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) 2000 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

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 
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17366 None - 29 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17232 None - 27 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17279 None - 24 1 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17349 None - 15 0 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
17298 None - 18 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17364 None - 12 0 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17230 None - 27 0 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17277 None - 24 1 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17194 None - 28 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17362 None - 12 0 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
6459 None - 16 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)