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)H31
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge-1
Forcefieldmultiple
Molecule ID17395
Tautomer Group IDNone
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 633)

The highlighted row is the currently viewed molecule with the following conditions:
Green: the current molecule has the lowest QM energy in the set.
Yellow: the current molecule is within 2 kJ.mol-1 of the minimum energy.
Red: the current molecule is above 2 kJ.mol-1 of the minimum energy.

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac > Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17497 None - 25 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
17414 None - 24 1 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17446 None - 28 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17512 None - 27 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
1556 None - 143 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
3587 None - 9 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
17412 None - 18 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17444 None - 28 1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17361 None - 12 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
30988 None - 1456 0 Template N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
207 None - 20 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
17410 None - 18 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17442 None - 28 1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17527 None - 18 0 Manual N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
17193 None - 28 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)