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 
17153 None - 17 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17165 None - 27 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)