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Processing Stage | Template | Semi-Empirical QM (QM0) | DFT QM (QM1) | DFT Hessian QM (QM2) | |
---|---|---|---|---|---|
Calculation | None | Energy Minization | Energy Minization | Hessian | |
Level of Theory | None | Semi-Empirical / SCF | DFT (B3LYP/6-31G*) | DFT (B3LYP/6-31G*) | |
Default Size Limit (Atoms) | 2000 | 500 | 50 | 40 | |
Content of MD Topology | |||||
Charges Derived From | None | MOPAC | Merz-Singh-Kollman | Merz-Singh-Kollman | |
Geometry | User Provided | Optimized | Optimized | Optimized | |
Non-Bonded Interactions | Bonds | Rule Based: Parameters are asigned from existing parameters with a set of rules based on atom types and geometry. | Hessian Based: Force constant are calculated from the QM potential. New parameters are created when no suitable parameters exists. | ||
Angles | |||||
Dihedrals |
Current Processing State | Template |
Total Processing Time | NA (hh:mm:ss) |
Molecule Type | nucleic acid |
Residue Name (RNME) | 5XS6 |
Formula | 2C98H113N37O58P9 |
IUPAC InChI Key | KMALPVUMMVVAGK-XNWYNHHESA-N |
IUPAC InChI | InChI=1S/2C98H124N37O58P9/c2*1-39-18-128(96(145)123-87(39)138)66-11-45(187-196(152,153)168-23-54-44(10-65(177-54)127-7-5-63(100)118-95(127)144)186-194(148,149)166-22-53-42(137)8-64(176-53)126-6-4-62(99)117-94(126)143)55(178-66)24-169-199(158,159)190-48-14-69(131-34-112-74-79(101)106-31-109-82(74)131)181-58(48)27-172-197(154,155)188-46-12-67(129-19-40(2)88(139)124-97(129)146)179-56(46)25-170-200(160,161)191-49-15-70(132-35-113-75-80(102)107-32-110-83(75)132)182-59(49)28-173-198(156,157)189-47-13-68(130-20-41(3)89(140)125-98(130)147)180-57(47)26-171-201(162,163)192-50-16-71(133-36-114-76-81(103)108-33-111-84(76)133)183-60(50)29-174-202(164,165)193-51-17-73(135-38-116-78-86(135)120-93(105)122-91(78)142)184-61(51)30-167-195(150,151)185-43-9-72(175-52(43)21-136)134-37-115-77-85(134)119-92(104)121-90(77)141/h2*4-7,18-20,31-38,42-61,64-73,136-137H,8-17,21-30,99-105H2,1-3H3,(H,121,141)(H,122,142)(H,148,149)(H,150,151)(H,152,153)(H,154,155)(H,156,157)(H,158,159)(H,160,161)(H,162,163)(H,164,165)(H,123,138,145)(H,124,139,146)(H,125,140,147)/t2*42-,43-,44-,45-,46-,47-,48-,49-,50-,51-,52+,53+,54+,55+,56+,57+,58+,59+,60+,61+,64+,65+,66+,67+,68+,69+,70+,71+,72+,73+/m00/s1 |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=[N]=[C]1=O)N)O)N1C=CC(=[N]=[C]1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)N1C=[N]=C2C1=[N]=[CH]=[N]=C2N)O)n1cc(C)c(=O)[nH]c1=O)O)N1C=[N]=C2C1=[N]=[CH]=[N]=C2N)O)n1cc(C)c(=O)[nH]c1=O)O)N1C=[N]=C2C1=[N]=[CH]=[N]=C2N)O)N1C=[N]=C2C1=[N]=C(N)NC2=O)O)N1C=[N]=C2C1=[N]=C(N)NC2=O.OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O[P@@](=O)(OC[C@H]1O[C@H](C[C@@H]1O)N1C=CC(=[N]=[C]1=O)N)O)N1C=CC(=[N]=[C]1=O)N)O)n1cc(C)c(=O)[nH]c1=O)O)N1C=[N]=C2C1=[N]=[CH]=[N]=C2N)O)n1cc(C)c(=O)[nH]c1=O)O)N1C=[N]=C2C1=[N]=[CH]=[N]=C2N)O)n1cc(C)c(=O)[nH]c1=O)O)N1C=[N]=C2C1=[N]=[CH]=[N]=C2N)O)N1C=[N]=C2C1=[N]=C(N)NC2=O)O)N1C=[N]=C2C1=[N]=C(N)NC2=O |
Number of atoms | 630 |
Net Charge | -15 |
Forcefield | multiple |
Molecule ID | 365206 |
Visibility | Public |
Molecule Tags |
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The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.