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)LH5
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17475
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 (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 
1554 None - 155 0 Manual* N/A Compare with
17293 None - 9 -1 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17325 None - 25 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17327 None - 25 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
17297 None - 18 0 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17299 None - 18 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17331 None - 17 -2 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17397 None - 21 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
1655 None - 9 0 Manual* N/A Compare with
3408 None - 24 0 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
1677 None - 34 0 Manual* N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
1679 None - 31 0 Manual* N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
3486 None - 9 0 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
1731 None - 74 0 Manual* N/A Compare with
17349 None - 15 0 Manual N/A Compare with
3488 None - 12 0 Manual* N/A Compare with
17381 None - 23 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
17351 None - 15 0 Manual N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17383 None - 23 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
17353 None - 23 0 Manual N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
17355 None - 23 0 Manual N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
2109 None - 171 -2 Manual* N/A Compare with
17357 None - 30 0 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
2172 None - 26 -1 Manual* N/A Compare with
17359 None - 30 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
17361 None - 12 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17415 None - 24 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)