011: Renamed 56A6_CARBO to 56A6@CARBO (@: force-field variant; _: auxiliary mtb). PHH, 09.11.2011: Reintroduced a FORCEFIELD block in all GROMOS11 files. PHH, 09.11.2011: Removed all MTBUILDBLSOLVENT blocks from all auxiliary mtb files (now only included in the main mtb file). As a result, make_top must now always be called with inclusion of the main mtb file (in addition to the possible auxiliary ones). PHH, 22.11.2011: Fixed the trehalo-uronate patches (they were corrupted due to a mistake in the generating script) PHH, 22.11.2011: Finalized the #@BLOCKTYPE comments in mtb files listing file name, residue code (BLK=...), function (SOL,INI,TER,SVT), type (TYPE=APEP,BPEP,DNUC,RNUC, HEXP,HEXU,MOLE), and full name (NAME=...): intended for later use by make_top. PHH, 26.06.2012: Introduced MAKETOPVERSION blocks in all GROMOS11 files PHH, 12.07.2012: Removed all LINKEXCLUSIONS and PHYSICALCONSTANTS blocks from GROMOS11 auxiliary mtb files (now only included in the main mtb file). As a result (and also since MTBUILBLSOLVENT is only to be found there), make_top must always be called with inclusion of the main mtb file (in addition to the possible auxiliary ones). END FORCEFIELD 56A6@CARBO END MAKETOPVERSION 1.1 END # # # Force-field construction: # ========================= # # The parameter set 56A6@CARBO is the successor of 45A4 # (nearly identical to 56A5 and 56A6 in the context of carbohydrates), # and also encompass a general description carbohydrates, including # residues for all simple (i.e. unfunctionalized) aldohexopyranoses, # as well as aldohexouronates. # # The calibration and parameters of this set in the # context of carbohydrates are documented in # # Hansen, H.S. & Hunenberger, P.H. # A reoptimized GROMOS force field for hexopyranose-based carbohydrates # accounting for the relative free energies of ring conformers, anomers, # epimers, hydroxymethyl rotamers and glycosidic linkage conformers. # # for aldohexopyranoses. # # Note the small erratum entries in http://www.csms.ethz.ch/research/typos # [84] Hansen & Hunenberger, J. Comput. Chem. 32 998 (2011) # - Table 2, last line, improper dihedrals for beta-Glc: C2-C1-O1-C2 must # be changed to C2-C3-C1-O2, and C5-O5-C6-C4 to C5-C4-O5-C6 # - Table 3, entry C6: 45A4/53A6 as well as 56ACARBO atom types are # incorrect and should both be CH2 # - Tables 3 and 4: the atom type HO actually does not exist in # GROMOS - in the force-field files, it is listed simply as H # - Table 6, entry T1, dihedrals for beta-Glc: O5-C5-C6-O6 should rather # be defined as C4-C5-C6-O6 to follow the the IUPAC definition of omega; # this does not matter much in practice since T1 is a 3-fold term # (the definition C4-C5-C6-O6 is adopted in the current GROMOS # force-field files) # - Table 6, entry T3, dihedrals for beta-Glc: C5-C4-O4-H4 should # rather be defined as C3-C4-O4-H4 to follow the systematism of # the other dihedrals and the IUPAC definition of chi4; this does not # matter much in practice since T3 is a 3-fold term (the definition # C3-C4-O4-H4 is adopted in the current GROMOS force-field files) # # The adjutments for for aldohexouronates remain close to those of # 45A4, their principles being described in # # Peric, L., Pereira, C.S., Perez, S. & Hunenberger, P.H. # Conformation, dynamics and ion-binding properties of # single-chain polyuronates: a molecular dynamics study # Mol. Simul., 34, 421-446 (2008) # # This set adheres to well-defined build-up rules, that are # specified in details in the above reference. # # Some additional rules are specified here that complements this # information. Note that these rules are designed for unambiguous # choices in the case of the common sugars, not of all possible # compounds that are within the scope of the force field. # # A) Unique definition of improper dihedral angles involving exocyclic groups: # # In 56A6@CARBO, an improper dihedral angle term involving an exocyclic group # is uniquely defined as Xr-Yr-Zr-E with a reference value of +35 deg, where Xr # is the chiral center, Yr and Zr its ring neighbors, and E the exocyclic # substituent. Note that depending on the atom numbering, this angle may # also be found as E-Zr-Yr-Xr in the topology file (which of the two is listed # is determined by the requirement that the sequence number of the 2nd atom # is lower than that of the 3rd atom). # # The chirality can be inverted by swapping the order of Yr and Zr. # # Thus: the chiral center is the 1st or 4th atom in sequence - the one neighbor to # the three other ones - while the exocyclic atom is the other one, i.e. the 4th # or 1st atom. # # This differs from earlier force field-versions where the chiral center was also # the 1st or 4th atom in sequence - the one neighbor to the three other ones - but # the exocyclic atom was the 2nd or 3rd atom. # # B) Unique definition of dihedral angles: # # The dihedral angles of types T1, T2 and T3 are to be applied only # once around each central bond (see footnote a in Table 6). All other # torsional terms are to be applied for all occurrences, so there is # no choice to make there. # # For term T1, there is no ambiguity in the ring (i.e. only one choice), # except C3-C4-C5-O5 (which is taken rather than C3-C4-C5-C6), # i.e. we give priority to atoms in the ring over C6. # For the hydroxymethyl, we take omega as defined by IUPAC # (C4-C5-C6-O6) and not omega-tilde (O5-C5-C6-O6). # # For the term T2, there is no ambiguity in the ring (i.e. only one # choice), except C4-C5-O5-C1 (which is taken rather than C6-C5-O5-C1), # i.e. we give priority to atoms in the ring over C6. # This term is also used for the phi dihedral angle (methylated or # glycosylated sugar) and for the psi dihedral angle # (connection to a previous residue). In both cases, we use # phi and psi as defined by IUPAC. # # For term T3, which concerns exocyclic hydroxyl groups, the term # is applied to the chi_n dihedral angle (n=2,3,4,6) or to the phi # dihedral angle (free lactol group), as defined by IUPAC. # # We can now summarize the rules very simply for the choices in T1-T3, # namely: (1) give priority to atoms in the ring; (2) follow IUPAC # definitions for chi_n, phi and psi # # Note the use of special rules for the uronates (see rule F below) # # C) Mapping of footnotes (e)-(h) in Table 6 # # These footnotes are correct but may appear a bit confusing at first sight. # Here is a reformulated rule: # # If there is an improper dihedral CH*r-Xr-Xr'-O (or O-Xr'-Xr-CH*r) in the # topology (see point A above) and O has a substituent Cx, then: # # T6 is applied to Xr-CH*r-O-Cx and T7 is applied to Xr'-CH*r-O-Cx # # In simple hexopyranoses, a T6/T7 pair applies to the phi/phi-tilde dihedral # pair of an O1-substituted residue, and another T6/T7 pair applies to the dihedral # psi/psi-tilde pair of an O2-, O3-, or O4-substituted residue. # # If there is an improper dihedral CH*r-Xr-Xr'-CH* (or CH*-Xr'-Xr-CH*r) in the # topology (see point A above) and CH* has a substituent Cx, then: # # T8 is applied to Xr-CH*r-CH*-Cx and T9 is applied to Xr'-CH*r-CH*-Cx # # In simple hexopyranoses, no T8/T9 pair is used # # If there is an improper dihedral CH*r-Xr-Xr'-CH* (or CH*-Xr'-Xr-CH*r) in the # topology (see point A above) and CH* has a substituent O, then: # # T9 is applied to Xr-CH*r-CH*-O and T10 is applied to Xr'-CH*r-CH*-O # # In simple hexopyranoses, a T10/T11 pair applies to the omega/omega-tilde # dihedral pair; D-series: T10 for omega and T11 for omega-tilde; # L-series: opposite. # # D) The atom sequence order in the residues was altered relative to the earlier # force-field files # # OLD NEW # # 2-linked C2-C4-C3-C6(-C5-O5-C1) C2-C3-C4-C6(-C5-O5-C1) # 3-linked C3-C4-C2-C6(-C5-O5-C1) C3-C2-C4-C6(-C5-O5-C1) # 4-linked C4-C3-C2-C6(-C5-O5-C1) C4-C2-C3-C6(-C5-O5-C1) # 6-linked C6-C3-C2-C4(-C5-O5-C1) C6-C2-C3-C4(-C5-O5-C1) # # E) The inclusion scheme for the connecting bonds was altered relative to the earlier # force-field files # # Previously, a residue would include definition of the two tail bonds C1-O1 # and O1-C#_next. Now, a residue includes definition of the head bond # C1_prev-O# and of the tail bond C1-O1. # # In other words, O1-C#_next is no longer defined in the residue, while # C1_prev-O# is now defined. This also has some influence on the bonds # included in the patches. # # F) Special dihedral rules for the uronates: # # For the CH2OH in an hexopyranose, we would have terms of type # T1 (omega), T3 (chi_6) + T10/T11 and T12. We could think of # keeping T1 (only once), killing T3, keeping T10/11 (one for O61 # and one for O62), and keeping T12 (one for O61 and one for O62). # # I am not sure this mixture makes any sense for the COO- group in # uronates. So, for now, I killed all of them and simply # use the same gamma potential as in 45A4, namely a single # type 40. Unlike for the previous ff version, however, # I apply it on C4-C5-C6-O61 instead of O5-C5-C6-O61. # This is a 6-fold term, so it does not matter. But it is # more consistent to define gamma, the analog of omega for a # carboxylate group. # # The B-version of the force field are also available for (approximate) # simulations in vacuum. The only change between A- and B-versions # is a a neutralization of the carboxylate charge in uronate # residues. # # Naming convention for carbohydrate residues : # ============================================= # # First letter (stereochemistry): # # N: D-allose n: L-allose # E: D-altrose e: L-altrose # G: D-glucose g: L-glucose # M: D-mannose m: L-mannose # K: D-gulose k: L-gulose # I: D-idose i: L-idose # L: D-galactose l: L-galactose # T: D-talose t: L-talose # # Second letter (anomery): # A: alpha # B: beta # # Third letter (connectivity): # 2: at 2-OH # 3: at 3-OH # 4: at 4-OH # 6: at 6-OH # # Fourth letter (functionalization): # P hexopyranose # U uronate # # -> only the four most relevant residues, # GB4U, LA4U, MB4U, kA4U (glucuronates, alginates, # pectinates) and iA4U (dermatan sulfate) # are available at present for the uronates # # In the following, we use the generic notations: # @ : stereochemistry [N,E,G,M,K,I,L,T,n,e,g,m,k,i,l,t] # * : anomery [A,B] # # : connectivity [1,2,3,4,6] # # Patches: # # HO#C : initial HO#-O#-C#- group (# not equal to 1; for patching a # residue of type @*#) # C1OH : terminal -C1-O1-HO1 (HO1=hydrogen) # C1OC : terminal -C1-O1-CM (CM=methyl) # C@*P : terminal -C1-O1-C1'-... (trehalo 1->1' linkage with additional # terminal residue of type @*) # # Residue and patch construction: # =============================== # # The residues are assembled in the direction # # non-reducing end -> reducing end # # (for a chain terminated by a trehalo linkage, # leading to a formally non-reducing oligosaccharide, # the trehalo linkage is also at the chain end) # # The (linear) sequence is defined as # # initial patch - [residues] - terminal patch # # For each residue @*#P: # (prev -> previous residue or initial patch; # next -> next residue or terminal patch) # # - the C1_prev-O# bond is *not* defined in the residue (but in the prev) # - the O#-C# bond *is* defined in the residue (not in the prev) # - the C1_prev-O#-C# angle is *not* defined in the residue (but in the prev) # - the O5_prev-C1_prev-O#-C# dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # - the C1_prev-O#-C#-C# dihedral (prev glycosidic psi dihedral) *is* defined in the residue # - the exclusions of C1_prev and O# *are* defined in the residue # # and # # - the O1-C1 bond *is* defined in the residue (not in the next) # - the O1-C#_next bonds is *not* defined in the residue (but in the next) # - the C1-O1-C#_next angle *is* defined in the residue # - the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # - the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # - the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # # For each initial patches C#OH: # # - the HO#-O# bond *is* defined in the patch # - the O#-C# bonds is *not* defined in the patch (but in the residue) # - the HO#-O#-C# angle *is* defined in the patch # - the HO#-O#-C#-C(#-1) (chi# dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO# and O# *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C# are *not* defined in the patch (but in the residue) # # For the terminal patch C1OH: # # - the C1-O1 bond is *not* defined in the patch (but in the residue) # - the O1-H1 bond *is* defined in the patch (not in the residue) # - the C1-O1-H1 angle *is* defined in the patch as a replacement # - the O5-C1-O1-H1 dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of O5, C1, O1 and HO1 *are* defined in the patch (replace those defined in the residue, # which are identical up to one exception: a special 1-4 exclusion (ring oxygen O5 to lactol hydrogen HO1 # specific to this force-field is introduced) # # For the terminal patch C1OC: # # - the C1-O1 bond is *not* defined in the patch (but in the residue) # - the O1-CM bond *is* defined in the patch (not in the residue) # - the C1-O1-CM angle is *not* defined in the patch (but in the residue) # - the O5-C1-O1-CM dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of C1, O1 and CM *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # For the terminal patches C@*P: # # - the C1-O1 bond is *not* defined in the patch (but in the residue) # - the O1-CM bond *is* defined in the patch (not in the residue) # - the C1-O1-CM angle is *not* defined in the patch (but in the residue) # - the O5-C1-O1-CM dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of C1, O1 and CM *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # The above slightly differs from 45A4: # # Previously, a residue would include definition of the two tail bonds C1-O1 # and O1-C#_next. Now, a residue includes definition of the head bond # C1_prev-O# and of the tail bond C1-O1. # # In other words, O1-C#_next is no longer defined in the residue, while # C1_prev-O# is now defined. This also has some influence on the bonds # included in the patches. # # Residue and patch assembly: # =========================== # # The residues are assembled in the direction # # non-reducing end -> reducing end # # (for a chain terminated by a trehalo linkage, # leading to a formally non-reducing oligosaccharide, # the trehalo linkage is also at the chain end) # # The (linear) sequence is defined as # # initial patch - [residues] - terminal patch # # Examples: # # beta-D-glucopyranose: HO4C GB4P C1OH # alpha-D-glucopyranose: HO4C GA4P C1OH # Me-beta-D-glucopyranoside: HO4C GB4P C1OC # Me-alpha-D-glucopyranoside: HO4C GA4P C1OC # beta-cellobiose: HO4C GB4P GB4P C1OH # beta-maltose: HO4C GA4P GB4P C1OH # trehalose (alpha,alpha): HO4C GA4P CGAP # isotrehalose (alpha,beta): HO4C GA4P CGBP [or HO4C GB4P CGAP] # neotrehalose (beta,beta): HO4C GB4P CGBP # # Note that the first residue can be initiated in different # ways. For example, HO2C GB2P GB4P C1OH is also beta-cellobiose. # MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NA2P SOL TYPE HEXP(2:1) NAME -2-D-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME NA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NA3P SOL TYPE HEXP(3:1) NAME -3-D-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME NA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NA4P SOL TYPE HEXP(4:1) NAME -4-D-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME NA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NA6P SOL TYPE HEXP(6:1) NAME -6-D-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME NA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CNAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(NA), i.e. trehalo-linked residue NA # building block (residue, nucleotide, etc.) # RNME CNAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NB2P SOL TYPE HEXP(2:1) NAME -2-D-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME NB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NB3P SOL TYPE HEXP(3:1) NAME -3-D-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME NB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NB4P SOL TYPE HEXP(4:1) NAME -4-D-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME NB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK NB6P SOL TYPE HEXP(6:1) NAME -6-D-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME NB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CNBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(NB), i.e. trehalo-linked residue NB # building block (residue, nucleotide, etc.) # RNME CNBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EA2P SOL TYPE HEXP(2:1) NAME -2-D-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME EA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EA3P SOL TYPE HEXP(3:1) NAME -3-D-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME EA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EA4P SOL TYPE HEXP(4:1) NAME -4-D-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME EA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EA6P SOL TYPE HEXP(6:1) NAME -6-D-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME EA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CEAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(EA), i.e. trehalo-linked residue EA # building block (residue, nucleotide, etc.) # RNME CEAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EB2P SOL TYPE HEXP(2:1) NAME -2-D-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME EB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EB3P SOL TYPE HEXP(3:1) NAME -3-D-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME EB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EB4P SOL TYPE HEXP(4:1) NAME -4-D-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME EB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK EB6P SOL TYPE HEXP(6:1) NAME -6-D-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME EB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CEBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(EB), i.e. trehalo-linked residue EB # building block (residue, nucleotide, etc.) # RNME CEBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GA2P SOL TYPE HEXP(2:1) NAME -2-D-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME GA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GA3P SOL TYPE HEXP(3:1) NAME -3-D-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME GA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GA4P SOL TYPE HEXP(4:1) NAME -4-D-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME GA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GA6P SOL TYPE HEXP(6:1) NAME -6-D-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME GA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CGAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(GA), i.e. trehalo-linked residue GA # building block (residue, nucleotide, etc.) # RNME CGAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GB2P SOL TYPE HEXP(2:1) NAME -2-D-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME GB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GB3P SOL TYPE HEXP(3:1) NAME -3-D-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME GB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GB4P SOL TYPE HEXP(4:1) NAME -4-D-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME GB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GB6P SOL TYPE HEXP(6:1) NAME -6-D-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME GB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CGBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(GB), i.e. trehalo-linked residue GB # building block (residue, nucleotide, etc.) # RNME CGBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MA2P SOL TYPE HEXP(2:1) NAME -2-D-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME MA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MA3P SOL TYPE HEXP(3:1) NAME -3-D-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME MA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MA4P SOL TYPE HEXP(4:1) NAME -4-D-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME MA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MA6P SOL TYPE HEXP(6:1) NAME -6-D-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME MA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CMAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(MA), i.e. trehalo-linked residue MA # building block (residue, nucleotide, etc.) # RNME CMAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MB2P SOL TYPE HEXP(2:1) NAME -2-D-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME MB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MB3P SOL TYPE HEXP(3:1) NAME -3-D-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME MB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MB4P SOL TYPE HEXP(4:1) NAME -4-D-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME MB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MB6P SOL TYPE HEXP(6:1) NAME -6-D-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME