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
Residue Name (RNME)YCH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge0
Forcefieldmultiple
Molecule ID17533
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:19
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 
17246 None - 27 -2 Manual N/A Compare with
17245 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
17509 None - 27 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17501 None - 32 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)