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 Typeheteromolecule
Residue Name (RNME)URA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms12
Net Charge0
Forcefieldmultiple
Molecule ID6460
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS96 Files

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

Topology Information

Force Field Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2012-10-30 23:45:42
Literature Reference

Topology History

Other conformers for this molecule (1-100 of 633)

Compare All Topologies (634)RMSD Matrix (634)

Molid  Formula  Iupac  Atoms  Charge  Curation  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17196 None - 28 0 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17209 None - 27 -2 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)