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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) | LH5 |
| Formula | None |
| IUPAC InChI Key | None |
| IUPAC InChI | None |
| IUPAC Name | |
| Common Name | |
| Canonical SMILES (Daylight) | NULL |
| Number of atoms | 23 |
| Net Charge | 0 |
| Forcefield | multiple |
| Molecule ID | 17475 |
| Tautomer Group ID | None |
| Visibility | Public |
| Molecule Tags |
| Force Field Version | 45A3 (IFP45A3.dat) |
| Upload Date | 2014-02-03 13:07:18 |
| 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 |
Compare All Topologies (633)RMSD Matrix (633)
| Molid | Formula | Iupac | Atoms | Charge | Curation | Δ Qm Optimized Energy (kJ.mol-1) | Compare |
|---|---|---|---|---|---|---|---|
| 17503 | None | - | 32 | 0 | Manual | N/A | Compare with |
| 3504 | None | - | 15 | 0 | Manual* | N/A | Compare with |
| 17472 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 2018 | None | - | 90 | -1 | Manual* | N/A | Compare with |
| 17505 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 3587 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 17474 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 2166 | None | - | 186 | -1 | Manual* | N/A | Compare with |
| 17507 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 3924 | None | - | 176 | 0 | Manual | N/A | Compare with |
| 17477 | None | - | 27 | -1 | Manual | N/A | Compare with |
| 2182 | None | - | 41 | -4 | Manual* | N/A | Compare with |
| 17509 | None | - | 27 | 0 | Manual | N/A | Compare with |
| 4013 | None | - | 176 | 0 | Manual* | N/A | Compare with |
| 17479 | None | - | 27 | -1 | Manual | N/A | Compare with |
| 2280 | None | - | 186 | -1 | Manual* | N/A | Compare with |
| 17511 | None | - | 27 | 0 | Manual | N/A | Compare with |
| 4213 | None | - | 61 | 0 | Manual | N/A | Compare with |
| 17481 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 2672 | None | - | 39 | 0 | Manual | N/A | Compare with |
| 17513 | None | - | 26 | 0 | Manual | N/A | Compare with |
| 4579 | None | - | 161 | -8 | Manual* | N/A | Compare with |
| 17483 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 2745 | None | - | 24 | 0 | Manual* | N/A | Compare with |
| 17515 | None | - | 26 | 0 | Manual | N/A | Compare with |
| 4581 | None | - | 161 | -8 | Manual* | N/A | Compare with |
| 17485 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 2749 | None | - | 14 | 0 | Manual* | N/A | Compare with |
| 17517 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17487 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 2919 | None | - | 52 | -1 | Manual | N/A | Compare with |
| 1651 | None | - | 10 | 0 | Manual* | N/A | Compare with |
| 17519 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17489 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 2921 | None | - | 75 | -2 | Manual | N/A | Compare with |
| 1657 | None | - | 5 | 0 | Manual* | N/A | Compare with |
| 17491 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 3409 | None | - | 27 | 0 | Manual* | N/A | Compare with |
| 17460 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 1668 | None | - | 27 | 0 | Manual* | N/A | Compare with |
| 17493 | None | - | 19 | 0 | Manual | N/A | Compare with |
| 3411 | None | - | 18 | 0 | Manual* | N/A | Compare with |
| 17462 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 1678 | None | - | 35 | 0 | Manual* | N/A | Compare with |
| 17495 | None | - | 19 | 0 | Manual | N/A | Compare with |
| 3485 | None | - | 6 | 0 | Manual* | N/A | Compare with |
| 17464 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 1680 | None | - | 30 | 0 | Manual* | N/A | Compare with |
| 17497 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 3487 | None | - | 12 | 0 | Manual* | N/A | Compare with |
| 17466 | None | - | 31 | 0 | Manual | N/A | Compare with |
| 1732 | None | - | 73 | 0 | Manual* | N/A | Compare with |
| 17499 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 3496 | None | - | 15 | 0 | Manual* | N/A | Compare with |
| 17468 | None | - | 31 | 0 | Manual | N/A | Compare with |
| 1736 | None | - | 80 | 0 | Manual* | N/A | Compare with |
| 17501 | None | - | 32 | 0 | Manual | N/A | Compare with |
| 3501 | None | - | 21 | 0 | Manual* | N/A | Compare with |
| 17470 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 1771 | None | - | 186 | -1 | Manual* | N/A | Compare with |
| 17153 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 17533 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 5797 | None | - | 18 | -1 | Manual* | N/A | Compare with |
| 17155 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 17535 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 5810 | None | - | 156 | -12 | Manual* | N/A | Compare with |
| 17157 | None | - | 20 | 0 | Manual | N/A | Compare with |
| 17537 | None | - | 19 | -2 | Manual | N/A | Compare with |
| 5838 | None | - | 43 | -1 | Manual* | N/A | Compare with |
| 17159 | None | - | 20 | 0 | Manual | N/A | Compare with |
| 17539 | None | - | 19 | -2 | Manual | N/A | Compare with |
| 6451 | None | - | 27 | 0 | Manual | N/A | Compare with |
| 17161 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17541 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 6459 | None | - | 16 | 0 | Manual | N/A | Compare with |
| 17163 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17543 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 6461 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 17545 | None | - | 26 | 1 | Manual | N/A | Compare with |
| 6871 | None | - | 108 | 0 | Manual* | N/A | Compare with |
| 17547 | None | - | 26 | 1 | Manual | N/A | Compare with |
| 7282 | None | - | 113 | 0 | Manual* | N/A | Compare with |
| 4592 | None | - | 161 | -8 | Manual* | N/A | Compare with |
| 17549 | None | - | 15 | -1 | Manual | N/A | Compare with |
| 7284 | None | - | 71 | 1 | Manual* | N/A | Compare with |
| 4602 | None | - | 113 | 0 | Manual* | N/A | Compare with |
| 17551 | None | - | 15 | -1 | Manual | N/A | Compare with |
| 9371 | None | - | 11 | -2 | Manual* | N/A | Compare with |
| 17521 | None | - | 21 | -1 | Manual | N/A | Compare with |
| 4604 | None | - | 217 | 0 | Manual* | N/A | Compare with |
| 18619 | None | - | 49 | -3 | Manual | N/A | Compare with |
| 9411 | None | - | 17 | -2 | Manual* | N/A | Compare with |
| 17523 | None | - | 21 | -1 | Manual | N/A | Compare with |
| 5011 | None | - | 40 | -4 | Manual* | N/A | Compare with |
| 18621 | None | - | 49 | -3 | Manual* | N/A | Compare with |
| 17145 | None | - | 33 | 1 | Manual | N/A | Compare with |
| 17525 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 5089 | None | - | 41 | 1 | Manual* | N/A | Compare with |
| 18623 | None | - | 139 | -3 | Manual | N/A | Compare with |
| 17147 | None | - | 33 | 1 | Manual | N/A | Compare with |
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The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.
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