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)EME
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms22
Net Charge0
Forcefieldmultiple
Molecule ID17464
Tautomer Group IDNone
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 (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 
17288 None - 17 0 Manual N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
17320 None - 24 0 Manual N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17473 None - 23 0 Manual N/A Compare with
17505 None - 29 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17269 None - 18 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17422 None - 21 0 Manual N/A Compare with
6451 None - 27 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
17437 None - 25 0 Manual N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
17303 None - 25 0 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17488 None - 21 0 Manual N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
1540 None - 143 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
1586 None - 149 0 Manual* N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
17235 None - 26 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17267 None - 19 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
17420 None - 21 0 Manual N/A Compare with
5838 None - 43 -1 Manual* N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 Manual N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
17352 None - 15 0 Manual N/A Compare with
1736 None - 80 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
3501 None - 21 0 Manual* N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17301 None - 25 0 Manual N/A Compare with
1563 None - 137 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
1605 None - 23 0 Manual* N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17518 None - 28 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
1538 None - 161 0 Manual* N/A Compare with
17316 None - 32 0 Manual N/A Compare with
1583 None - 125 0 Manual* N/A Compare with
17469 None - 24 0 Manual N/A Compare with
17501 None - 32 0 Manual N/A Compare with
17233 None - 26 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17265 None - 19 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
17418 None - 21 0 Manual N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17450 None - 23 0 Manual N/A Compare with
17157 None - 20 0 Manual N/A Compare with
17182 None - 23 0 Manual N/A Compare with
17214 None - 29 0 Manual N/A Compare with
17367 None - 29 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17399 None - 21 0 Manual N/A Compare with
17520 None - 28 0 Manual N/A Compare with
17552 None - 15 -1 Manual N/A Compare with
17284 None - 23 0 Manual N/A Compare with
17165 None - 27 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)