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)KH5
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17440
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:17
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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
1548 None - 24 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17308 None - 23 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)