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)TDH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms15
Net Charge0
Forcefieldmultiple
Molecule ID17352
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
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 (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 
17529 None - 18 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
30988 None - 1456 0 Template 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)