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 (601-633 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 
17364 None - 12 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
6460 None - 12 0 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
570 None - 11 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
567 None - 10 0 Manual* N/A Compare with
578 None - 10 0 Manual* N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1596 None - 3 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)