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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) | H3M |
| 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 | 17356 |
| 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 |
|---|---|---|---|---|---|---|---|
| 17466 | None | - | 31 | 0 | Manual | N/A | Compare with |
| 1642 | None | - | 18 | 0 | Manual* | N/A | Compare with |
| 1571 | None | - | 147 | 0 | Manual* | N/A | Compare with |
| 17498 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17468 | None | - | 31 | 0 | Manual | N/A | Compare with |
| 1649 | None | - | 5 | 0 | Manual* | N/A | Compare with |
| 1574 | None | - | 123 | 0 | Manual* | N/A | Compare with |
| 17500 | None | - | 25 | 0 | Manual | N/A | Compare with |
| 17470 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 1577 | None | - | 138 | 0 | Manual* | N/A | Compare with |
| 1525 | None | - | 147 | 0 | Manual* | N/A | Compare with |
| 17502 | None | - | 32 | 0 | Manual | N/A | Compare with |
| 17472 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 1579 | None | - | 143 | 0 | Manual* | N/A | Compare with |
| 1532 | None | - | 149 | 0 | Manual* | N/A | Compare with |
| 17504 | None | - | 32 | 0 | Manual | N/A | Compare with |
| 17474 | None | - | 23 | 0 | Manual | N/A | Compare with |
| 1582 | None | - | 119 | 0 | Manual* | N/A | Compare with |
| 17536 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 3412 | None | - | 18 | 0 | Manual* | N/A | Compare with |
| 1679 | None | - | 31 | 0 | Manual* | N/A | Compare with |
| 17538 | None | - | 19 | -2 | Manual | N/A | Compare with |
| 3486 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 1731 | None | - | 74 | 0 | Manual* | N/A | Compare with |
| 17540 | None | - | 19 | -2 | Manual | N/A | Compare with |
| 3488 | None | - | 12 | 0 | Manual* | N/A | Compare with |
| 1733 | None | - | 81 | 0 | Manual* | N/A | Compare with |
| 17542 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 3500 | None | - | 18 | 0 | Manual* | N/A | Compare with |
| 1738 | None | - | 77 | 0 | Manual* | N/A | Compare with |
| 17544 | None | - | 29 | 0 | Manual | N/A | Compare with |
| 3502 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 2002 | None | - | 24 | 0 | Manual* | N/A | Compare with |
| 17546 | None | - | 26 | 1 | Manual | N/A | Compare with |
| 3505 | None | - | 18 | 0 | Manual* | N/A | Compare with |
| 2109 | None | - | 171 | -2 | Manual* | N/A | Compare with |
| 17548 | None | - | 26 | 1 | Manual | N/A | Compare with |
| 3923 | None | - | 4 | 0 | Manual | N/A | Compare with |
| 2172 | None | - | 26 | -1 | Manual* | N/A | Compare with |
| 17550 | None | - | 15 | -1 | Manual | N/A | Compare with |
| 17520 | None | - | 28 | 0 | Manual | N/A | Compare with |
| 3947 | None | - | 127 | -1 | Manual | N/A | Compare with |
| 2276 | None | - | 363 | -2 | Manual* | N/A | Compare with |
| 17552 | None | - | 15 | -1 | Manual | N/A | Compare with |
| 17522 | None | - | 21 | -1 | Manual | N/A | Compare with |
| 4182 | None | - | 5 | 0 | Manual* | N/A | Compare with |
| 2671 | None | - | 47 | -3 | Manual | N/A | Compare with |
| 18620 | None | - | 49 | -3 | Manual | N/A | Compare with |
| 17524 | None | - | 21 | -1 | Manual | N/A | Compare with |
| 4578 | None | - | 161 | -8 | Manual* | N/A | Compare with |
| 2694 | None | - | 77 | -3 | Manual | N/A | Compare with |
| 18622 | None | - | 49 | -3 | Manual* | N/A | Compare with |
| 17526 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 4580 | None | - | 161 | -8 | Manual* | N/A | Compare with |
| 2747 | None | - | 20 | 0 | Manual* | N/A | Compare with |
| 18660 | None | - | 49 | -3 | Manual* | N/A | Compare with |
| 17528 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 2752 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 21025 | None | - | 209 | -4 | Manual* | N/A | Compare with |
| 17530 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 2920 | None | - | 27 | 1 | Manual | N/A | Compare with |
| 1655 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 17532 | None | - | 18 | 0 | Manual | N/A | Compare with |
| 3408 | None | - | 24 | 0 | Manual* | N/A | Compare with |
| 1664 | None | - | 8 | 0 | Manual* | N/A | Compare with |
| 17534 | None | - | 24 | 0 | Manual | N/A | Compare with |
| 3410 | None | - | 15 | 0 | Manual* | N/A | Compare with |
| 1677 | None | - | 34 | 0 | Manual* | N/A | Compare with |
| 9643 | None | - | 103 | 1 | Manual | N/A | Compare with |
| 1502 | None | - | 106 | 0 | Manual* | N/A | Compare with |
| 5031 | None | - | 78 | 0 | Manual* | N/A | Compare with |
| 208 | None | - | 23 | 0 | Manual* | N/A | Compare with |
| 17146 | None | - | 33 | 1 | Manual | N/A | Compare with |
| 1505 | None | - | 130 | 0 | Manual* | N/A | Compare with |
| 5100 | None | - | 58 | -6 | Manual* | N/A | Compare with |
| 211 | None | - | 14 | 0 | Manual* | N/A | Compare with |
| 17148 | None | - | 33 | 1 | Manual | N/A | Compare with |
| 1507 | None | - | 138 | 0 | Manual* | N/A | Compare with |
| 5182 | None | - | 110 | -8 | Manual* | N/A | Compare with |
| 213 | None | - | 27 | 0 | Manual* | N/A | Compare with |
| 17150 | None | - | 16 | -1 | Manual | N/A | Compare with |
| 1511 | None | - | 131 | 0 | Manual* | N/A | Compare with |
| 5639 | None | - | 127 | 0 | Manual | N/A | Compare with |
| 215 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 17152 | None | - | 16 | -1 | Manual | N/A | Compare with |
| 5796 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 562 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 17154 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 5798 | None | - | 19 | 0 | Manual* | N/A | Compare with |
| 565 | None | - | 9 | 0 | Manual* | N/A | Compare with |
| 164 | None | - | 27 | 1 | Manual* | N/A | Compare with |
| 17156 | None | - | 17 | 0 | Manual | N/A | Compare with |
| 5814 | None | - | 381 | 1 | Manual* | N/A | Compare with |
| 567 | None | - | 10 | 0 | Manual* | N/A | Compare with |
| 166 | None | - | 17 | 0 | Manual* | N/A | Compare with |
| 17158 | None | - | 20 | 0 | Manual | N/A | Compare with |
| 6252 | None | - | 89 | 0 | Manual* | N/A | Compare with |
| 569 | None | - | 8 | 0 | Manual* | N/A | Compare with |
| 168 | None | - | 15 | 0 | Manual* | N/A | Compare with |
| 17160 | None | - | 20 | 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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