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)WNI
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms29
Net Charge0
Forcefieldmultiple
Molecule ID17367
Tautomer Group IDNone
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 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 
2749 None - 14 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
578 None - 10 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17232 None - 27 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17381 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)