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)SEP
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms11
Net Charge-2
Forcefieldmultiple
Molecule ID9371
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

GROMOS96 Files

Topology Files Structure Files
GROMOS96 United-Atom MTB
United-Atom PDB (optimised geometry)

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2013-07-01 10:47:42
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 
566 None - 12 0 Manual* N/A Compare with
165 None - 26 0 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
568 None - 16 0 Manual* N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
570 None - 11 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
171 None - 14 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
173 None - 20 0 Manual* N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17532 None - 18 0 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17534 None - 24 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17161 None - 23 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17163 None - 23 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
1646 None - 3 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)