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
Residue Name (RNME)H1C
FormulaNone
IUPAC InChI Key
None
IUPAC InChI
None
IUPAC Name
Common Name
Canonical SMILES (Daylight)
NULL
Number of atoms24
Net Charge1
Forcefieldmultiple
Molecule ID17277
Tautomer Group IDNone
Visibility Public
Molecule Tags

Molecular Dynamics (MD) Files

Topology Information

Force Field Version54A7 (IFP54A7.dat / 54A7.ifp)
Upload Date2014-02-03 13:07:16
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 (201-300 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 
6451 None - 27 0 Manual N/A Compare with
17161 None - 23 0 Manual N/A Compare with
17314 None - 32 0 Manual N/A Compare with
17422 None - 21 0 Manual N/A Compare with
17454 None - 28 0 Manual N/A Compare with
2920 None - 27 1 Manual N/A Compare with
17231 None - 27 0 Manual N/A Compare with
17263 None - 17 0 Manual N/A Compare with
17371 None - 18 -1 Manual N/A Compare with
17524 None - 21 -1 Manual N/A Compare with
18622 None - 49 -3 Manual* N/A Compare with
1548 None - 24 0 Manual* N/A Compare with
1588 None - 125 0 Manual* N/A Compare with
17180 None - 20 -1 Manual N/A Compare with
17212 None - 27 -2 Manual N/A Compare with
17473 None - 23 0 Manual N/A Compare with
178 None - 21 1 Manual* N/A Compare with
17505 None - 29 0 Manual N/A Compare with
582 None - 12 0 Manual* N/A Compare with
17539 None - 19 -2 Manual N/A Compare with
1565 None - 113 0 Manual* N/A Compare with
1608 None - 20 0 Manual* N/A Compare with
17195 None - 28 0 Manual N/A Compare with
17488 None - 21 0 Manual N/A Compare with
564 None - 6 0 Manual* N/A Compare with
4908 None - 40 -4 Manual* N/A Compare with
9643 None - 103 1 Manual N/A Compare with
17297 None - 18 0 Manual N/A Compare with
17405 None - 28 -1 Manual N/A Compare with
17329 None - 17 -2 Manual N/A Compare with
17437 None - 25 0 Manual N/A Compare with
1771 None - 186 -1 Manual* N/A Compare with
3504 None - 15 0 Manual* N/A Compare with
17246 None - 27 -2 Manual N/A Compare with
17354 None - 23 0 Manual N/A Compare with
17278 None - 24 1 Manual N/A Compare with
17386 None - 20 -2 Manual N/A Compare with
17159 None - 20 0 Manual N/A Compare with
17312 None - 25 -1 Manual N/A Compare with
17420 None - 21 0 Manual N/A Compare with
17452 None - 23 0 Manual N/A Compare with
2752 None - 19 0 Manual* N/A Compare with
17229 None - 27 0 Manual N/A Compare with
17261 None - 17 0 Manual N/A Compare with
17369 None - 18 -1 Manual N/A Compare with
17522 None - 21 -1 Manual N/A Compare with
18620 None - 49 -3 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
17210 None - 27 -2 Manual N/A Compare with
17471 None - 24 0 Manual N/A Compare with
176 None - 20 0 Manual* N/A Compare with
17503 None - 32 0 Manual N/A Compare with
580 None - 12 0 Manual* N/A Compare with
5838 None - 43 -1 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
17486 None - 21 0 Manual N/A Compare with
216 None - 13 0 Manual* N/A Compare with
17518 None - 28 0 Manual N/A Compare with
4603 None - 113 0 Manual* N/A Compare with
9377 None - 12 -2 Manual* N/A Compare with
17295 None - 9 -1 Manual N/A Compare with
17403 None - 16 -1 Manual N/A Compare with
17327 None - 25 0 Manual N/A Compare with
17435 None - 21 -1 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
17352 None - 15 0 Manual N/A Compare with
17276 None - 24 -1 Manual N/A Compare with
17384 None - 23 0 Manual N/A Compare with
17537 None - 19 -2 Manual N/A Compare with
17310 None - 25 -1 Manual N/A Compare with
17418 None - 21 0 Manual N/A Compare with
17450 None - 23 0 Manual N/A Compare with
2747 None - 20 0 Manual* N/A Compare with
17227 None - 20 0 Manual N/A Compare with
17259 None - 15 -1 Manual N/A Compare with
17367 None - 29 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
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
17208 None - 18 0 Manual N/A Compare with
17469 None - 24 0 Manual N/A Compare with
174 None - 19 -1 Manual* N/A Compare with
17501 None - 32 0 Manual N/A Compare with
577 None - 37 0 Manual* N/A Compare with
5810 None - 156 -12 Manual* N/A Compare with
17157 None - 20 0 Manual N/A Compare with
1603 None - 17 0 Manual* N/A Compare with
17191 None - 44 0 Manual N/A Compare with
17223 None - 22 0 Manual N/A Compare with
17484 None - 15 0 Manual N/A Compare with
214 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)