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)W7H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms28
Net Charge0
Forcefieldmultiple
Molecule ID17456
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:18
Literature ReferenceDrazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic; A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications; PLOS Computational Biology, 2013, 9 (7), e1003154

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 
17260 None - 15 -1 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17232 None - 27 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17264 None - 17 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17306 None - 23 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17340 None - 18 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)

Column Lengths: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] Column Lengths: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] Column Lengths: [4, 4, 4, 4] Column Lengths: [3, 3, 3, 3] Column Lengths: [3, 3, 3]