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)YNB
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge0
Forcefieldmultiple
Molecule ID17516
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 
1505 None - 130 0 Manual* N/A Compare with
211 None - 14 0 Manual* N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
1507 None - 138 0 Manual* N/A Compare with
213 None - 27 0 Manual* N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
1511 None - 131 0 Manual* N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17439 None - 25 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17441 None - 28 1 Manual N/A Compare with
17411 None - 18 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17443 None - 28 1 Manual N/A Compare with
17413 None - 24 1 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
166 None - 17 0 Manual* N/A Compare with
17445 None - 28 0 Manual N/A Compare with
17415 None - 24 1 Manual N/A Compare with
569 None - 8 0 Manual* N/A Compare with
168 None - 15 0 Manual* N/A Compare with
17447 None - 28 0 Manual N/A Compare with
17417 None - 21 0 Manual N/A Compare with
571 None - 14 0 Manual* N/A Compare with
170 None - 14 0 Manual* N/A Compare with
17449 None - 23 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
573 None - 20 0 Manual* N/A Compare with
172 None - 14 0 Manual* N/A Compare with
17451 None - 23 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
575 None - 20 0 Manual* N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17453 None - 28 0 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17455 None - 28 0 Manual N/A Compare with
17425 None - 34 1 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17457 None - 28 0 Manual N/A Compare with
17427 None - 34 1 Manual N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
17489 None - 22 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17491 None - 22 0 Manual N/A Compare with
17461 None - 22 0 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17493 None - 19 0 Manual N/A Compare with
17463 None - 22 0 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
1567 None - 119 0 Manual* N/A Compare with
17495 None - 19 0 Manual N/A Compare with
17465 None - 31 0 Manual N/A Compare with
1642 None - 18 0 Manual* N/A Compare with
1571 None - 147 0 Manual* N/A Compare with
17497 None - 25 0 Manual N/A Compare with
17467 None - 31 0 Manual N/A Compare with
1649 None - 5 0 Manual* N/A Compare with
1574 None - 123 0 Manual* N/A Compare with
17499 None - 25 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
1577 None - 138 0 Manual* N/A Compare with
1525 None - 147 0 Manual* N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
1579 None - 143 0 Manual* N/A Compare with
1532 None - 149 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
1582 None - 119 0 Manual* N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17507 None - 29 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17509 None - 27 0 Manual N/A Compare with
17479 None - 27 -1 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17511 None - 27 0 Manual N/A Compare with
17481 None - 15 0 Manual N/A Compare with
1591 None - 137 0 Manual* N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
17513 None - 26 0 Manual N/A Compare with
17483 None - 15 0 Manual N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
1556 None - 143 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