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 (101-200 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms > Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
210 None - 17 0 Manual* N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
177 None - 20 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17159 None - 20 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)