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)UREA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms8
Net Charge0
Forcefieldmultiple
Molecule ID1664
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS96 Files

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

Additional Structure Files

Files
United-Atom G96 (optimised geometry)

Consistency Check of Topology

Files
Check Top Result for GROMOS96 United-Atom Topology

Topology Information

Force Field Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2010-08-04 17:18:15
Literature ReferenceLink

Topology History

Other conformers for this molecule (1-100 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula > Iupac  Atoms  Charge  Curation  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
213 None - 27 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17491 None - 22 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17533 None - 24 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17486 None - 21 0 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17508 None - 29 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17226 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)