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)R1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms30
Net Charge-1
Forcefieldmultiple
Molecule ID17375
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
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 (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 
17357 None - 30 0 Manual N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17424 None - 21 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17187 None - 15 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
17219 None - 31 1 Manual N/A Compare with
566 None - 12 0 Manual* N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
17321 None - 18 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17475 None - 23 0 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17422 None - 21 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17473 None - 23 0 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
5181 None - 56 -6 Manual* N/A Compare with
17149 None - 16 -1 Manual N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17353 None - 23 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17420 None - 21 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
6460 None - 12 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17147 None - 33 1 Manual N/A Compare with
17300 None - 18 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)