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)P5H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17322
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:16
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 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 
17546 None - 26 1 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17427 None - 34 1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17510 None - 27 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17493 None - 19 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17425 None - 34 1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17457 None - 28 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17508 None - 29 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17491 None - 22 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17440 None - 25 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
2920 None - 27 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)