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)SEP
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms11
Net Charge-2
Forcefieldmultiple
Molecule ID9371
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2013-07-01 10:47:42
Literature Reference

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 
17321 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17431 None - 15 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)