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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 building block |
| Residue Name (RNME) | F3H |
| Formula | None |
| IUPAC InChI Key | None |
| IUPAC InChI | None |
| IUPAC Name | |
| Common Name | |
| Canonical SMILES (Daylight) | NULL |
| Number of atoms | 24 |
| Net Charge | 0 |
| Forcefield | multiple |
| Molecule ID | 17320 |
| Tautomer Group ID | None |
| Visibility | Public |
| Molecule Tags |
| Force Field Version | 45A3 (IFP45A3.dat) |
| Upload Date | 2014-02-03 13:07:16 |
| 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 |
|---|---|---|---|---|---|---|---|
| 1602 | None | - | 20 | 0 | Manual* | N/A | Compare with |
| 17190 | None | - | 44 | 0 | Manual | N/A | Compare with |
| 17222 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 17344 | None | - | 23 | -2 | Manual | N/A | Compare with |
| 562 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 17376 | None | - | 30 | -1 | Manual | N/A | Compare with |
| 17529 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 30988 | None | - | 1456 | 0 | Template | N/A | Compare with |
| 4592 | None | - | 161 | -8 | Manual* | N/A | Compare with |
| 7284 | None | - | 71 | 1 | Manual* | N/A | Compare with |
| 17292 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17325 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17478 | None | - | 27 | -1 | Manual | N/A | Compare with |
| 17510 | None | - | 27 | 0 | Manual | N/A | Compare with |
| 1731 | None | - | 74 | 0 | Manual* | N/A | Compare with |
| 3488 | None | - | 12 | 0 | Manual* | N/A | Compare with |
| 17241 | None | - | 26 | -1 | Manual | N/A | Compare with |
| 17273 | None | - | 24 | -1 | Manual | N/A | Compare with |
| 17427 | None | - | 34 | 1 | Manual | N/A | Compare with |
| 17459 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 1560 | None | - | 123 | 0 | Manual* | N/A | Compare with |
| 17340 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17461 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 17493 | None | - | 19 | 0 | Manual | N/A | Compare with |
| 2672 | None | - | 39 | 0 | Manual | N/A | Compare with |
| 4579 | None | - | 161 | -8 | Manual* | N/A | Compare with |
| 17224 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 17256 | None | - | 27 | 0 | Manual | N/A | Compare with |
| 17410 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17442 | None | - | 28 | 1 | Manual | N/A | Compare with |
| 1525 | None | - | 147 | 0 | Manual* | N/A | Compare with |
| 1579 | None | - | 143 | 0 | Manual* | N/A | Compare with |
| 17173 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17205 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 175 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 17359 | None | - | 30 | 0 | Manual | N/A | Compare with |
| 578 | None | - | 10 | 0 | Manual* | N/A | Compare with |
| 17391 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17544 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 5796 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 17154 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 17307 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17188 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 17220 | None | - | 31 | 1 | Manual | N/A | Compare with |
| 215 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 17374 | None | - | 30 | -1 | Manual | N/A | Compare with |
| 17527 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 18675 | None | - | 140 | -3 | Manual | N/A | Compare with |
| 7282 | None | - | 113 | 0 | Manual* | N/A | Compare with |
| 17290 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17323 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17476 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17508 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 1679 | None | - | 31 | 0 | Manual* | N/A | Compare with |
| 3486 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 17239 | None | - | 16 | -1 | Manual | N/A | Compare with |
| 17271 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17425 | None | - | 34 | 1 | Manual | N/A | Compare with |
| 17457 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 1557 | None | - | 131 | 0 | Manual* | N/A | Compare with |
| 1598 | None | - | 6 | 0 | Manual* | N/A | Compare with |
| 17491 | 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 |
| 17408 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 17440 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 1577 | None | - | 138 | 0 | Manual* | N/A | Compare with |
| 17171 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17203 | None | - | 33 | 1 | Manual | N/A | Compare with |
| 173 | None | - | 20 | 0 | Manual* | N/A | Compare with |
| 17357 | None | - | 30 | 0 | Manual | N/A | Compare with |
| 576 | None | - | 26 | 0 | Manual* | N/A | Compare with |
| 17389 | None | - | 18 | 0 | 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 |
| 17305 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17338 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17218 | None | - | 31 | 1 | Manual | N/A | Compare with |
| 213 | None | - | 27 | 0 | Manual* | N/A | Compare with |
| 17372 | None | - | 18 | -1 | Manual | N/A | Compare with |
| 1511 | None | - | 131 | 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 |
| 17288 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 17321 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17474 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17506 | 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 |
| 17237 | None | - | 16 | -1 | Manual | N/A | Compare with |
| 17269 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17423 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 17455 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 1555 | None | - | 167 | 0 | Manual* | N/A | Compare with |
| 1595 | None | - | 5 | 0 | Manual* | N/A | Compare with |
| 17186 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 2182 | None | - | 41 | -4 | 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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