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 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
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 (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 
21025 None - 209 -4 Manual* N/A Compare with
4582 None - 161 -8 Manual* N/A Compare with
7283 None - 87 1 Manual* N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17291 None - 28 0 Manual N/A Compare with
17323 None - 18 0 Manual N/A Compare with
17477 None - 27 -1 Manual N/A Compare with
17509 None - 27 0 Manual N/A Compare with
1680 None - 30 0 Manual* N/A Compare with
3487 None - 12 0 Manual* N/A Compare with
17240 None - 16 -1 Manual N/A Compare with
17272 None - 18 0 Manual N/A Compare with
17426 None - 34 1 Manual N/A Compare with
17458 None - 28 0 Manual N/A Compare with
1558 None - 137 0 Manual* N/A Compare with
1601 None - 17 0 Manual* N/A Compare with
17189 None - 44 0 Manual N/A Compare with
17221 None - 22 0 Manual N/A Compare with
17342 None - 23 -2 Manual N/A Compare with
4578 None - 161 -8 Manual* N/A Compare with
17255 None - 27 0 Manual N/A Compare with
17409 None - 18 0 Manual N/A Compare with
17441 None - 28 1 Manual N/A Compare with
1578 None - 144 0 Manual* N/A Compare with
17172 None - 28 0 Manual N/A Compare with
17204 None - 33 1 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17543 None - 29 0 Manual N/A Compare with
5795 None - 18 -1 Manual* N/A Compare with
17153 None - 17 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17492 None - 22 0 Manual N/A Compare with
2671 None - 47 -3 Manual N/A Compare with
17526 None - 18 0 Manual N/A Compare with
18660 None - 49 -3 Manual* N/A Compare with
7281 None - 62 1 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17475 None - 23 0 Manual N/A Compare with
17507 None - 29 0 Manual N/A Compare with
1678 None - 35 0 Manual* N/A Compare with
3485 None - 6 0 Manual* N/A Compare with
17238 None - 16 -1 Manual N/A Compare with
17270 None - 18 0 Manual N/A Compare with
17424 None - 21 0 Manual N/A Compare with
17456 None - 28 0 Manual N/A Compare with
1556 None - 143 0 Manual* N/A Compare with
1596 None - 3 0 Manual* N/A Compare with
17187 None - 15 0 Manual N/A Compare with
17219 None - 31 1 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17253 None - 27 0 Manual N/A Compare with
17407 None - 28 -1 Manual N/A Compare with
17439 None - 25 0 Manual N/A Compare with
1576 None - 129 0 Manual* N/A Compare with
17170 None - 28 0 Manual N/A Compare with
17202 None - 33 1 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17541 None - 29 0 Manual N/A Compare with
5471 None - 130 -10 Manual* N/A Compare with
17151 None - 16 -1 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
2276 None - 363 -2 Manual* N/A Compare with
4182 None - 5 0 Manual* N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
6870 None - 24 0 Manual* N/A Compare with
212 None - 17 0 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
1510 None - 161 0 Manual* N/A Compare with
17319 None - 24 0 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
1668 None - 27 0 Manual* N/A Compare with
3411 None - 18 0 Manual* N/A Compare with
17236 None - 26 0 Manual N/A Compare with
17268 None - 19 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
1554 None - 155 0 Manual* N/A Compare with
1594 None - 10 0 Manual* N/A Compare with
17185 None - 15 0 Manual N/A Compare with
17217 None - 31 1 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17524 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
1572 None - 153 0 Manual* N/A Compare with
17168 None - 27 0 Manual N/A Compare with
17200 None - 26 1 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)