MD Topology | NMR | X-Ray

Visualize with JSmol

Processing Information

QM Processing Stage

Click table to toggle details.

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)GLG
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID1668
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 Date2010-08-05 22:22:39
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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17408 None - 28 -1 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17531 None - 18 0 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17162 None - 23 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
Previous Page Next Page

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)