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)L3H
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms23
Net Charge0
Forcefieldmultiple
Molecule ID17384
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 
17229 None - 27 0 Manual N/A Compare with
17408 None - 28 -1 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17440 None - 25 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17178 None - 20 -1 Manual N/A Compare with
17357 None - 30 0 Manual N/A Compare with
17210 None - 27 -2 Manual N/A Compare with
17389 None - 18 0 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
580 None - 12 0 Manual* N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17306 None - 23 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17338 None - 18 0 Manual N/A Compare with
17491 None - 22 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17289 None - 28 0 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17321 None - 18 0 Manual N/A Compare with
17474 None - 23 0 Manual N/A Compare with
17506 None - 29 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17244 None - 26 -1 Manual N/A Compare with
17423 None - 21 0 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17455 None - 28 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17193 None - 28 0 Manual N/A Compare with
17372 None - 18 -1 Manual N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17438 None - 25 0 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17176 None - 25 0 Manual N/A Compare with
17355 None - 23 0 Manual N/A Compare with
17208 None - 18 0 Manual N/A Compare with
17387 None - 20 -2 Manual N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
577 None - 37 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17304 None - 25 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17336 None - 30 1 Manual N/A Compare with
17489 None - 22 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17406 None - 28 -1 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
4593 None - 161 -8 Manual* N/A Compare with
17287 None - 17 0 Manual N/A Compare with
8099 None - 3218 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
1732 None - 73 0 Manual* N/A Compare with
3496 None - 15 0 Manual* N/A Compare with
17242 None - 26 -1 Manual N/A Compare with
17421 None - 21 0 Manual N/A Compare with
17274 None - 24 -1 Manual N/A Compare with
17453 None - 28 0 Manual N/A Compare with
1561 None - 119 0 Manual* N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17370 None - 18 -1 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
214 None - 24 0 Manual* N/A Compare with
1524 None - 137 0 Manual* N/A Compare with
1526 None - 143 0 Manual* N/A Compare with
1581 None - 149 0 Manual* N/A Compare with
17174 None - 25 0 Manual N/A Compare with
17353 None - 23 0 Manual N/A Compare with
17206 None - 18 0 Manual N/A Compare with
17385 None - 20 -2 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
172 None - 14 0 Manual* N/A Compare with
575 None - 20 0 Manual* N/A Compare with
5797 None - 18 -1 Manual* N/A Compare with
17302 None - 25 0 Manual N/A Compare with
17155 None - 17 0 Manual N/A Compare with
17334 None - 30 1 Manual N/A Compare with
17487 None - 21 0 Manual N/A Compare with
2694 None - 77 -3 Manual N/A Compare with
4580 None - 161 -8 Manual* N/A Compare with
17225 None - 20 0 Manual N/A Compare with
17404 None - 16 -1 Manual N/A Compare with
17257 None - 15 -1 Manual N/A Compare with
17436 None - 21 -1 Manual N/A Compare with
17317 None - 24 0 Manual N/A Compare with
17470 None - 24 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)