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 ID17304
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 (1-100 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17265 None - 19 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17422 None - 21 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)