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)KCN
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms27
Net Charge0
Forcefieldmultiple
Molecule ID17231
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
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 (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 
7284 None - 71 1 Manual* N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17335 None - 30 1 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17220 None - 31 1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17413 None - 24 1 Manual N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17278 None - 24 1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
5089 None - 41 1 Manual* N/A Compare with
17426 None - 34 1 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
564 None - 6 0 Manual* N/A Compare with
562 None - 9 0 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
210 None - 17 0 Manual* N/A Compare with
30988 None - 1456 0 Template N/A Compare with
177 None - 20 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
175 None - 19 0 Manual* N/A Compare with
169 None - 13 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
578 None - 10 0 Manual* N/A Compare with
580 None - 12 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
1506 None - 134 0 Manual* N/A Compare with
1505 None - 130 0 Manual* N/A Compare with
1503 None - 118 0 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
619 None - 16 0 Manual* N/A Compare with
584 None - 15 0 Manual* N/A Compare with
583 None - 15 0 Manual* N/A Compare with
582 None - 12 0 Manual* N/A Compare with
581 None - 16 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)