MD Topology | NMR | X-Ray

Visualize with JSmol

Processing Information

QM Processing Stage

Click table to toggle details.

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)L5H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17163
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 (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 
17426 None - 34 1 Manual N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17292 None - 28 0 Manual N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17324 None - 18 0 Manual N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
167 None - 14 -1 Manual* N/A Compare with
17543 None - 29 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
1553 None - 155 0 Manual* N/A Compare with
17307 None - 23 0 Manual N/A Compare with
1593 None - 3 0 Manual* N/A Compare with
17339 None - 18 0 Manual N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
206 None - 25 1 Manual* N/A Compare with
1502 None - 106 0 Manual* N/A Compare with
17409 None - 18 0 Manual N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17358 None - 30 0 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17148 None - 33 1 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17283 None - 23 0 Manual N/A Compare with
17290 None - 28 0 Manual N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17322 None - 18 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17200 None - 26 1 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
165 None - 26 0 Manual* N/A Compare with
568 None - 16 0 Manual* N/A Compare with
1551 None - 153 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
1590 None - 147 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17183 None - 23 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
17215 None - 29 0 Manual N/A Compare with
204 None - 22 0 Manual* N/A Compare with
584 None - 15 0 Manual* N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
6459 None - 16 0 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17164 None - 23 0 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17146 None - 33 1 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
2018 None - 90 -1 Manual* N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
3587 None - 9 0 Manual* N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17288 None - 17 0 Manual N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
17166 None - 27 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17198 None - 26 1 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
163 None - 13 0 Manual* N/A Compare with
566 None - 12 0 Manual* N/A Compare with
5031 None - 78 0 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
Previous Page Next Page

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)