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)N3H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms18
Net Charge0
Forcefieldmultiple
Molecule ID17392
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version45A3 (IFP45A3.dat)
Upload Date2014-02-03 13:07:17
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 (1-100 of 633)

The highlighted row is the currently viewed molecule with the following conditions:
Green: the current molecule has the lowest QM energy in the set.
Yellow: the current molecule is within 2 kJ.mol-1 of the minimum energy.
Red: the current molecule is above 2 kJ.mol-1 of the minimum energy.

Compare All Topologies (633)RMSD Matrix (633)

Molid  Formula  Iupac  Atoms  Charge  Curation  Δ Qm Optimized Energy
(kJ.mol-1
Compare 
17406 None - 28 -1 Manual N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17196 None - 28 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
5011 None - 40 -4 Manual* N/A Compare with
17145 None - 33 1 Manual N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
2002 None - 24 0 Manual* N/A Compare with
3505 None - 18 0 Manual* N/A Compare with
17253 None - 27 0 Manual N/A Compare with
6252 None - 89 0 Manual* N/A Compare with
17160 None - 20 0 Manual N/A Compare with
17287 None - 17 0 Manual N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17472 None - 24 0 Manual N/A Compare with
17504 None - 32 0 Manual N/A Compare with
2919 None - 52 -1 Manual N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17179 None - 20 -1 Manual N/A Compare with
17211 None - 27 -2 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
1564 None - 143 0 Manual* N/A Compare with
1606 None - 20 0 Manual* N/A Compare with
17194 None - 28 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
562 None - 9 0 Manual* N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
4604 None - 217 0 Manual* N/A Compare with
9411 None - 17 -2 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
1738 None - 77 0 Manual* N/A Compare with
3502 None - 19 0 Manual* N/A Compare with
17251 None - 23 -2 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17158 None - 20 0 Manual N/A Compare with
17285 None - 17 0 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17470 None - 24 0 Manual N/A Compare with
17502 None - 32 0 Manual N/A Compare with
2749 None - 14 0 Manual* N/A Compare with
17234 None - 26 0 Manual N/A Compare with
17266 None - 19 0 Manual N/A Compare with
17419 None - 21 0 Manual N/A Compare with
17451 None - 23 0 Manual N/A Compare with
1539 None - 137 0 Manual* N/A Compare with
1584 None - 137 0 Manual* N/A Compare with
17177 None - 20 -1 Manual N/A Compare with
17209 None - 27 -2 Manual N/A Compare with
17368 None - 29 0 Manual N/A Compare with
175 None - 19 0 Manual* N/A Compare with
17400 None - 21 0 Manual N/A Compare with
17521 None - 21 -1 Manual N/A Compare with
578 None - 10 0 Manual* N/A Compare with
18619 None - 49 -3 Manual N/A Compare with
5814 None - 381 1 Manual* N/A Compare with
1562 None - 125 0 Manual* N/A Compare with
1604 None - 16 0 Manual* N/A Compare with
17192 None - 44 0 Manual N/A Compare with
17351 None - 15 0 Manual N/A Compare with
17383 None - 23 0 Manual N/A Compare with
215 None - 19 0 Manual* N/A Compare with
17536 None - 24 0 Manual N/A Compare with
4602 None - 113 0 Manual* N/A Compare with
9371 None - 11 -2 Manual* N/A Compare with
17300 None - 18 0 Manual N/A Compare with
17332 None - 17 -2 Manual N/A Compare with
17485 None - 21 0 Manual N/A Compare with
17517 None - 28 0 Manual N/A Compare with
1733 None - 81 0 Manual* N/A Compare with
3500 None - 18 0 Manual* N/A Compare with
17249 None - 23 -2 Manual N/A Compare with
17281 None - 23 0 Manual N/A Compare with
17402 None - 16 -1 Manual N/A Compare with
17434 None - 21 -1 Manual N/A Compare with
17315 None - 32 0 Manual N/A Compare with
17468 None - 31 0 Manual N/A Compare with
17500 None - 25 0 Manual N/A Compare with
2745 None - 24 0 Manual* N/A Compare with
4581 None - 161 -8 Manual* N/A Compare with
17232 None - 27 0 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)