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)F23
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17302
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
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 
1594 None - 10 0 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
2018 None - 90 -1 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)