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)P5H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17324
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:16
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 
5810 None - 156 -12 Manual* N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
4592 None - 161 -8 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
18675 None - 140 -3 Manual N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17258 None - 15 -1 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17260 None - 15 -1 Manual N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17242 None - 26 -1 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)