MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

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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

Data

Current Processing StateCompleted
Total Processing TimeNA (hh:mm:ss)

Molecule Information

Molecule Typeamino acid building block
Residue Name (RNME)PYA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms9
Net Charge-1
Forcefieldmultiple
Molecule ID17296
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:16
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

Topology History

Other conformers for this molecule (401-500 of 633)

The highlighted row is the currently viewed molecule with the following conditions:
Green: the current molecule has the lowest QM energy in the set.
Yellow: the current molecule is within 2 kJ.mol-1 of the minimum energy.
Red: the current molecule is above 2 kJ.mol-1 of the minimum energy.

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation > Δ Qm Optimized Energy
(kJ.mol-1
Compare 
5639 None - 127 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
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ATB Pipeline Setting

Access to this feature is currently restricted

The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.

Experimental Solvation Free Energies (0-0 of 0)