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)WBR
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID17256
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:15
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 
17491 None - 22 0 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17389 None - 18 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17235 None - 26 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
1566 None - 129 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17400 None - 21 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)