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
Residue Name (RNME)H2X
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge0
Forcefieldmultiple
Molecule ID17487
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 (201-300 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac > Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17196 None - 28 0 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17535 None - 24 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17499 None - 25 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17313 None - 32 0 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17328 None - 25 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
1657 None - 5 0 Manual* N/A Compare with
3409 None - 27 0 Manual* N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17548 None - 26 1 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
1550 None - 24 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)