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
Residue Name (RNME)HTY
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17173
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:14
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 (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation > Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17399 None - 21 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17277 None - 24 1 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)