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  Details  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17177 None - 20 -1 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17325 None - 25 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17515 None - 26 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
208 None - 23 0 Manual* N/A Compare with
17547 None - 26 1 Manual N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17199 None - 26 1 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17510 None - 27 0 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17542 None - 29 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
5810 None - 156 -12 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)