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)T1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge-1
Forcefieldmultiple
Molecule ID17521
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:18
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 
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
1576 None - 129 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
168 None - 15 0 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17363 None - 12 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1572 None - 153 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
166 None - 17 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17361 None - 12 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
6458 None - 13 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)