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)KPH
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge1
Forcefieldmultiple
Molecule ID17545
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:19
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 
17304 None - 25 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17336 None - 30 1 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17472 None - 24 0 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
1732 None - 73 0 Manual* N/A Compare with
17421 None - 21 0 Manual N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
17353 None - 23 0 Manual N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17368 None - 29 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17317 None - 24 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17470 None - 24 0 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
17419 None - 21 0 Manual N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
5795 None - 18 -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)