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)K2P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge-2
Forcefieldmultiple
Molecule ID17246
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:15
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 (201-300 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 
17503 None - 32 0 Manual N/A Compare with
1560 None - 123 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
1602 None - 20 0 Manual* N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17190 None - 44 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
7284 None - 71 1 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
1557 None - 131 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17233 None - 26 0 Manual N/A Compare with
1598 None - 6 0 Manual* N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17188 None - 15 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
7282 None - 113 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17284 None - 23 0 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17350 None - 15 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
1555 None - 167 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17231 None - 27 0 Manual N/A Compare with
1595 None - 5 0 Manual* N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17314 None - 32 0 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17348 None - 20 -2 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)