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)KH5
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17440
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:17
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 
17241 None - 26 -1 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17529 None - 18 0 Manual N/A Compare with
30988 None - 1456 0 Template N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17154 None - 17 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
17256 None - 27 0 Manual N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17205 None - 18 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17358 None - 30 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17271 None - 18 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
17254 None - 27 0 Manual N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17203 None - 33 1 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17320 None - 24 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
5182 None - 110 -8 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)