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)T1P
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms21
Net Charge-1
Forcefieldmultiple
Molecule ID17523
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:19
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 >
17460 None - 28 0 Manual N/A Compare with
17459 None - 28 0 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17448 None - 28 0 Manual N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17446 None - 28 0 Manual N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17444 None - 28 1 Manual N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17442 None - 28 1 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17433 None - 21 -1 Manual N/A Compare with
17432 None - 15 0 Manual N/A Compare with
17431 None - 15 0 Manual N/A Compare with
17430 None - 15 0 Manual N/A Compare with
17429 None - 15 0 Manual N/A Compare with
17428 None - 34 1 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
17416 None - 24 1 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
17414 None - 24 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
17412 None - 18 0 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
17410 None - 18 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17401 None - 16 -1 Manual N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17398 None - 21 0 Manual N/A Compare with
17397 None - 21 0 Manual N/A Compare with
17396 None - 24 -1 Manual N/A Compare with
17395 None - 24 -1 Manual N/A Compare with
17394 None - 24 -1 Manual N/A Compare with
17393 None - 24 -1 Manual N/A Compare with
17392 None - 18 0 Manual N/A Compare with
17391 None - 18 0 Manual N/A Compare with
17390 None - 18 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
17382 None - 23 0 Manual N/A Compare with
17381 None - 23 0 Manual N/A Compare with
17380 None - 28 -1 Manual N/A Compare with
17379 None - 28 -1 Manual N/A Compare with
17378 None - 28 -1 Manual N/A Compare with
17377 None - 28 -1 Manual N/A Compare with
17376 None - 30 -1 Manual N/A Compare with
17375 None - 30 -1 Manual N/A Compare with
17374 None - 30 -1 Manual N/A Compare with
17373 None - 30 -1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
17366 None - 29 0 Manual N/A Compare with
17365 None - 29 0 Manual N/A Compare with
17364 None - 12 0 Manual N/A Compare with
17363 None - 12 0 Manual N/A Compare with
17362 None - 12 0 Manual N/A Compare with
17361 None - 12 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)