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) 1000 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

GROMOS96 Files

Topology Files Structure Files
GROMOS96 United-Atom MTB
United-Atom PDB (optimised geometry)

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 
17439 None - 25 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17459 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
17433 None - 21 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17545 None - 26 1 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
4213 None - 61 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)