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 building block
Residue Name (RNME)W7H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms28
Net Charge0
Forcefieldmultiple
Molecule ID17456
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 (301-400 of 632)

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation > Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17467 None - 31 0 Manual N/A Compare with
2921 None - 75 -2 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
3923 None - 4 0 Manual N/A Compare with
3924 None - 176 0 Manual N/A Compare with
3947 None - 127 -1 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17462 None - 22 0 Manual N/A Compare with
17464 None - 22 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17482 None - 15 0 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17494 None - 19 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17498 None - 25 0 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
17528 None - 18 0 Manual N/A Compare with
17359 None - 30 0 Manual N/A Compare with
17360 None - 30 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17340 None - 18 0 Manual N/A Compare with
17341 None - 23 -2 Manual N/A Compare with
17344 None - 23 -2 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
17348 None - 20 -2 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
2920 None - 27 1 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)