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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) | S2P |
| Formula | None |
| IUPAC InChI Key | None |
| IUPAC InChI | None |
| IUPAC Name | |
| Common Name | |
| Canonical SMILES (Daylight) | NULL |
| Number of atoms | 17 |
| Net Charge | -2 |
| Forcefield | multiple |
| Molecule ID | 17329 |
| 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 |
|---|---|---|---|---|---|---|---|
| 17314 | None | - | 32 | 0 | Manual | N/A | Compare with |
| 17284 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17316 | None | - | 32 | 0 | Manual | N/A | Compare with |
| 17286 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 17318 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 17288 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 17320 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 17290 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17322 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17292 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17324 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17294 | None | - | 9 | -1 | Manual | N/A | Compare with |
| 17326 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17296 | None | - | 9 | -1 | Manual | N/A | Compare with |
| 17328 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17298 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17331 | None | - | 17 | -2 | Manual | N/A | Compare with |
| 17300 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17333 | None | - | 30 | 1 | Manual | N/A | Compare with |
| 17302 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17335 | None | - | 30 | 1 | Manual | N/A | Compare with |
| 17304 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17337 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17306 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17339 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17308 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17341 | None | - | 23 | -2 | Manual | N/A | Compare with |
| 17310 | None | - | 25 | -1 | Manual | N/A | Compare with |
| 17312 | None | - | 25 | -1 | Manual | N/A | Compare with |
| 17375 | None | - | 30 | -1 | Manual | N/A | Compare with |
| 17345 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17377 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 17347 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17379 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 17349 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 17381 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17351 | None | - | 15 | 0 | Manual | N/A | Compare with |
| 17383 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17353 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17385 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17355 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17387 | None | - | 20 | -2 | Manual | N/A | Compare with |
| 17357 | None | - | 30 | 0 | Manual | N/A | Compare with |
| 17389 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17359 | None | - | 30 | 0 | Manual | N/A | Compare with |
| 17391 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 17361 | None | - | 12 | 0 | Manual | N/A | Compare with |
| 17393 | None | - | 24 | -1 | Manual | N/A | Compare with |
| 17363 | None | - | 12 | 0 | Manual | N/A | Compare with |
| 17395 | None | - | 24 | -1 | Manual | N/A | Compare with |
| 17365 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 17397 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 17367 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 17399 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 17369 | None | - | 18 | -1 | Manual | N/A | Compare with |
| 17401 | None | - | 16 | -1 | Manual | N/A | Compare with |
| 17371 | None | - | 18 | -1 | Manual | N/A | Compare with |
| 17373 | None | - | 30 | -1 | Manual | N/A | Compare with |
| 17343 | None | - | 23 | -2 | Manual | N/A | Compare with |
| 17435 | None | - | 21 | -1 | Manual | N/A | Compare with |
| 17405 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 1506 | None | - | 134 | 0 | Manual* | N/A | Compare with |
| 212 | None | - | 17 | 0 | Manual* | N/A | Compare with |
| 17437 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17407 | None | - | 28 | -1 | Manual | N/A | Compare with |
| 1510 | None | - | 161 | 0 | Manual* | N/A | Compare with |
| 214 | None | - | 24 | 0 | Manual* | N/A | Compare with |
| 17439 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17409 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 1524 | None | - | 137 | 0 | Manual* | N/A | Compare with |
| 216 | None | - | 13 | 0 | Manual* | N/A | Compare with |
| 17441 | None | - | 28 | 1 | Manual | N/A | Compare with |
| 17411 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 564 | None | - | 6 | 0 | Manual* | N/A | Compare with |
| 163 | None | - | 13 | 0 | Manual* | N/A | Compare with |
| 17443 | None | - | 28 | 1 | Manual | N/A | Compare with |
| 17413 | None | - | 24 | 1 | Manual | N/A | Compare with |
| 566 | None | - | 12 | 0 | Manual* | N/A | Compare with |
| 165 | None | - | 26 | 0 | Manual* | N/A | Compare with |
| 17445 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17415 | None | - | 24 | 1 | Manual | N/A | Compare with |
| 568 | None | - | 16 | 0 | Manual* | N/A | Compare with |
| 167 | None | - | 14 | -1 | Manual* | N/A | Compare with |
| 17447 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17417 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 570 | None | - | 11 | 0 | Manual* | N/A | Compare with |
| 169 | None | - | 13 | 0 | Manual* | N/A | Compare with |
| 17449 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17419 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 572 | None | - | 17 | 0 | Manual* | N/A | Compare with |
| 171 | None | - | 14 | 0 | Manual* | N/A | Compare with |
| 17451 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 17421 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 574 | None | - | 17 | 0 | Manual* | N/A | Compare with |
| 173 | None | - | 20 | 0 | Manual* | N/A | Compare with |
| 17453 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 17423 | None | - | 21 | 0 | Manual | N/A | Compare with |
| 576 | None | - | 26 | 0 | Manual* | N/A | Compare with |
| 175 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 17455 | None | - | 28 | 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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