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 ID17523
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:19
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 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation > Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17276 None - 24 -1 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17322 None - 18 0 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17307 None - 23 0 Manual N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17262 None - 17 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17298 None - 18 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17299 None - 18 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17228 None - 20 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17173 None - 25 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
6458 None - 13 0 Manual N/A Compare with
17280 None - 24 1 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17222 None - 22 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17224 None - 22 0 Manual N/A Compare with
17230 None - 27 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17265 None - 19 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17316 None - 32 0 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17308 None - 23 0 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17292 None - 28 0 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
17326 None - 25 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17175 None - 25 0 Manual N/A Compare with
17171 None - 28 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17156 None - 17 0 Manual N/A Compare with
17153 None - 17 0 Manual N/A Compare with
17285 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)