MB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CMBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(MB), i.e. trehalo-linked residue MB # building block (residue, nucleotide, etc.) # RNME CMBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KA2P SOL TYPE HEXP(2:1) NAME -2-D-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME KA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KA3P SOL TYPE HEXP(3:1) NAME -3-D-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME KA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KA4P SOL TYPE HEXP(4:1) NAME -4-D-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME KA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KA6P SOL TYPE HEXP(6:1) NAME -6-D-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME KA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CKAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(KA), i.e. trehalo-linked residue KA # building block (residue, nucleotide, etc.) # RNME CKAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KB2P SOL TYPE HEXP(2:1) NAME -2-D-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME KB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KB3P SOL TYPE HEXP(3:1) NAME -3-D-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME KB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KB4P SOL TYPE HEXP(4:1) NAME -4-D-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME KB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK KB6P SOL TYPE HEXP(6:1) NAME -6-D-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME KB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CKBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(KB), i.e. trehalo-linked residue KB # building block (residue, nucleotide, etc.) # RNME CKBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IA2P SOL TYPE HEXP(2:1) NAME -2-D-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME IA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IA3P SOL TYPE HEXP(3:1) NAME -3-D-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME IA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IA4P SOL TYPE HEXP(4:1) NAME -4-D-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME IA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IA6P SOL TYPE HEXP(6:1) NAME -6-D-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME IA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CIAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(IA), i.e. trehalo-linked residue IA # building block (residue, nucleotide, etc.) # RNME CIAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IB2P SOL TYPE HEXP(2:1) NAME -2-D-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME IB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IB3P SOL TYPE HEXP(3:1) NAME -3-D-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME IB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IB4P SOL TYPE HEXP(4:1) NAME -4-D-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME IB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK IB6P SOL TYPE HEXP(6:1) NAME -6-D-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME IB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CIBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(IB), i.e. trehalo-linked residue IB # building block (residue, nucleotide, etc.) # RNME CIBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LA2P SOL TYPE HEXP(2:1) NAME -2-D-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME LA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LA3P SOL TYPE HEXP(3:1) NAME -3-D-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME LA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LA4P SOL TYPE HEXP(4:1) NAME -4-D-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME LA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LA6P SOL TYPE HEXP(6:1) NAME -6-D-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME LA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CLAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(LA), i.e. trehalo-linked residue LA # building block (residue, nucleotide, etc.) # RNME CLAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LB2P SOL TYPE HEXP(2:1) NAME -2-D-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME LB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LB3P SOL TYPE HEXP(3:1) NAME -3-D-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME LB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LB4P SOL TYPE HEXP(4:1) NAME -4-D-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME LB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LB6P SOL TYPE HEXP(6:1) NAME -6-D-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME LB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CLBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(LB), i.e. trehalo-linked residue LB # building block (residue, nucleotide, etc.) # RNME CLBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TA2P SOL TYPE HEXP(2:1) NAME -2-D-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME TA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TA3P SOL TYPE HEXP(3:1) NAME -3-D-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME TA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TA4P SOL TYPE HEXP(4:1) NAME -4-D-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME TA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TA6P SOL TYPE HEXP(6:1) NAME -6-D-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME TA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CTAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(TA), i.e. trehalo-linked residue TA # building block (residue, nucleotide, etc.) # RNME CTAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TB2P SOL TYPE HEXP(2:1) NAME -2-D-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME TB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TB3P SOL TYPE HEXP(3:1) NAME -3-D-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME TB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C5-C4-O5-C6 11 5 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TB4P SOL TYPE HEXP(4:1) NAME -4-D-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME TB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK TB6P SOL TYPE HEXP(6:1) NAME -6-D-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME TB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C5-C4-O5-C6 11 8 12 1 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CTBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(TB), i.e. trehalo-linked residue TB # building block (residue, nucleotide, etc.) # RNME CTBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nA2P SOL TYPE HEXP(2:1) NAME -2-L-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME nA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nA3P SOL TYPE HEXP(3:1) NAME -3-L-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME nA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nA4P SOL TYPE HEXP(4:1) NAME -4-L-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME nA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nA6P SOL TYPE HEXP(6:1) NAME -6-L-allopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME nA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CnAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(nA), i.e. trehalo-linked residue nA # building block (residue, nucleotide, etc.) # RNME CnAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nB2P SOL TYPE HEXP(2:1) NAME -2-L-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME nB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nB3P SOL TYPE HEXP(3:1) NAME -3-L-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME nB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nB4P SOL TYPE HEXP(4:1) NAME -4-L-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME nB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK nB6P SOL TYPE HEXP(6:1) NAME -6-L-allopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME nB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CnBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(nB), i.e. trehalo-linked residue nB # building block (residue, nucleotide, etc.) # RNME CnBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eA2P SOL TYPE HEXP(2:1) NAME -2-L-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME eA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eA3P SOL TYPE HEXP(3:1) NAME -3-L-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME eA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eA4P SOL TYPE HEXP(4:1) NAME -4-L-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME eA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eA6P SOL TYPE HEXP(6:1) NAME -6-L-altropyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME eA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CeAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(eA), i.e. trehalo-linked residue eA # building block (residue, nucleotide, etc.) # RNME CeAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eB2P SOL TYPE HEXP(2:1) NAME -2-L-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME eB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eB3P SOL TYPE HEXP(3:1) NAME -3-L-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME eB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eB4P SOL TYPE HEXP(4:1) NAME -4-L-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME eB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK eB6P SOL TYPE HEXP(6:1) NAME -6-L-altropyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME eB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CeBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(eB), i.e. trehalo-linked residue eB # building block (residue, nucleotide, etc.) # RNME CeBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gA2P SOL TYPE HEXP(2:1) NAME -2-L-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME gA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gA3P SOL TYPE HEXP(3:1) NAME -3-L-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME gA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gA4P SOL TYPE HEXP(4:1) NAME -4-L-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME gA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gA6P SOL TYPE HEXP(6:1) NAME -6-L-glucopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME gA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CgAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(gA), i.e. trehalo-linked