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)D1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms20
Net Charge-1
Forcefieldmultiple
Molecule ID17180
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:14
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 
17207 None - 18 0 Manual N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17181 None - 23 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17213 None - 29 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17431 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
17433 None - 21 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17197 None - 26 1 Manual N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17205 None - 18 0 Manual N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17239 None - 16 -1 Manual N/A Compare with
17515 None - 26 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17271 None - 18 0 Manual N/A Compare with
17241 None - 26 -1 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17273 None - 24 -1 Manual N/A Compare with
17243 None - 26 -1 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17275 None - 24 -1 Manual N/A Compare with
17245 None - 27 -2 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17277 None - 24 1 Manual N/A Compare with
17247 None - 27 -2 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17279 None - 24 1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17227 None - 20 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)