MD Topology | NMR | X-Ray

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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 Typeamino acid building block
Residue Name (RNME)CYS
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms13
Net Charge0
Forcefieldmultiple
Molecule ID169
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 Date2009-08-10 17:13:25
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  Details  Δ Qm Optimized Energy
(kJ.mol-1)  		Compare 
17154 None - 17 0 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17360 None - 30 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
1502 None - 106 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
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
215 None - 19 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
1651 None - 10 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
165 None - 26 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
569 None - 8 0 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
3487 None - 12 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
577 None - 37 0 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
17480 None - 27 -1 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17274 None - 24 -1 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
1567 None - 119 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17496 None - 19 0 Manual N/A Compare with
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Conditions of Use

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)

Solvent > Experimental Value
(kJ.mol-1)  		Experimental Uncertainty
(kJ.mol-1)  		Doi 
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