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)KPH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge1
Forcefieldmultiple
Molecule ID17545
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 (1-100 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac > Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17263 None - 17 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17514 None - 26 0 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17512 None - 27 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 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)