MD Topology | NMR | X-Ray

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Processing Information

QM Processing Stage

Click table to toggle details.

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)L5H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17162
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:14
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 (201-300 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 
17289 None - 28 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17416 None - 24 1 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)