MD Topology | NMR | X-Ray

Visualize with JSmol

Show Structure

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)WKF
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms29
Net Charge0
Forcefieldmultiple
Molecule ID17506
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
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 
4013 None - 176 0 Manual* N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17343 None - 23 -2 Manual N/A Compare with
4213 None - 61 0 Manual N/A Compare with
2672 None - 39 0 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17345 None - 20 -2 Manual N/A Compare with
4579 None - 161 -8 Manual* N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17347 None - 20 -2 Manual N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17349 None - 15 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
1651 None - 10 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
17447 None - 28 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17421 None - 21 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
17503 None - 32 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17508 None - 29 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17510 None - 27 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
17512 None - 27 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
17514 None - 26 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
17516 None - 26 0 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17534 None - 24 0 Manual N/A Compare with
17536 None - 24 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
17544 None - 29 0 Manual N/A Compare with
17546 None - 26 1 Manual N/A Compare with
17548 None - 26 1 Manual N/A Compare with
17550 None - 15 -1 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
17528 None - 18 0 Manual N/A Compare with
21025 None - 209 -4 Manual* N/A Compare with
17530 None - 18 0 Manual N/A Compare with
17532 None - 18 0 Manual N/A Compare with
8099 None - 3218 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
Previous Page Next Page

Conditions of Use

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)

Solvent  Experimental Value
(kJ.mol-1)  		Experimental Uncertainty
(kJ.mol-1)  		Doi >
Previous Page Next Page