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)K1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms28
Net Charge-1
Forcefieldmultiple
Molecule ID17408
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 
17265 None - 19 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17163 None - 23 0 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17165 None - 27 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17466 None - 31 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17295 None - 9 -1 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)