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 Typeheteromolecule
Residue Name (RNME)ALG5
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms161
Net Charge-8
Forcefieldmultiple
Molecule ID4582
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 Date2012-01-04 14:25:14
Literature Reference

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 
17545 None - 26 1 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17411 None - 18 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17207 None - 18 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17409 None - 18 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17220 None - 31 1 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17254 None - 27 0 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17186 None - 15 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)