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)ECN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge-1
Forcefieldmultiple
Molecule ID17435
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 
1578 None - 144 0 Manual* N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17226 None - 20 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
210 None - 17 0 Manual* N/A Compare with
17392 None - 18 0 Manual N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
17546 None - 26 1 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
30988 None - 1456 0 Template N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17256 None - 27 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17358 None - 30 0 Manual N/A Compare with
207 None - 20 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
17544 None - 29 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17476 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
1572 None - 153 0 Manual* N/A Compare with
17168 None - 27 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)