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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) | P5H |
| Formula | None |
| IUPAC InChI Key | None |
| IUPAC InChI | None |
| IUPAC Name | |
| Common Name | |
| Canonical SMILES (Daylight) | NULL |
| Number of atoms | 18 |
| Net Charge | 0 |
| Forcefield | multiple |
| Molecule ID | 17322 |
| Tautomer Group ID | None |
| Visibility | Public |
| Molecule Tags |
| Force Field Version | 54A7 (IFP54A7.dat / 54A7.ifp) |
| 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 |
|---|---|---|---|---|---|---|---|
| 17396 | None | - | 24 | -1 | Manual | N/A | Compare with |
| 17366 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 17398 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 17368 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 17400 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 17370 | None | - | 18 | -1 | Manual | N/A | Compare with |
| 17372 | None | - | 18 | -1 | Manual | N/A | Compare with |
| 17374 | None | - | 30 | -1 | Manual | N/A | Compare with |
| 17344 | None | - | 23 | -2 | Manual | N/A | Compare with |
| 17376 | None | - | 30 | -1 | Manual | N/A | Compare with |
| 17346 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17378 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 17348 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17380 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 17350 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 17382 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17352 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 17384 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17354 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17386 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17356 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17388 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17358 | None | - | 30 | 0 | Manual | N/A | Compare with |
| 17390 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17360 | None | - | 30 | 0 | Manual | N/A | Compare with |
| 17392 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17362 | None | - | 12 | 0 | Manual | N/A | Compare with |
| 17394 | None | - | 24 | -1 | Manual | N/A | Compare with |
| 17364 | None | - | 12 | 0 | Manual | N/A | Compare with |
| 176 | None | - | 20 | 0 | Manual* | N/A | Compare with |
| 17456 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17426 | None | - | 34 | 1 | Manual | N/A | Compare with |
| 580 | None | - | 12 | 0 | Manual* | N/A | Compare with |
| 178 | None | - | 21 | 1 | Manual* | N/A | Compare with |
| 17458 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17428 | None | - | 34 | 1 | Manual | N/A | Compare with |
| 582 | None | - | 12 | 0 | Manual* | N/A | Compare with |
| 204 | None | - | 22 | 0 | Manual* | N/A | Compare with |
| 17460 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17430 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 584 | None | - | 15 | 0 | Manual* | N/A | Compare with |
| 206 | None | - | 25 | 1 | Manual* | N/A | Compare with |
| 17432 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 17402 | None | - | 16 | -1 | Manual | N/A | Compare with |
| 1502 | None | - | 106 | 0 | Manual* | N/A | Compare with |
| 208 | None | - | 23 | 0 | Manual* | N/A | Compare with |
| 17434 | None | - | 21 | -1 | Manual | N/A | Compare with |
| 17404 | None | - | 16 | -1 | Manual | N/A | Compare with |
| 1505 | None | - | 130 | 0 | Manual* | N/A | Compare with |
| 211 | None | - | 14 | 0 | Manual* | N/A | Compare with |
| 17436 | None | - | 21 | -1 | Manual | N/A | Compare with |
| 17406 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 1507 | None | - | 138 | 0 | Manual* | N/A | Compare with |
| 213 | None | - | 27 | 0 | Manual* | N/A | Compare with |
| 17438 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17408 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 1511 | None | - | 131 | 0 | Manual* | N/A | Compare with |
| 215 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 17440 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17410 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 562 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 17442 | None | - | 28 | 1 | Manual | N/A | Compare with |
| 17412 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 565 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 164 | None | - | 27 | 1 | Manual* | N/A | Compare with |
| 17444 | None | - | 28 | 1 | Manual | N/A | Compare with |
| 17414 | None | - | 24 | 1 | Manual | N/A | Compare with |
| 567 | None | - | 10 | 0 | Manual* | N/A | Compare with |
| 166 | None | - | 17 | 0 | Manual* | N/A | Compare with |
| 17446 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17416 | None | - | 24 | 1 | Manual | N/A | Compare with |
| 569 | None | - | 8 | 0 | Manual* | N/A | Compare with |
| 168 | None | - | 15 | 0 | Manual* | N/A | Compare with |
| 17448 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17418 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 571 | None | - | 14 | 0 | Manual* | N/A | Compare with |
| 170 | None | - | 14 | 0 | Manual* | N/A | Compare with |
| 17450 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17420 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 573 | None | - | 20 | 0 | Manual* | N/A | Compare with |
| 172 | None | - | 14 | 0 | Manual* | N/A | Compare with |
| 17452 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17422 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 575 | None | - | 20 | 0 | Manual* | N/A | Compare with |
| 174 | None | - | 19 | -1 | Manual* | N/A | Compare with |
| 17454 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17424 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 577 | None | - | 37 | 0 | Manual* | N/A | Compare with |
| 1594 | None | - | 10 | 0 | Manual* | N/A | Compare with |
| 1556 | None | - | 143 | 0 | Manual* | N/A | Compare with |
| 17516 | None | - | 26 | 0 | Manual | N/A | Compare with |
| 17486 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 1596 | None | - | 3 | 0 | Manual* | N/A | Compare with |
| 1558 | None | - | 137 | 0 | Manual* | N/A | Compare with |
| 17518 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17488 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 1601 | None | - | 17 | 0 | Manual* | N/A | Compare with |
| 1561 | None | - | 119 | 0 | Manual* | N/A | Compare with |
| 17490 | None | - | 22 | 0 | Manual | N/A | Compare with |
| 1603 | None | - | 17 | 0 | 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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