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)KH5
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms25
Net Charge0
Forcefieldmultiple
Molecule ID17437
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
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 
17160 None - 20 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17545 None - 26 1 Manual N/A Compare with
17162 None - 23 0 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17547 None - 26 1 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17527 None - 18 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
17529 None - 18 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17531 None - 18 0 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17533 None - 24 0 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17535 None - 24 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
5796 None - 19 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17154 None - 17 0 Manual N/A Compare with
5798 None - 19 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
17541 None - 29 0 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17165 None - 27 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17207 None - 18 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 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)