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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 |
Access to this feature is currently restricted
The maximum QM level is computed using the ATB Pipeline atom limits but can be manually increased on a case by case basis.