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)ECN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge-1
Forcefieldmultiple
Molecule ID17433
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:17
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 
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
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
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
17450 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17546 None - 26 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)