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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 |
Current Processing State | Completed |
Total Processing Time | NA (hh:mm:ss) |
Molecule Type | amino acid |
Residue Name (RNME) | KPH |
Formula | None |
IUPAC InChI Key | None |
IUPAC InChI | None |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | NULL |
Number of atoms | 26 |
Net Charge | 1 |
Forcefield | multiple |
Molecule ID | 17547 |
Visibility | Public |
Molecule Tags |
Force Field Version | 45A3 (IFP45A3.dat) |
Upload Date | 2014-02-03 13:07:19 |
Literature Reference | Drazen 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 |
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.
Molid | Formula | Iupac > | Atoms | Charge | Curation | Δ Qm Optimized Energy (kJ.mol-1) | Compare |
---|---|---|---|---|---|---|---|
17418 | None | - | 21 | 0 | Manual | N/A | Compare with |
17299 | None | - | 18 | 0 | Manual | N/A | Compare with |
17331 | None | - | 17 | -2 | Manual | N/A | Compare with |
17484 | None | - | 15 | 0 | Manual | N/A | Compare with |
17516 | None | - | 26 | 0 | Manual | N/A | Compare with |
2749 | None | - | 14 | 0 | Manual* | N/A | Compare with |
17248 | None | - | 27 | -2 | Manual | N/A | Compare with |
17280 | None | - | 24 | 1 | Manual | N/A | Compare with |
17401 | None | - | 16 | -1 | Manual | N/A | Compare with |
17433 | None | - | 21 | -1 | Manual | N/A | Compare with |
1539 | None | - | 137 | 0 | Manual* | N/A | Compare with |
1584 | None | - | 137 | 0 | Manual* | N/A | Compare with |
17165 | None | - | 27 | 0 | Manual | N/A | Compare with |
17197 | None | - | 26 | 1 | Manual | N/A | Compare with |
17350 | None | - | 15 | 0 | Manual | N/A | Compare with |
17382 | None | - | 23 | 0 | Manual | N/A | Compare with |
175 | None | - | 19 | 0 | Manual* | N/A | Compare with |
17535 | None | - | 24 | 0 | Manual | N/A | Compare with |
578 | None | - | 10 | 0 | Manual* | N/A | Compare with |
5814 | None | - | 381 | 1 | Manual* | N/A | Compare with |
17158 | None | - | 20 | 0 | Manual | N/A | Compare with |
1604 | None | - | 16 | 0 | Manual* | N/A | Compare with |
17180 | None | - | 20 | -1 | Manual | N/A | Compare with |
17212 | None | - | 27 | -2 | Manual | N/A | Compare with |
17365 | None | - | 29 | 0 | Manual | N/A | Compare with |
17397 | None | - | 21 | 0 | Manual | N/A | Compare with |
215 | None | - | 19 | 0 | Manual* | N/A | Compare with |
17550 | None | - | 15 | -1 | Manual | N/A | Compare with |
4602 | None | - | 113 | 0 | Manual* | N/A | Compare with |
9371 | None | - | 11 | -2 | Manual* | N/A | Compare with |
17314 | None | - | 32 | 0 | Manual | N/A | Compare with |
17467 | None | - | 31 | 0 | Manual | N/A | Compare with |
17499 | None | - | 25 | 0 | Manual | N/A | Compare with |
1733 | None | - | 81 | 0 | Manual* | N/A | Compare with |
3500 | None | - | 18 | 0 | Manual* | N/A | Compare with |
17231 | None | - | 27 | 0 | Manual | N/A | Compare with |
17263 | None | - | 17 | 0 | Manual | N/A | Compare with |
17416 | None | - | 24 | 1 | Manual | N/A | Compare with |
17448 | None | - | 28 | 0 | Manual | N/A | Compare with |
1562 | None | - | 125 | 0 | Manual* | N/A | Compare with |
17329 | None | - | 17 | -2 | Manual | N/A | Compare with |
17482 | None | - | 15 | 0 | Manual | N/A | Compare with |
17514 | None | - | 26 | 0 | Manual | N/A | Compare with |
