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)KPH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge1
Forcefieldmultiple
Molecule ID17548
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:19
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 
17247 None - 27 -2 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
2694 None - 77 -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
18619 None - 49 -3 Manual N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
5810 None - 156 -12 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)