residue gA # building block (residue, nucleotide, etc.) # RNME CgAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gB2P SOL TYPE HEXP(2:1) NAME -2-L-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME gB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gB3P SOL TYPE HEXP(3:1) NAME -3-L-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME gB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gB4P SOL TYPE HEXP(4:1) NAME -4-L-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME gB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK gB6P SOL TYPE HEXP(6:1) NAME -6-L-glucopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME gB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CgBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(gB), i.e. trehalo-linked residue gB # building block (residue, nucleotide, etc.) # RNME CgBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mA2P SOL TYPE HEXP(2:1) NAME -2-L-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME mA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mA3P SOL TYPE HEXP(3:1) NAME -3-L-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME mA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mA4P SOL TYPE HEXP(4:1) NAME -4-L-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME mA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mA6P SOL TYPE HEXP(6:1) NAME -6-L-mannopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME mA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CmAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(mA), i.e. trehalo-linked residue mA # building block (residue, nucleotide, etc.) # RNME CmAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mB2P SOL TYPE HEXP(2:1) NAME -2-L-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME mB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # C4-C3-C5-O4 5 2 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mB3P SOL TYPE HEXP(3:1) NAME -3-L-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME mB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # C4-C3-C5-O4 5 1 11 6 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mB4P SOL TYPE HEXP(4:1) NAME -4-L-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME mB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # C4-C3-C5-O4 1 5 11 0 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK mB6P SOL TYPE HEXP(6:1) NAME -6-L-mannopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME mB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # C4-C3-C5-O4 8 5 11 9 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CmBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(mB), i.e. trehalo-linked residue mB # building block (residue, nucleotide, etc.) # RNME CmBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # O4'-C5'-C3'-C4' 9 7 11 8 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kA2P SOL TYPE HEXP(2:1) NAME -2-L-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME kA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kA3P SOL TYPE HEXP(3:1) NAME -3-L-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME kA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kA4P SOL TYPE HEXP(4:1) NAME -4-L-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME kA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kA6P SOL TYPE HEXP(6:1) NAME -6-L-gulopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME kA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CkAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(kA), i.e. trehalo-linked residue kA # building block (residue, nucleotide, etc.) # RNME CkAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kB2P SOL TYPE HEXP(2:1) NAME -2-L-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME kB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kB3P SOL TYPE HEXP(3:1) NAME -3-L-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME kB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kB4P SOL TYPE HEXP(4:1) NAME -4-L-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME kB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kB6P SOL TYPE HEXP(6:1) NAME -6-L-gulopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME kB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CkBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(kB), i.e. trehalo-linked residue kB # building block (residue, nucleotide, etc.) # RNME CkBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iA2P SOL TYPE HEXP(2:1) NAME -2-L-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME iA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iA3P SOL TYPE HEXP(3:1) NAME -3-L-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME iA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iA4P SOL TYPE HEXP(4:1) NAME -4-L-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME iA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iA6P SOL TYPE HEXP(6:1) NAME -6-L-idopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME iA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CiAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(iA), i.e. trehalo-linked residue iA # building block (residue, nucleotide, etc.) # RNME CiAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iB2P SOL TYPE HEXP(2:1) NAME -2-L-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME iB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # C3-C2-C4-O3 2 1 5 3 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iB3P SOL TYPE HEXP(3:1) NAME -3-L-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME iB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # C3-C2-C4-O3 1 2 5 0 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iB4P SOL TYPE HEXP(4:1) NAME -4-L-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME iB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iB6P SOL TYPE HEXP(6:1) NAME -6-L-idopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME iB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C2-C4-O3 5 2 8 6 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CiBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(iB), i.e. trehalo-linked residue iB # building block (residue, nucleotide, etc.) # RNME CiBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lA2P SOL TYPE HEXP(2:1) NAME -2-L-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME lA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lA3P SOL TYPE HEXP(3:1) NAME -3-L-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME lA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lA4P SOL TYPE HEXP(4:1) NAME -4-L-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME lA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lA6P SOL TYPE HEXP(6:1) NAME -6-L-galactopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME lA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK ClAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(lA), i.e. trehalo-linked residue lA # building block (residue, nucleotide, etc.) # RNME ClAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lB2P SOL TYPE HEXP(2:1) NAME -2-L-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME lB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # O2-C3-C1-C2 0 2 13 1 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lB3P SOL TYPE HEXP(3:1) NAME -3-L-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME lB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 1 13 2 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lB4P SOL TYPE HEXP(4:1) NAME -4-L-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME lB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK lB6P SOL TYPE HEXP(6:1) NAME -6-L-galactopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME lB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK ClBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(lB), i.e. trehalo-linked residue lB # building block (residue, nucleotide, etc.) # RNME ClBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # C2'-C1'-C3'-O2' 14 5 11 15 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tA2P SOL TYPE HEXP(2:1) NAME -2-L-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME tA2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 1 12 13 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tA3P SOL TYPE HEXP(3:1) NAME -3-L-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME tA3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tA4P SOL TYPE HEXP(4:1) NAME -4-L-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME tA4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tA6P SOL TYPE HEXP(6:1) NAME -6-L-talopyranose-alpha-1- # building block (residue, nucleotide, etc.) # RNME tA6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CtAP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(tA), i.e. trehalo-linked residue tA # building block (residue, nucleotide, etc.) # RNME CtAP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tB2P SOL TYPE HEXP(2:1) NAME -2-L-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME tB2P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O2) # [or initial patch HO2C (HO2, O2)] # the C1_prev-O2 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O2-C2 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O2-C2 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O2-C2-C1 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O2 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 13 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C2 56 3 0.23200 1 6 2 3 5 12 13 14 2 C3 56 3 0.23200 0 6 3 4 5 6 11 13 3 O3 3 16 -0.64200 0 2 4 5 4 HO3 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O2 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 2 5 26 # C4-C5 5 11 26 # C2-C3 1 2 26 # C2-C1 1 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C3-O3 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O2 # this term is skipped: included in prev residue or initial patch # O2-C2 0 1 20 # # terms of type : O-H # # O3-HO3 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 2 5 11 8 # C2-C3-C4 1 2 5 8 # C3-C2-C1 2 1 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 2 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 3 2 5 9 # C2-C3-O3 1 2 3 9 # O2-C2-C3 0 1 2 9 # O2-C2-C1 0 1 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 1 13 12 9 # C2-C1-O1 1 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O2-C2 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C3-O3-HO3 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 1 12 14 2 # C2-C3-C1-O2 1 2 13 0 2 # O3-C2-C4-C3 3 1 5 2 2 # O4-C3-C5-C4 6 2 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 2 1 13 12 34 # C1-C2-C3-C4 13 1 2 5 34 # C2-C3-C4-C5 1 2 5 11 34 # C3-C4-C5-O5 2 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 1 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 13 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C2-C3-O3-HO3 (chi3 dihedral) 1 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O2-C2 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 1 13 14 15 46 # C1_prev-O2-C2-C3 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O2-C2-C1 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 13 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 0 1 13 14 52 # O2-C2-C3-O3 0 1 2 3 52 # O3-C3-C4-O4 3 2 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 0 1 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 2 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C1_prev-C4 -1 5 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # HO3-C1 4 13 2 0 # HO3-C5 4 11 2 0 # C2-HO4 1 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 2 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 2 14 4 0 # C5-O1 11 14 4 0 # O2-C4 0 5 4 0 # O3-C1 3 13 4 0 # O3-C5 3 11 4 0 # C2-O4 1 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 3 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tB3P SOL TYPE HEXP(3:1) NAME -3-L-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME tB3P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O3) # [or initial patch HO3C (HO3, O3)] # the C1_prev-O3 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O3-C3 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O3-C3 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O3-C3-C2 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O3 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 2 5 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C3 56 3 0.23200 1 6 2 3 5 6 11 13 2 C2 56 3 0.23200 0 6 3 4 5 12 13 14 3 O2 3 16 -0.64200 0 2 4 13 4 HO2 21 1 0.41000 1 0 5 C4 56 3 0.23200 0 5 6 7 8 11 12 6 O4 3 16 -0.64200 0 2 7 11 7 HO4 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O3 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 1 5 26 # C4-C5 5 11 26 # C3-C2 1 2 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C4-O4 5 6 20 # C6-O6 8 9 20 # C1_prev-O3 # this term is skipped: included in prev residue or initial patch # O3-C3 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O4-HO4 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 1 5 11 8 # C2-C3-C4 2 1 5 8 # C3-C2-C1 1 2 13 8 # C4-C5-C6 5 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 1 5 6 9 # O4-C4-C5 6 5 11 9 # O3-C3-C4 0 1 5 9 # O3-C3-C2 0 1 2 9 # C3-C2-O2 1 2 3 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 5 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O3-C3 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C4-O4-HO4 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 1 13 3 2 # O3-C2-C4-C3 0 2 5 1 2 # O4-C3-C5-C4 6 1 11 5 2 # C6-C4-O5-C5 8 5 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 1 2 13 12 34 # C4-C3-C2-C1 5 1 2 13 34 # C2-C3-C4-C5 2 1 5 11 34 # C3-C4-C5-O5 1 5 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 5 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 5 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 2 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C3-C4-O4-HO4 (chi4 dihedral) 1 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O3-C3 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O3-C3-C4 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O3-C3-C2 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 2 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 5 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O3-C3-C2-O2 0 1 2 3 52 # O3-C3-C4-O4 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 6 5 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 1 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 5 2 0 # HO2-O5 4 12 2 0 # C1_prev-C1 -1 13 2 1 1 21 # C1_prev-C5 -1 11 2 1 1 21 # C2-HO4 2 7 2 0 # HO4-O5 7 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 1 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 1 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 5 4 0 # O3-C1 0 13 4 0 # O3-C5 0 11 4 0 # C2-O4 2 6 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 0 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tB4P SOL TYPE HEXP(4:1) NAME -4-L-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME tB4P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 15 4 0.23200 0 4 9 10 11 12 9 O6 3 16 -0.64200 0 2 10 11 10 HO6 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 8 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C6-O6 8 9 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O6-HO6 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 9 8 11 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C6-O6-HO6 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # C3-C4-C2-O3 5 1 2 6 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # --- dihedrals --- # # NDA 26 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 9 8 11 1 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C5-C6-O6-HO6 (chi6 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 9 8 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 9 8 11 1 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # O6-C6-C5-O5 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK tB6P SOL TYPE HEXP(6:1) NAME -6-L-talopyranose-beta-1- # building block (residue, nucleotide, etc.) # RNME tB6P # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O6) # [or initial patch HO6C (HO6, O6)] # the C1_prev-O6 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O6-C6 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O6-C6 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O6-C6-C5 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O6 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 2 1 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C6 15 4 0.23200 1 3 8 11 12 2 C2 56 3 0.23200 0 8 3 4 5 6 8 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 6 6 7 8 9 11 13 6 O3 3 16 -0.64200 0 2 7 8 7 HO3 21 1 0.41000 1 0 8 C4 56 3 0.23200 0 4 9 10 11 12 9 O4 3 16 -0.64200 0 2 10 11 10 HO4 21 1 0.41000 1 0 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O6 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C3-C4 5 8 26 # C4-C5 8 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # C6-C5 1 11 26 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C4-O4 8 9 20 # C1_prev-O6 # this term is skipped: included in prev residue or initial patch # O6-C6 0 1 20 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # O4-HO4 9 10 1 # # --- bond angles --- # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 8 11 8 # C2-C3-C4 2 5 8 8 # C3-C2-C1 5 2 13 8 # C6-C5-C4 1 11 8 8 # # terms of type : C-C-O # # C3-C4-O4 5 8 9 9 # O4-C4-C5 9 8 11 9 # O3-C3-C4 6 5 8 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # O6-C6-C5 0 1 11 9 # C4-C5-O5 8 11 12 9 # C6-C5-O5 1 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O6-C6 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # C4-O4-HO4 8 9 10 12 # # --- improper dihedrals --- # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C2-C4-C3 6 2 8 5 2 # O4-C3-C5-C4 9 5 11 8 2 # C6-C4-O5-C5 1 8 12 11 2 # # --- dihedrals --- # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 8 34 # C2-C3-C4-C5 2 5 8 11 34 # C3-C4-C5-O5 5 8 11 12 34 # O6-C6-C5-C4 (omega dihedral angle for hydroxymethyl group) 0 1 11 8 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 8 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O6-C6-C5 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 11 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # C3-C4-O4-HO4 (chi4 dihedral) 5 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O6-C6 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-O5 (omega-tilde dihedral angle) 0 1 11 12 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O6-C6-C5-C4 (omega dihedral angle) 0 1 11 8 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O3-C3-C4-O4 6 5 8 9 52 # O6-C6-C5-O5 0 1 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 9 8 11 12 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # HO2-C4 4 8 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C2-HO4 2 10 2 0 # HO4-O5 10 12 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 1 13 3 0 # C6-C3 1 5 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # O2-C4 3 8 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # C2-O4 2 9 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 1 14 5 0 # C6-O3 1 6 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CtBP TER TYPE HEXP(1:-) NAME terminal -C1-O1-C1'(tB), i.e. trehalo-linked residue tB # building block (residue, nucleotide, etc.) # RNME CtBP # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 5 8 9 11 17 18 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 15 4 0.23200 0 2 18 19 18 O6' 3 16 -0.64200 0 1 19 19 HO6' 21 1 0.41000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # C5'-C6' 7 17 26 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # C6'-O6' 17 18 20 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # O6'-HO6' 18 19 1 # # --- bond angles --- # (new or replacement) # # NBA 21 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # C5'-C6'-O6' 7 17 18 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # C6'-O6'-HO6' 17 18 19 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 5 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # C3'-C4'-C2'-O3' 11 8 14 12 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C5'-O5'-C4'-C6' 7 6 8 17 2 # # --- dihedrals --- # (new or replacement) # # NDA 24 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # C4'-C5'-C6'-O6' (omega dihedral angle for hydroxymethyl group) 8 7 17 18 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # C5'-C6'-O6'-HO6' (chi6 dihedral) 7 17 18 19 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T10 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # O5'-C5'-C6'-O6' (omega-tilde dihedral angle) 6 7 17 18 50 # # terms of type : T11 Xr-CH*r-CH*-O (exocyclic oxymethyl) # # C4'-C5'-C6'-O6' (omega dihedral angle) 8 7 17 18 51 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # O5'-C5'-C6'-O6' 6 7 17 18 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK GB4U SOL TYPE HEXU(4:1) NAME -4-D-glucuronate-beta-1- # building block (residue, nucleotide, etc.) # RNME GB4U # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 12 12 0.36000 0 4 9 10 11 12 9 O61 2 16 -0.68000 0 2 10 11 10 O62 2 16 -0.68000 1 1 11 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 22 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # terms of type : C4-C5-C6-O61 (gamma dihedral) for carboxylate # # O61-C6-C5-C4 9 8 11 1 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CGBU TER TYPE HEXU(1:-) NAME terminal -C1-O1-C1'(GB), i.e. trehalo-linked residue GB # building block (residue, nucleotide, etc.) # RNME CGBU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 6 8 9 11 17 18 19 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.36000 0 2 18 19 18 O61' 2 16 -0.68000 0 1 19 19 O62' 2 16 -0.68000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # # terms of type : C-C(carboxylate) # # C5'-C6' 7 17 27 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # # terms of type : C-O(carboxylate) # # C6'-O61' 17 18 6 # C6'-O62' 17 19 6 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # # --- bond angles --- # (new or replacement) # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O(carboxylate) # # C5'-C6'-O61' 7 17 18 22 # C5'-C6'-O62' 7 17 19 22 # # terms of type : O-C-O(carboxylate) # # O61'-C6'-O62' 18 17 19 38 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # terms of type : planar geometry around C6'(carboxylate group) # # C6'-O61'-O62'-C5' 17 18 19 7 1 # # --- dihedrals --- # (new or replacement) # # NDA 20 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # terms of type : C4'-C5'-C6'-O61' (gamma dihedral) for carboxylate # # C4'-C5'-C6'-O61' 8 7 17 18 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK LA4U SOL TYPE HEXU(4:1) NAME -4-D-galacturonate-alpha-1- # building block (residue, nucleotide, etc.) # RNME LA4U # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 12 12 0.36000 0 4 9 10 11 12 9 O61 2 16 -0.68000 0 2 10 11 10 O62 2 16 -0.68000 1 1 11 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1-C2-O5-O1 13 2 12 14 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # C4-C3-C5-O4 1 5 11 0 2 # C5-C4-O5-C6 11 1 12 8 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 22 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 46 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 47 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # terms of type : C4-C5-C6-O61 (gamma dihedral) for carboxylate # # O61-C6-C5-C4 9 8 11 1 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CLAU TER TYPE HEXU(1:-) NAME terminal -C1-O1-C1'(LA), i.e. trehalo-linked residue LA # building block (residue, nucleotide, etc.) # RNME CLAU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 6 8 9 11 17 18 19 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.36000 0 2 18 19 18 O61' 2 16 -0.68000 0 1 19 19 O62' 2 16 -0.68000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # # terms of type : C-C(carboxylate) # # C5'-C6' 7 17 27 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # # terms of type : C-O(carboxylate) # # C6'-O61' 17 18 6 # C6'-O62' 17 19 6 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # # --- bond angles --- # (new or replacement) # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O(carboxylate) # # C5'-C6'-O61' 7 17 18 22 # C5'-C6'-O62' 7 17 19 22 # # terms of type : O-C-O(carboxylate) # # O61'-C6'-O62' 18 17 19 38 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # terms of type : planar geometry around C6'(carboxylate group) # # C6'-O61'-O62'-C5' 17 18 19 7 1 # # --- dihedrals --- # (new or replacement) # # NDA 20 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # terms of type : C4'-C5'-C6'-O61' (gamma dihedral) for carboxylate # # C4'-C5'-C6'-O61' 8 7 17 18 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK MB4U SOL TYPE HEXU(4:1) NAME -4-D-mannuronate-beta-1- # building block (residue, nucleotide, etc.) # RNME MB4U # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 12 12 0.36000 0 4 9 10 11 12 9 O61 2 16 -0.68000 0 2 10 11 10 O62 2 16 -0.68000 1 1 11 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C5-C4-O5-C6 11 1 12 8 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 22 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # terms of type : C4-C5-C6-O61 (gamma dihedral) for carboxylate # # O61-C6-C5-C4 9 8 11 1 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CMBU TER TYPE HEXU(1:-) NAME terminal -C1-O1-C1'(MB), i.e. trehalo-linked residue MB # building block (residue, nucleotide, etc.) # RNME CMBU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 6 8 9 11 17 18 19 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.36000 0 2 18 19 18 O61' 2 16 -0.68000 0 1 19 19 O62' 2 16 -0.68000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # # terms of type : C-C(carboxylate) # # C5'-C6' 7 17 27 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # # terms of type : C-O(carboxylate) # # C6'-O61' 17 18 6 # C6'-O62' 17 19 6 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # # --- bond angles --- # (new or replacement) # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O(carboxylate) # # C5'-C6'-O61' 7 17 18 22 # C5'-C6'-O62' 7 17 19 22 # # terms of type : O-C-O(carboxylate) # # O61'-C6'-O62' 18 17 19 38 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # C1'-O5'-C2'-O1 5 6 14 4 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # terms of type : planar geometry around C6'(carboxylate group) # # C6'-O61'-O62'-C5' 17 18 19 7 1 # # --- dihedrals --- # (new or replacement) # # NDA 20 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # terms of type : C4'-C5'-C6'-O61' (gamma dihedral) for carboxylate # # C4'-C5'-C6'-O61' 8 7 17 18 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK kA4U SOL TYPE HEXU(4:1) NAME -4-L-guluronate-alpha-1 # building block (residue, nucleotide, etc.) # RNME kA4U # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 12 12 0.36000 0 4 9 10 11 12 9 O61 2 16 -0.68000 0 2 10 11 10 O62 2 16 -0.68000 1 1 11 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # O2-C3-C1-C2 3 5 13 2 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 22 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # terms of type : C4-C5-C6-O61 (gamma dihedral) for carboxylate # # O61-C6-C5-C4 9 8 11 1 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CkAU TER TYPE HEXU(1:-) NAME terminal -C1-O1-C1'(kA), i.e. trehalo-linked residue kA # building block (residue, nucleotide, etc.) # RNME CkAU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 6 8 9 11 17 18 19 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.36000 0 2 18 19 18 O61' 2 16 -0.68000 0 1 19 19 O62' 2 16 -0.68000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # # terms of type : C-C(carboxylate) # # C5'-C6' 7 17 27 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # # terms of type : C-O(carboxylate) # # C6'-O61' 17 18 6 # C6'-O62' 17 19 6 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # # --- bond angles --- # (new or replacement) # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O(carboxylate) # # C5'-C6'-O61' 7 17 18 22 # C5'-C6'-O62' 7 17 19 22 # # terms of type : O-C-O(carboxylate) # # O61'-C6'-O62' 18 17 19 38 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # terms of type : planar geometry around C6'(carboxylate group) # # C6'-O61'-O62'-C5' 17 18 19 7 1 # # --- dihedrals --- # (new or replacement) # # NDA 20 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # terms of type : C4'-C5'-C6'-O61' (gamma dihedral) for carboxylate # # C4'-C5'-C6'-O61' 8 7 17 18 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLSOLUTE #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK iA4U SOL TYPE HEXU(4:1) NAME -4-L-iduronate-alpha-1- # building block (residue, nucleotide, etc.) # RNME iA4U # # number of atoms, number of preceding exclusions # NMAT NLIN 14 2 # # -- preceding exclusions -- # # two atoms of the previous residue (C1_prev, O1_prev = O4) # [or initial patch HO4C (HO4, O4)] # the C1_prev-O4 and O1-C#_next bonds are *not* defined in the residue (but in the prev and next, respectively) # the C1_prev-O4-C4 angle is *not* defined in the residue (but in the prev) # the O5_prev-C1_prev-O4-C4 dihedral (prev glycosidic phi dihedral) is *not* defined in the residue (but in the prev) # the C1_prev-O4-C4-C3 dihedral (prev glycosidic psi dihedral) *is* defined in the residue # the exclusions of C1_prev and O4 *are* defined in the residue # #ATOM MAE MSAE -1 2 0 1 0 3 1 5 11 # # -- atoms -- # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 C4 56 3 0.23200 1 6 2 5 6 8 11 12 2 C2 56 3 0.23200 0 7 3 4 5 6 12 13 14 3 O2 3 16 -0.64200 0 3 4 5 13 4 HO2 21 1 0.41000 1 0 5 C3 56 3 0.23200 0 4 6 7 11 13 6 O3 3 16 -0.64200 0 1 7 7 HO3 21 1 0.41000 1 0 8 C6 12 12 0.36000 0 4 9 10 11 12 9 O61 2 16 -0.68000 0 2 10 11 10 O62 2 16 -0.68000 1 1 11 11 C5 56 3 0.23200 0 2 12 13 12 O5 54 16 -0.46400 0 2 13 14 # # -- trailing atoms -- # # two special atoms of the residue (C1, O1) preceding the first atom of the next residue (C#_next) # [or terminal patch C1OH (HO1), C1OC (CM) or CRR (C1'; for 1-1' linkage to residue of type RR)] # the C1_prev-O4 and O1-C#_next bonds *are* defined in the residue # the C1-O1-C#_next angle *is* defined in the residue # the O5-C1-O1-C#_next dihedral (glycosidic phi dihedral) *is* defined in the residue # the C1-O1-C#_next-C(#-1)_next (glycosidic psi dihedral) is *not* defined in the residue (but in the next) # the exclusions of C1 and O1 are *not* defined in the residue (but in the next) # #ATOM ANM IACM MASS CGM ICGM 13 C1 56 3 0.46400 0 14 O1 4 16 -0.46400 0 # # --- bonds --- # # NB 15 # IB JB MCB # # terms of type : C-C # # C4-C3 1 5 26 # C4-C5 1 11 26 # C2-C3 2 5 26 # C2-C1 2 13 26 # # terms of type : C-C(carboxylate) # # C6-C5 8 11 27 # # terms of type : C-O # # C1-O1 13 14 20 # O1-C#_next # this term is skipped: included in prev residue or initial patch # C5-O5 11 12 20 # O5-C1 12 13 20 # C2-O2 2 3 20 # C3-O3 5 6 20 # C1_prev-O4 # this term is skipped: included in prev residue or initial patch # O4-C4 0 1 20 # # terms of type : C-O(carboxylate) # # C6-O61 8 9 6 # C6-O62 8 10 6 # # terms of type : O-H # # O2-HO2 3 4 1 # O3-HO3 6 7 1 # # --- bond angles --- # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C3-C4-C5 5 1 11 8 # C4-C3-C2 1 5 2 8 # C3-C2-C1 5 2 13 8 # C4-C5-C6 1 11 8 8 # # terms of type : C-C-O(carboxylate) # # O61-C6-C5 9 8 11 22 # O62-C6-C5 10 8 11 22 # # terms of type : O-C-O(carboxylate) # # O61-C6-O62 9 8 10 38 # # terms of type : C-C-O # # O4-C4-C3 0 1 5 9 # O4-C4-C5 0 1 11 9 # C4-C3-O3 1 5 6 9 # C2-C3-O3 2 5 6 9 # O2-C2-C3 3 2 5 9 # O2-C2-C1 3 2 13 9 # C4-C5-O5 1 11 12 9 # C6-C5-O5 8 11 12 9 # C2-C1-O5 2 13 12 9 # C2-C1-O1 2 13 14 9 # # terms of type : O-C-O # # O5-C1-O1 12 13 14 9 # # terms of type : C-O-C # # C5-O5-C1 11 12 13 10 # C1-O1-C#_next 13 14 15 10 # C1_prev-O4-C4 # this term is skipped: included in prev residue or initial patch # # terms of type : C-O-H # # C2-O2-HO2 2 3 4 12 # C3-O3-HO3 5 6 7 12 # # --- improper dihedrals --- # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5 (1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-C2-O5-C1 14 2 12 13 2 # C2-C3-C1-O2 2 5 13 3 2 # O3-C4-C2-C3 6 1 2 5 2 # O4-C3-C5-C4 0 5 11 1 2 # C6-C4-O5-C5 8 1 12 11 2 # # terms of type : planar geometry around C6 (carboxylate group) # # C6-O61-O62-C5 8 9 10 11 1 # # --- dihedrals --- # # NDA 22 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # C3-C2-C1-O5 5 2 13 12 34 # C1-C2-C3-C4 13 2 5 1 34 # C5-C4-C3-C2 11 1 5 2 34 # C3-C4-C5-O5 5 1 11 12 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C5-O5-C1-C2 11 12 13 2 42 # C4-C5-O5-C1 1 11 12 13 42 # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 12 13 14 15 42 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (generic CO term) - not appropriate for OH) -1 0 1 5 42 # C1-O1-C#_next-C(#-1)_next # this term is skipped: glycosidic psi dihedral - included in next residue or terminal patch # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1-C2-O2-HO2 (chi2 dihedral) 13 2 3 4 43 # C2-C3-O3-HO3 (chi3 dihedral) 2 5 6 7 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 12 13 14 15 44 # O5_prev-C1_prev-O4-C4 # this term is skipped: prev glycosidic phi dihedral - included in prev residue or initial patch # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # C5-O5-C1-O1 11 12 13 14 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # O5-C1-O1-C#_next (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 12 13 14 15 46 # C1_prev-O4-C4-C5 (glycosidic psi-tilde dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 11 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C2-C1-O1-C#_next (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 2 13 14 15 47 # C1_prev-O4-C4-C3 (glycosidic psi dihedral to prev residue (exocyclic methoxyl term) - not appropriate for OH) -1 0 1 5 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O2-C2-C1-O1 3 2 13 14 52 # O2-C2-C3-O3 3 2 5 6 52 # O4-C4-C3-O3 0 1 5 6 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O2-C2-C1-O5 3 2 13 12 53 # O4-C4-C5-O5 0 1 11 12 53 # # terms of type : C4-C5-C6-O61 (gamma dihedral) for carboxylate # # O61-C6-C5-C4 9 8 11 1 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # O5-C#_next 12 15 1 1 2 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C3-C#_next 5 15 2 1 2 21 # C5-C#_next 11 15 2 1 2 21 # C4-HO2 1 4 2 0 # HO2-O5 4 12 2 0 # HO3-C1 7 13 2 0 # HO3-C5 7 11 2 0 # C1_prev-C2 -1 2 2 1 1 21 # C1_prev-O5 -1 12 2 1 1 21 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C6-C1 8 13 3 0 # C3-C6 5 8 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # C3-O1 5 14 4 0 # C5-O1 11 14 4 0 # C4-O2 1 3 4 0 # O3-C1 6 13 4 0 # O3-C5 6 11 4 0 # O4-C2 0 2 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # C6-O1 8 14 5 0 # O3-C6 6 8 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK CiAU TER TYPE HEXU(1:-) NAME terminal -C1-O1-C1'(iA), i.e. trehalo-linked residue iA # building block (residue, nucleotide, etc.) # RNME CiAU # # number of atoms, number of atoms to be replaced # NMAT NREP 19 -4 # # - the O1-C1' bond *is* defined in the patch (not in the residue) # - the C1-O1-C1' angle is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the O5-C1-O1-C1' dihedral (phi dihedral) is *not* defined in the patch (but in the residue); # recall that there is no psi dihedral in a trehalo linkage, but a phi' instead # - the C1-O1-C1'-O5 dihedral (phi' dihedral) *is* defined in the patch (but in the residue) # - the exclusions of C5, O5, C1 and O1 *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch, O5'is not listed here because there is no special 1-4 exclusion # specific to this force-field in the case of a methyl group (only for hydrogen) # # excluded: O5 and C1 1 C5 56 3 0.23200 0 2 2 3 # excluded: C1 and O1 2 O5 3 16 -0.46400 0 2 3 4 # excluded: O1 and C1' 3 C1 56 3 0.46400 0 2 4 5 # excluded: C1', O5' and C2' 4 O1 4 16 -0.46400 0 3 5 6 14 # # -- new atoms -- # (exclusions defined here) # 5 C1' 56 3 0.46400 0 5 6 7 11 14 15 6 O5' 54 16 -0.46400 0 4 7 8 14 17 7 C5' 56 3 0.23200 1 6 8 9 11 17 18 19 8 C4' 56 3 0.23200 0 6 9 10 11 12 14 17 9 O4' 3 16 -0.64200 0 2 10 11 10 HO4' 21 1 0.41000 1 0 11 C3' 56 3 0.23200 0 4 12 13 14 15 12 O3' 3 16 -0.64200 0 2 13 14 13 HO3' 21 1 0.41000 1 0 14 C2' 56 3 0.23200 0 2 15 16 15 O2' 3 16 -0.64200 0 1 16 16 HO2' 21 1 0.41000 1 0 17 C6' 12 12 0.36000 0 2 18 19 18 O61' 2 16 -0.68000 0 1 19 19 O62' 2 16 -0.68000 1 0 # # --- bonds --- # (new or replacement) # # NB 16 # IB JB MCB # # terms of type : C-C # # C4'-C3' 8 11 26 # C5'-C4' 7 8 26 # C3'-C2' 11 14 26 # C1'-C2' 5 14 26 # # terms of type : C-C(carboxylate) # # C5'-C6' 7 17 27 # # terms of type : C-O # # C5-O5 # this term is skipped: already included appropriately in the patched residue # O5-C1 # this term is skipped: already included appropriately in the patched residue # C1-O1 # this term is skipped: already included appropriately in the patched residue # O1-C1' 4 5 20 # O5'-C5' 6 7 20 # C1'-O5' 5 6 20 # C2'-O2' 14 15 20 # C3'-O3' 11 12 20 # C4'-O4' 8 9 20 # # terms of type : C-O(carboxylate) # # C6'-O61' 17 18 6 # C6'-O62' 17 19 6 # # terms of type : O-H # # O2'-HO2' 15 16 1 # O3'-HO3' 12 13 1 # O4'-HO4' 9 10 1 # # --- bond angles --- # (new or replacement) # # NBA 22 # IB JB KB MCB # # terms of type : C-C-C # # C5'-C4'-C3' 7 8 11 8 # C4'-C3'-C2' 8 11 14 8 # C1'-C2'-C3' 5 14 11 8 # C4'-C5'-C6' 8 7 17 8 # # terms of type : C-C-O(carboxylate) # # C5'-C6'-O61' 7 17 18 22 # C5'-C6'-O62' 7 17 19 22 # # terms of type : O-C-O(carboxylate) # # O61'-C6'-O62' 18 17 19 38 # # terms of type : C-C-O # # O4'-C4'-C3' 9 8 11 9 # C5'-C4'-O4' 7 8 9 9 # C4'-C3'-O3' 8 11 12 9 # O3'-C3'-C2' 12 11 14 9 # C3'-C2'-O2' 11 14 15 9 # C1'-C2'-O2' 5 14 15 9 # O5'-C5'-C4' 6 7 8 9 # O5'-C5'-C6' 6 7 17 9 # O5'-C1'-C2' 6 5 14 9 # O1-C1'-C2' 4 5 14 9 # # terms of type : O-C-O # # O1-C1'-O5' 4 5 6 9 # # terms of type : C-O-C # # C1'-O5'-C5' 5 6 7 10 # C5-O5-C1 # this term is skipped: already included appropriately in the patched residue # O5-C1-O1 # this term is skipped: already included appropriately in the patched residue # C1-O1-C1' # this term is skipped: already included appropriately in the patched residue # PHH, May 2011: the C1-O1-C1' angle was listed in the previous files and is now removed; # this removal should not affect the built topologies - it just replaced the identical term of the patched residue # # terms of type : C-O-H # # C2'-O2'-HO2' 14 15 16 12 # C3'-O3'-HO3' 11 12 13 12 # C4'-O4'-HO4' 8 9 10 12 # # --- improper dihedrals --- # (new or replacement) # # NIDA 6 # IB JB KB LB MCB # # terms of type : tetrahedral geometry around C1,C2,C3,C4 and C5'(1st or 4th atom in sequence - # the one neighbor to the three other ones; the exocyclic atom is the other one, i.e. 4th or 1st) # # O1-O5'-C2'-C1' 4 6 14 5 2 # O2'-C1'-C3'-C2' 15 5 11 14 2 # O3'-C4'-C2'-C3' 12 8 14 11 2 # C4'-C5'-C3'-O4' 8 7 11 9 2 # C6'-O5'-C4'-C5' 17 6 8 7 2 # # terms of type : planar geometry around C6'(carboxylate group) # # C6'-O61'-O62'-C5' 17 18 19 7 1 # # --- dihedrals --- # (new or replacement) # # NDA 20 # IB JB KB LB MCB # # terms of type : T1 X-C-C-X; X not H (generic CC - unaltered from 53A6) # # O5'-C1'-C2'-C3' 6 5 14 11 34 # C4'-C3'-C2'-C1' 8 11 14 5 34 # C5'-C4'-C3'-C2' 7 8 11 14 34 # O5'-C5'-C4'-C3' 6 7 8 11 34 # # terms of type : T2 X-C-O-X; X not H (generic CO) # # C2'-C1'-O5'-C5' 14 5 6 7 42 # C1'-O5'-C5'-C4' 5 6 7 8 42 # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (generic CO term) - not appropriate for OH) 3 4 5 6 42 # C2-C1-O1-C1' # this term does not exist: there is no psi dihedral in a trehalo linkage, but a phi' instead # # terms of type : T3 X-C-O-H (generic hydroxyl) # # C1'-C2'-O2'-HO2' (chi2 dihedral) 5 14 15 16 43 # C2'-C3'-O3'-HO3' (chi3 dihedral) 14 11 12 13 43 # C3'-C4'-O4'-HO4' (chi4 dihedral) 11 8 9 10 43 # # terms of type : T4 Or-CH*r-O-X (exo-anomeric) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exo-anomeric term) - appropriate for both OC and OH) 3 4 5 6 44 # # terms of type : T5 CH*r-Or-CH*r-O (anomeric) # # O1-C1'-O5'-C5' 4 5 6 7 45 # # terms of type : T6 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-C2' (glycosidic phi-tilde dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 14 46 # # terms of type : T7 Xr-CH*r-O-CH* (exocyclic methoxyl) # # C1-O1-C1'-O5' (glycosidic phi dihedral to next residue (exocyclic methoxyl term) - not appropriate for OH) 3 4 5 6 47 # # terms of type : T12 Ox-X-X-Ox; not type T13 (oxygen-oxygen gauche) # # O1-C1'-C2'-O2' 4 5 14 15 52 # O3'-C3'-C2'-O2' 12 11 14 15 52 # O4'-C4'-C3'-O3' 9 8 11 12 52 # # terms of type : T13 Ox-X-X-Or (oxygen-oxygen intracyclic) # # O5'-C1'-C2'-O2' 6 5 14 15 53 # O5'-C5'-C4'-O4' 6 7 8 9 53 # # terms of type : C4'-C5'-C6'-O61' (gamma dihedral) for carboxylate # # C4'-C5'-C6'-O61' 8 7 17 18 40 # # --- LJ exceptions --- # # NEXP 19 # IE JE MCE condition # # terms of type : N1 H-Xr (lactol) # # C1-O5' 3 6 1 1 1 21 # # terms of type : N2 H-Xr (hydroxyl) [corresponding terms only apply if C#_next / C1_prev are actually hydrogens] # # C1-C3' 3 11 2 1 1 21 # C1-C5' 3 7 2 1 1 21 # C4'-HO2' 8 16 2 0 # O5'-HO2' 6 16 2 0 # C1'-HO3' 5 13 2 0 # C5'-HO3' 7 13 2 0 # HO4'-C2' 10 14 2 0 # O5'-HO4' 6 10 2 0 # # terms of type : N3 CH*-CH*r (substituent-to-ring) # # C1'-C6' 5 17 3 0 # C3'-C6' 11 17 3 0 # # terms of type : N4 O-CH*r (substituent-to-ring) # # O1-C3' 4 11 4 0 # O1-C5' 4 7 4 0 # C4'-O2' 8 15 4 0 # C1'-O3' 5 12 4 0 # C5'-O3' 7 12 4 0 # O4'-C2' 9 14 4 0 # # terms of type : N5 O-CH* (Hassel-Ottar) # # O1-C6' 4 17 5 0 # O3'-C6' 12 17 5 0 #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK C1OC TER TYPE HEXP(1:-) NAME terminal -C1-O1-CH3 group for carbohydrates # building block (residue, nucleotide, etc.) # RNME C1OC # # number of atoms, number of atoms to be replaced # NMAT NREP 3 -2 # # - the O1-CM bond *is* defined in the patch (not included in the residue) # - the C1-O1-CM angle is *not* defined in the