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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) | ECN |
Formula | None |
IUPAC InChI Key | None |
IUPAC InChI | None |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | NULL |
Number of atoms | 21 |
Net Charge | -1 |
Forcefield | multiple |
Molecule ID | 17435 |
Visibility | Public |
Molecule Tags |
Force Field Version | 45A3 (IFP45A3.dat) |
Upload Date | 2014-02-03 13:07:17 |
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 |
---|---|---|---|---|---|---|---|
1578 | None | - | 144 | 0 | Manual* | N/A | Compare with |
17172 | None | - | 28 | 0 | Manual | N/A | Compare with |
17204 | None | - | 33 | 1 | Manual | N/A | Compare with |
17345 | None | - | 20 | -2 | Manual | N/A | Compare with |
170 | None | - | 14 | 0 | Manual* | N/A | Compare with |
17377 | None | - | 28 | -1 | Manual | N/A | Compare with |
573 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17531 | None | - | 18 | 0 | Manual | N/A | Compare with |
5795 | None | - | 18 | -1 | Manual* | N/A | Compare with |
17153 | None | - | 17 | 0 | Manual | N/A | Compare with |
17294 | None | - | 9 | -1 | Manual | N/A | Compare with |
17326 | None | - | 25 | 0 | Manual | N/A | Compare with |
17480 | None | - | 27 | -1 | Manual | N/A | Compare with |
17512 | None | - | 27 | 0 | Manual | N/A | Compare with |
2671 | None | - | 47 | -3 | Manual | N/A | Compare with |
4578 | None | - | 161 | -8 | Manual* | N/A | Compare with |
17243 | None | - | 26 | -1 | Manual | N/A | Compare with |
17275 | None | - | 24 | -1 | Manual | N/A | Compare with |
17428 | None | - | 34 | 1 | Manual | N/A | Compare with |
17309 | None | - | 25 | -1 | Manual | N/A | Compare with |
17341 | None | - | 23 | -2 | Manual | N/A | Compare with |
17463 | None | - | 22 | 0 | Manual | N/A | Compare with |
17495 | None | - | 19 | 0 | Manual | N/A | Compare with |
1678 | None | - | 35 | 0 | Manual* | N/A | Compare with |
3485 | None | - | 6 | 0 | Manual* | N/A | Compare with |
17226 | None | - | 20 | 0 | Manual | N/A | Compare with |
17258 | None | - | 15 | -1 | Manual | N/A | Compare with |
17411 | None | - | 18 | 0 | Manual | N/A | Compare with |
17444 | None | - | 28 | 1 | Manual | N/A | Compare with |
1556 | None | - | 143 | 0 | Manual* | N/A | Compare with |
1596 | None | - | 3 | 0 | Manual* | N/A | Compare with |
17187 | None | - | 15 | 0 | Manual | N/A | Compare with |
17219 | None | - | 31 | 1 | Manual | N/A | Compare with |
17360 | None | - | 30 | 0 | Manual | N/A | Compare with |
210 | None | - | 17 | 0 | Manual* | N/A | Compare with |
17392 | None | - | 18 | 0 | Manual | N/A | Compare with |
1506 | None | - | 134 | 0 | Manual* | N/A | Compare with |
17546 | None | - | 26 | 1 | Manual | N/A | Compare with |
7281 | None | - | 62 | 1 | Manual* | N/A | Compare with |
17170 | None | - | 28 | 0 | Manual | N/A | Compare with |
17202 | None | - | 33 | 1 | Manual | N/A | Compare with |
17343 | None | - | 23 | -2 | Manual | N/A | Compare with |
168 | None | - | 15 | 0 | Manual* | N/A | Compare with |
17375 | None | - | 30 | -1 | Manual | N/A | Compare with |
571 | None | - | 14 | 0 | Manual* | N/A | Compare with |
17529 | None | - | 18 | 0 | Manual | N/A | Compare with |
30988 | None | - | 1456 | 0 | Template | N/A | Compare with |
5471 | None | - | 130 | -10 | Manual* | N/A | Compare with |
17151 | None | - | 16 | -1 | Manual | N/A | Compare with |
17292 | None | - | 28 | 0 | Manual | N/A | Compare with |
17324 | None | - | 18 | 0 | Manual | N/A | Compare with |
17478 | None | - | 27 | -1 | Manual | N/A | Compare with |
17510 | None | - | 27 | 0 | Manual | N/A | Compare with |
2276 | None | - | 363 | -2 | Manual* | N/A | Compare with |
4182 | None | - | 5 | 0 | Manual* | N/A | Compare with |
17241 | None | - | 26 | -1 | Manual | N/A | Compare with |
17273 | None | - | 24 | -1 | Manual | N/A | Compare with |
17426 | None | - | 34 | 1 | Manual | N/A | Compare with |
17459 | None | - | 28 | 0 | Manual | N/A | Compare with |
1576 | None | - | 129 | 0 | Manual* | N/A | Compare with |
17339 | 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 |
1668 | None | - | 27 | 0 | Manual* | N/A | Compare with |
3411 | None | - | 18 | 0 | Manual* | N/A | Compare with |
17224 | None | - | 22 | 0 | Manual | N/A | Compare with |
17256 | None | - | 27 | 0 | Manual | N/A | Compare with |
17409 | None | - | 18 | 0 | Manual | N/A | Compare with |
17442 | None | - | 28 | 1 | Manual | N/A | Compare with |
1554 | None | - | 155 | 0 | Manual* | N/A | Compare with |
1594 | None | - | 10 | 0 | Manual* | N/A | Compare with |
17185 | None | - | 15 | 0 | Manual | N/A | Compare with |
17217 | None | - | 31 | 1 | Manual | N/A | Compare with |
17358 | None | - | 30 | 0 | Manual | N/A | Compare with |
207 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17390 | None | - | 18 | 0 | Manual | N/A | Compare with |
1503 | None | - | 118 | 0 | Manual* | N/A | Compare with |
17544 | None | - | 29 | 0 | Manual | N/A | Compare with |
6870 | None | - | 24 | 0 | Manual* | N/A | Compare with |
17307 | None | - | 23 | 0 | Manual | N/A | Compare with |
17200 | None | - | 26 | 1 | Manual | N/A | Compare with |
166 | None | - | 17 | 0 | Manual* | N/A | Compare with |
17373 | None | - | 30 | -1 | Manual | N/A | Compare with |
569 | None | - | 8 | 0 | Manual* | N/A | Compare with |
17527 | None | - | 18 | 0 | Manual | N/A | Compare with |
18675 | None | - | 140 | -3 | Manual | N/A | Compare with |
5181 | None | - | 56 | -6 | Manual* | N/A | Compare with |
17149 | None | - | 16 | -1 | Manual | N/A | Compare with |
17290 | None | - | 28 | 0 | Manual | N/A | Compare with |
17322 | 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 |
2172 | None | - | 26 | -1 | Manual* | N/A | Compare with |
3947 | None | - | 127 | -1 | Manual | N/A | Compare with |
17239 | None | - | 16 | -1 | Manual | N/A | Compare with |
17271 | None | - | 18 | 0 | Manual | N/A | Compare with |
17424 | None | - | 21 | 0 | Manual | N/A | Compare with |
17457 | None | - | 28 | 0 | Manual | N/A | Compare with |
1572 | None | - | 153 | 0 | Manual* | N/A | Compare with |
17168 | None | - | 27 | 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.