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)H1M
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17451
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:18
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 (501-600 of 633)

The highlighted row is the currently viewed molecule with the following conditions:
Green: the current molecule has the lowest QM energy in the set.
Yellow: the current molecule is within 2 kJ.mol-1 of the minimum energy.
Red: the current molecule is above 2 kJ.mol-1 of the minimum energy.

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge > Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17244 None - 26 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17551 None - 15 -1 Manual N/A Compare with
17549 None - 15 -1 Manual N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17480 None - 27 -1 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17478 None - 27 -1 Manual N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17311 None - 25 -1 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17309 None - 25 -1 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17296 None - 9 -1 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
17294 None - 9 -1 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17346 None - 20 -2 Manual N/A Compare with
17330 None - 17 -2 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17248 None - 27 -2 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17252 None - 23 -2 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)