patch (but in the residue) # - the O5-C1-O1-CM dihedral (phi dihedral) is *not* defined in the patch (but in the residue) # - the exclusions of C1, O1 and CM *are* defined in the patch (replace those defined in the residue, which # are identical; here there is no exception like in the C1OH patch in the earlier force-field versions) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # # in contrast to the C1OH patch in the earlier force-field versions, O5 is not listed here because there is # no special 1-4 exclusion in the case of a methyl group (only for hydrogen) - was already the case before # # excluded: O1 and CM 1 C1 56 3 0.46400 0 2 2 3 # excluded: CM 2 O1 4 16 -0.46400 0 1 3 # # -- new atoms -- # (exclusions defined here) # 3 CM 16 5 0.23200 1 0 # # -- bonds -- # (new or replacement) # # NB 1 # IB JB MCB # C1-O1 skipped: already included appropriately in the patched residue # O1-CM (new) 2 3 20 # # -- bond angles -- # (new or replacement) # # NBA 0 # IB JB KB MCB # C1-O1-CM skipped: already included appropriately in the patched residue # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 0 # IB JB KB LB MCB # O5-C1-O1-CM skipped: already included appropriately in the patched residue # (same phi dihedral potential for all alkyl substitutions) # -- LJ exceptions -- # (new or replacement) # # NEXP 0 # IE JE MCE condition # #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK C1OH TER TYPE HEXP(1:-) NAME terminal -C1-O1-HO1 group for carbohydrates # building block (residue, nucleotide, etc.) # RNME C1OH # # number of atoms, number of atoms to be replaced # NMAT NREP 4 -3 # # - the O1-H1 bond *is* defined in the patch (not included in the residue) # - the C1-O1-H1 angle *is* defined in the patch as a replacement # - the O5-C1-O1-H1 dihedral (phi dihedral) *is* defined in the patch as a replacement (two terms) # - the exclusions of O5, C1, O1 and HO1 *are* defined in the patch (replace those defined in the residue, # which are identical; no special 1-4 exclusion here [ring oxygen O5 to lactol hydrogen HO1], as we had it # in the earlier force-field versions) # # -- replacement atoms -- # (their exclusions replace those defined in the residue concerning trailing atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE # excluded: C1, O1 and HO1 # no special 1-4 exclusion (ring oxygen to lactol hydrogen), as we had it in the earlier force-field versions 1 O5 54 16 -0.46400 0 2 2 3 # excluded: O1 and HO1 2 C1 56 3 0.46400 0 2 3 4 # excluded: HO1 3 O1 3 16 -0.64200 0 1 4 # # -- new atoms -- # (exclusions defined here) # 4 HO1 21 1 0.41000 1 0 # # -- bonds -- # (new or replacement) # # NB 1 # IB JB MCB # O1-HO1 (new) 3 4 1 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # O5-C1-O1 skipped: already included appropriately in the patched residue # C1-O1-H1 (replacement) 2 3 4 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 4 # IB JB KB LB MCB # O5-C1-O1-HO1 : T3 X-C-O-H (generic hydroxyl) as replacement for existing T2 X-C-O-X; X not H (generic CO) 1 2 3 4 43 # O5-C1-O1-HO1 : T4 Or-CH*r-O-X (exo-anomeric) was already there, but was deleted by the previous replacement 1 2 3 4 44 # C2-C1-O1-HO1 : T0 (dummy) as replacement for existing T6 or T7 phi-tilde dihedral to next residue (exocyclic methoxyl term) # DIHEDRAL KILLER FOR EXISTING T6 OR T7 (UNTIL MAKE_TOP IS FIXED) # kill existing T6 or T7 C2-C1-O1-C in termination patch C1OH; will not be replaced -1 2 3 4 -46 -1 2 3 4 -47 # -- LJ exceptions -- # (new or replacement) # # NEXP 0 # IE JE MCE condition # #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK HO2C INI TYPE HEXP(-:2) NAME initial HO2-O2-C2- group for carbohydrates # building block (residue, nucleotide, etc.) # RNME HO2C # # number of atoms, number of atoms to be replaced # NMAT NREP 2 0 # # - the HO2-O2 and O2-C2 bonds *are* defined in the patch # - the HO2-O2-C2 angle *is* defined in the patch # - the HO2-O2-C2-C1 (chi2 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO2 and O2 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C2 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 HO2 21 1 0.41000 0 1 2 2 O2 3 16 -0.64200 0 0 # # -- bonds -- # (new or replacement) # # NB 1 # IB JB MCB # HO2-O2 (new) 1 2 1 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO2-O2-C2 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 6 # IB JB KB LB MCB # DIHEDRAL KILLER FOR EXISTING T2 (UNTIL MAKE_TOP IS FIXED) # kill existing T2 C_(n-1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4,6); will be replaced by a T3 1 2 3 15 -42 # DIHEDRAL KILLER FOR EXISTING T6 OR T7 (UNTIL MAKE_TOP IS FIXED) # kill existing T6 or T7 C_(n-1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4); this is the psi dihedral # to prev residue (exocyclic methoxyl term), and it will be replaced by a T3 1 2 3 15 -46 1 2 3 15 -47 # DIHEDRAL KILLER FOR EXISTING T6 OR T7 (UNTIL MAKE_TOP IS FIXED) # kill existing T7 or T6 C_(n+1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4); this is the psi-tilde dihedral # to prev residue (exocyclic methoxyl term), and it will not be replaced 1 2 3 4 -46 1 2 3 4 -47 # HO2-O2-C2-C1 : T3 X-C-O-H (generic hydroxyl) as replacement for existing T2 and T6 or T7 (psi) terms 1 2 3 15 43 # -- LJ exceptions -- # (new or replacement) # # NEXP 0 # IE JE MCE condition # #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK HO3C INI TYPE HEXP(-:3) NAME initial HO3-O3-C3- group for carbohydrates # building block (residue, nucleotide, etc.) # RNME HO3C # # number of atoms, number of atoms to be replaced # NMAT NREP 2 0 # # - the HO3-O3 and O3-C3 bonds *are* defined in the patch # - the HO3-O3-C3 angle *is* defined in the patch # - the HO3-O3-C3-C2 (chi3 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO3 and O3 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C3 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 HO3 21 1 0.41000 0 1 2 2 O3 3 16 -0.64200 0 0 # # -- bonds -- # (new or replacement) # # NB 1 # IB JB MCB # HO3-O3 (new) 1 2 1 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO3-O3-C3 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 6 # IB JB KB LB MCB # DIHEDRAL KILLER FOR EXISTING T2 (UNTIL MAKE_TOP IS FIXED) # kill existing T2 C_(n-1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4,6); will be replaced by a T3 1 2 3 4 -42 # DIHEDRAL KILLER FOR EXISTING T6 OR T7 (UNTIL MAKE_TOP IS FIXED) # kill existing T6 or T7 C_(n-1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4); this is the psi dihedral # to prev residue (exocyclic methoxyl term), and it will be replaced by a T3 1 2 3 4 -46 1 2 3 4 -47 # DIHEDRAL KILLER FOR EXISTING T6 OR T7 (UNTIL MAKE_TOP IS FIXED) # kill existing T7 or T6 C_(n+1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4); this is the psi-tilde dihedral # to prev residue (exocyclic methoxyl term), and it will not be replaced 1 2 3 7 -46 1 2 3 7 -47 # HO3-O3-C3-C2 : T3 X-C-O-H (generic hydroxyl) as replacement for existing T2 and T6 or T7 (psi) terms 1 2 3 4 43 # -- LJ exceptions -- # (new or replacement) # # NEXP 0 # IE JE MCE condition # #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK HO4C INI TYPE HEXP(-:4) NAME initial HO4-O4-C4- group for carbohydrates # building block (residue, nucleotide, etc.) # RNME HO4C # # number of atoms, number of atoms to be replaced # NMAT NREP 2 0 # # - the HO4-O4 and O4-C4 bonds *are* defined in the patch # - the HO4-O4-C4 angle *is* defined in the patch # - the HO4-O4-C4-C3 (chi4 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO4 and O4 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C4 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 HO4 21 1 0.41000 0 1 2 2 O4 3 16 -0.64200 0 0 # # -- bonds -- # (new or replacement) # # NB 1 # IB JB MCB # HO4-O4 (new) 1 2 1 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO4-O4-C4 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 6 # IB JB KB LB MCB # DIHEDRAL KILLER FOR EXISTING T2 (UNTIL MAKE_TOP IS FIXED) # kill existing T2 C_(n-1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4,6); will be replaced by a T3 1 2 3 7 -42 # DIHEDRAL KILLER FOR EXISTING T6 OR T7 (UNTIL MAKE_TOP IS FIXED) # kill existing T6 or T7 C_(n-1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4); this is the psi dihedral # to prev residue (exocyclic methoxyl term), and it will be replaced by a T3 1 2 3 7 -46 1 2 3 7 -47 # DIHEDRAL KILLER FOR EXISTING T6 OR T7 (UNTIL MAKE_TOP IS FIXED) # kill existing T7 or T6 C_(n+1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4); this is the psi-tilde dihedral # to prev residue (exocyclic methoxyl term), and it will not be replaced 1 2 3 13 -46 1 2 3 13 -47 # HO4-O4-C4-C3 : T3 X-C-O-H (generic hydroxyl) as replacement for existing T2 and T6 or T7 (psi) terms 1 2 3 7 43 # -- LJ exceptions -- # (new or replacement) # # NEXP 0 # IE JE MCE condition # #@FREELINE END MTBUILDBLEND #@BLOCKTYPE 56a6@CARBO_carbo.mtb BLK HO6C INI TYPE HEXP(-:6) NAME initial HO6-O6-C6- group for carbohydrates # building block (residue, nucleotide, etc.) # RNME HO6C # # number of atoms, number of atoms to be replaced # NMAT NREP 2 0 # # - the HO6-O6 and O6-C6 bonds *are* defined in the patch # - the HO6-O6-C6 angle *is* defined in the patch # - the HO6-O6-C6-C5 (chi6 dihedral) is *not* defined in the patch (but in the residue) # [PHH, May 2011: this term was removed because unnecessary; should have no effect on built topologies] # - the exclusions of HO6 and O6 *are* defined in the patch (replace those defined in the residue, which are identical) # - the exclusions of C6 are *not* defined in the patch (but in the residue) # # -- new atoms -- # (their exclusions replace those defined in the residue concerning preceding atoms) # #ATOM ANM IACM MASS CGM ICGM MAE MSAE 1 HO6 21 1 0.41000 0 1 2 2 O6 3 16 -0.64200 0 0 # # -- bonds -- # (new or replacement) # # NB 1 # IB JB MCB # HO6-O6 (new) 1 2 1 # # -- bond angles -- # (new or replacement) # # NBA 1 # IB JB KB MCB # HO6-O6-C6 (new) 1 2 3 12 # # -- improper dihedrals -- # (new or replacement) # # NIDA 0 # IB JB KB LB MCB # # -- dihedrals -- # (new or replacement) # # NDA 2 # IB JB KB LB MCB # DIHEDRAL KILLER FOR EXISTING T2 (UNTIL MAKE_TOP IS FIXED) # kill existing T2 C_(n-1)-C_n-O_n-C in initiation patch HOnC (n=2,3,4,6); will be replaced by a T3 1 2 3 13 -42 # HO6-O6-C6-O5 : T3 X-C-O-H (generic hydroxyl) as replacement for existing T2 (psi) term 1 2 3 13 43 # -- LJ exceptions -- # (new or replacement) # # NEXP 0 # IE JE MCE condition # #@FREELINE END