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 >
566 None - 12 0 Manual* N/A Compare with
565 None - 9 0 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
562 None - 9 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
208 None - 23 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
206 None - 25 1 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
163 None - 13 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)