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 Typeamino acid building block
Residue Name (RNME)LYS
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge0
Forcefieldmultiple
Molecule ID205
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS96 Files

Topology Files Structure Files
GROMOS96 United-Atom MTB

Topology Information

Force Field Version53A6 (IFP53A6.dat / 53A6.ifp)
Upload Date2009-08-13 10:38:54
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  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17432 None - 15 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
204 None - 22 0 Manual* N/A Compare with
17460 None - 28 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17496 None - 19 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
1651 None - 10 0 Manual* N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17512 None - 27 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)