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 Typesugar
Residue Name (RNME)CRA
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms35
Net Charge0
Forcefieldmultiple
Molecule ID1678
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 Date2010-08-06 09:08:16
Literature ReferenceMalde AK and Mark AE. How much can be trust the binding modes of non-standard ligands in X-ray crystal complexes? J. Med. Chem., manuscript submitted.

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 
17313 None - 32 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17415 None - 24 1 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17413 None - 24 1 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17362 None - 12 0 Manual N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17411 None - 18 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
2002 None - 24 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)