2745 | None | - | 24 | 0 | Manual* | N/A | Compare with |
4581 | None | - | 161 | -8 | Manual* | N/A | Compare with |
17246 | None | - | 27 | -2 | Manual | N/A | Compare with |
17278 | None | - | 24 | 1 | Manual | N/A | Compare with |
17431 | None | - | 15 | 0 | Manual | N/A | Compare with |
1532 | None | - | 149 | 0 | Manual* | N/A | Compare with |
1582 | None | - | 119 | 0 | Manual* | N/A | Compare with |
17195 | None | - | 28 | 0 | Manual | N/A | Compare with |
17348 | None | - | 20 | -2 | Manual | N/A | Compare with |
17380 | None | - | 28 | -1 | Manual | N/A | Compare with |
173 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17533 | None | - | 24 | 0 | Manual | N/A | Compare with |
576 | None | - | 26 | 0 | Manual* | N/A | Compare with |
5798 | None | - | 19 | 0 | Manual* | N/A | Compare with |
17156 | None | - | 17 | 0 | Manual | N/A | Compare with |
17297 | None | - | 18 | 0 | Manual | N/A | Compare with |
17178 | None | - | 20 | -1 | Manual | N/A | Compare with |
17210 | None | - | 27 | -2 | Manual | N/A | Compare with |
17363 | None | - | 12 | 0 | Manual | N/A | Compare with |
17395 | None | - | 24 | -1 | Manual | N/A | Compare with |
213 | None | - | 27 | 0 | Manual* | N/A | Compare with |
17548 | None | - | 26 | 1 | Manual | N/A | Compare with |
1511 | None | - | 131 | 0 | Manual* | N/A | Compare with |
4592 | None | - | 161 | -8 | Manual* | N/A | Compare with |
7284 | None | - | 71 | 1 | Manual* | N/A | Compare with |
17312 | None | - | 25 | -1 | Manual | N/A | Compare with |
17465 | None | - | 31 | 0 | Manual | N/A | Compare with |
17497 | None | - | 25 | 0 | Manual | N/A | Compare with |
1731 | None | - | 74 | 0 | Manual* | N/A | Compare with |
3488 | None | - | 12 | 0 | Manual* | N/A | Compare with |
17229 | None | - | 27 | 0 | Manual | N/A | Compare with |
17261 | None | - | 17 | 0 | Manual | N/A | Compare with |
17414 | None | - | 24 | 1 | Manual | N/A | Compare with |
17446 | None | - | 28 | 0 | Manual | N/A | Compare with |
1560 | None | - | 123 | 0 | Manual* | N/A | Compare with |
1602 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17480 | None | - | 27 | -1 | Manual | N/A | Compare with |
17512 | None | - | 27 | 0 | Manual | N/A | Compare with |
2672 | None | - | 39 | 0 | Manual | N/A | Compare with |
4579 | None | - | 161 | -8 | Manual* | N/A | Compare with |
17244 | None | - | 26 | -1 | Manual | N/A | Compare with |
17276 | None | - | 24 | -1 | Manual | N/A | Compare with |
17429 | None | - | 15 | 0 | Manual | N/A | Compare with |
1525 | None | - | 147 | 0 | Manual* | N/A | Compare with |
1579 | None | - | 143 | 0 | Manual* | N/A | Compare with |
17193 | None | - | 28 | 0 | Manual | N/A | Compare with |
17346 | None | - | 20 | -2 | Manual | N/A | Compare with |
17378 | None | - | 28 | -1 | Manual | N/A | Compare with |
171 | None | - | 14 | 0 | Manual* | N/A | Compare with |
17531 | None | - | 18 | 0 | Manual | N/A | Compare with |
574 | None | - | 17 | 0 | Manual* | N/A | Compare with |
5796 | None | - | 19 | 0 | Manual* | N/A | Compare with |
17154 | None | - | 17 | 0 | Manual | N/A | Compare with |
17295 | None | - | 9 | -1 | Manual | N/A | Compare with |
17327 | None | - | 25 | 0 | Manual | N/A | Compare with |
17208 | None | - | 18 | 0 | Manual | N/A | Compare with |
17361 | None | - | 12 | 0 | Manual | N/A | Compare with |
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.