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)YNB
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms26
Net Charge0
Forcefieldmultiple
Molecule ID17514
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
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 
1591 None - 137 0 Manual* N/A Compare with
17388 None - 20 -2 Manual N/A Compare with
17542 None - 29 0 Manual N/A Compare with
5639 None - 127 0 Manual N/A Compare with
17152 None - 16 -1 Manual N/A Compare with
205 None - 24 0 Manual* N/A Compare with
17305 None - 23 0 Manual N/A Compare with
619 None - 16 0 Manual* N/A Compare with
17337 None - 18 0 Manual N/A Compare with
17490 None - 22 0 Manual N/A Compare with
2280 None - 186 -1 Manual* N/A Compare with
4213 None - 61 0 Manual N/A Compare with
17254 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
17171 None - 28 0 Manual N/A Compare with
17203 None - 33 1 Manual N/A Compare with
1552 None - 149 0 Manual* N/A Compare with
17356 None - 23 0 Manual N/A Compare with
17237 None - 16 -1 Manual N/A Compare with
17269 None - 18 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
17186 None - 15 0 Manual N/A Compare with
17218 None - 31 1 Manual N/A Compare with
1570 None - 125 0 Manual* N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
1646 None - 3 0 Manual* N/A Compare with
17525 None - 18 0 Manual N/A Compare with
18623 None - 139 -3 Manual N/A Compare with
6871 None - 108 0 Manual* N/A Compare with
164 None - 27 1 Manual* N/A Compare with
17288 None - 17 0 Manual N/A Compare with
567 None - 10 0 Manual* N/A Compare with
17320 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
1677 None - 34 0 Manual* N/A Compare with
3412 None - 18 0 Manual* N/A Compare with
17540 None - 19 -2 Manual N/A Compare with
5182 None - 110 -8 Manual* N/A Compare with
17150 None - 16 -1 Manual N/A Compare with
203 None - 22 0 Manual* N/A Compare with
17303 None - 25 0 Manual N/A Compare with
583 None - 15 0 Manual* N/A Compare with
17335 None - 30 1 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
2182 None - 41 -4 Manual* N/A Compare with
4013 None - 176 0 Manual* N/A Compare with
17252 None - 23 -2 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
17169 None - 28 0 Manual N/A Compare with
17201 None - 33 1 Manual N/A Compare with
1550 None - 24 0 Manual* N/A Compare with
17354 None - 23 0 Manual N/A Compare with
1589 None - 131 0 Manual* N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17267 None - 19 0 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
17184 None - 23 0 Manual N/A Compare with
17216 None - 29 0 Manual N/A Compare with
1566 None - 129 0 Manual* N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
1611 None - 18 0 Manual* N/A Compare with
17523 None - 21 -1 Manual N/A Compare with
18621 None - 49 -3 Manual* N/A Compare with
6461 None - 15 0 Manual N/A Compare with
17286 None - 17 0 Manual N/A Compare with
565 None - 9 0 Manual* N/A Compare with
17318 None - 24 0 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
17503 None - 32 0 Manual N/A Compare with
1664 None - 8 0 Manual* N/A Compare with
3410 None - 15 0 Manual* N/A Compare with
17235 None - 26 0 Manual N/A Compare with
5100 None - 58 -6 Manual* N/A Compare with
17148 None - 33 1 Manual N/A Compare with
177 None - 20 0 Manual* N/A Compare with
17301 None - 25 0 Manual N/A Compare with
581 None - 16 0 Manual* N/A Compare with
17333 None - 30 1 Manual N/A Compare with
17486 None - 21 0 Manual N/A Compare with
17519 None - 28 0 Manual N/A Compare with
2166 None - 186 -1 Manual* N/A Compare with
3924 None - 176 0 Manual N/A Compare with
17250 None - 23 -2 Manual N/A Compare with
17282 None - 23 0 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17435 None - 21 -1 Manual N/A Compare with
17167 None - 27 0 Manual N/A Compare with
17199 None - 26 1 Manual N/A Compare with
1547 None - 24 0 Manual* N/A Compare with
17352 None - 15 0 Manual N/A Compare with
1587 None - 155 0 Manual* N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17538 None - 19 -2 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 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)