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)T1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge-1
Forcefieldmultiple
Molecule ID17521
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:18
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 (101-200 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 
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
173 None - 20 0 Manual* N/A Compare with
17270 None - 18 0 Manual N/A Compare with
576 None - 26 0 Manual* N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
17336 None - 30 1 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
171 None - 14 0 Manual* N/A Compare with
17268 None - 19 0 Manual N/A Compare with
574 None - 17 0 Manual* N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
17334 None - 30 1 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
169 None - 13 0 Manual* N/A Compare with
17266 None - 19 0 Manual N/A Compare with
572 None - 17 0 Manual* N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
17485 None - 21 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)