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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) | ECA |
Formula | None |
IUPAC InChI Key | None |
IUPAC InChI | None |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | NULL |
Number of atoms | 20 |
Net Charge | -2 |
Forcefield | multiple |
Molecule ID | 17387 |
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 |
---|---|---|---|---|---|---|---|
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 |
17425 | None | - | 34 | 1 | Manual | N/A | Compare with |
578 | None | - | 10 | 0 | Manual* | N/A | Compare with |
177 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17457 | None | - | 28 | 0 | Manual | N/A | Compare with |
17427 | None | - | 34 | 1 | Manual | N/A | Compare with |
581 | None | - | 16 | 0 | Manual* | N/A | Compare with |
203 | None | - | 22 | 0 | Manual* | N/A | Compare with |
17459 | None | - | 28 | 0 | Manual | N/A | Compare with |
17429 | None | - | 15 | 0 | Manual | N/A | Compare with |
583 | None | - | 15 | 0 | Manual* | N/A | Compare with |
205 | None | - | 24 | 0 | Manual* | N/A | Compare with |
17431 | None | - | 15 | 0 | Manual | N/A | Compare with |
619 | None | - | 16 | 0 | Manual* | N/A | Compare with |
207 | None | - | 20 | 0 | Manual* | N/A | Compare with |
17433 | None | - | 21 | -1 | Manual | N/A | Compare with |
17403 | None | - | 16 | -1 | Manual | N/A | Compare with |
1503 | None | - | 118 | 0 | Manual* | N/A | Compare with |
210 | None | - | 17 | 0 | 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 |
17509 | None | - | 27 | 0 | Manual | N/A | Compare with |
17479 | None | - | 27 | -1 | Manual | N/A | Compare with |
1588 | None | - | 125 | 0 | Manual* | N/A | Compare with |
1551 | None | - | 153 | 0 | Manual* | N/A | Compare with |
17511 | None | - | 27 | 0 | Manual | N/A | Compare with |
17481 | None | - | 15 | 0 | Manual | N/A | Compare with |
1590 | None | - | 147 | 0 | Manual* | N/A | Compare with |
1553 | None | - | 155 | 0 | Manual* | N/A | Compare with |
17513 | None | - | 26 | 0 | Manual | N/A | Compare with |
17483 | None | - | 15 | 0 | Manual | N/A | Compare with |
1593 | None | - | 3 | 0 | Manual* | N/A | Compare with |
1555 | None | - | 167 | 0 | Manual* | N/A | Compare with |
17515 | None | - | 26 | 0 | Manual | N/A | Compare with |
17485 | None | - | 21 | 0 | Manual | N/A | Compare with |
1595 | None | - | 5 | 0 | Manual* | N/A | Compare with |
1557 | None | - | 131 | 0 | Manual* | N/A | Compare with |
17517 | None | - | 28 | 0 | Manual | N/A | Compare with |
17487 | None | - | 21 | 0 | Manual | N/A | Compare with |
1598 | None | - | 6 | 0 | Manual* | N/A | Compare with |
1560 | None | - | 123 | 0 | Manual* | N/A | Compare with |
17519 | None | - | 28 | 0 | Manual | N/A | Compare with |
17489 | None | - | 22 | 0 | Manual | N/A | Compare with |
1602 | None | - | 20 | 0 | Manual* | N/A | Compare with |
1562 | None | - | 125 | 0 | Manual* | N/A | Compare with |
17491 | None | - | 22 | 0 | Manual | N/A | Compare with |
17461 | None | - | 22 | 0 | Manual | N/A | Compare with |
1604 | None | - | 16 | 0 | Manual* | N/A | Compare with |
1564 | None | - | 143 | 0 | Manual* | N/A | Compare with |
17493 | None | - | 19 | 0 | Manual | N/A | Compare with |
17463 | None | - | 22 | 0 | Manual | N/A | Compare with |
1606 | None | - | 20 | 0 | Manual* | N/A | Compare with |
1566 | None | - | 129 | 0 | Manual* | N/A | Compare with |
17495 | None | - | 19 | 0 | Manual | N/A | Compare with |
17465 | None | - | 31 | 0 | Manual | N/A | Compare with |
1611 | None | - | 18 | 0 | Manual* | N/A | Compare with |
1570 | None | - | 125 | 0 | Manual* | N/A | Compare with |
17497 | None | - | 25 | 0 | Manual | N/A | Compare with |
17467 | None | - | 31 | 0 | Manual | N/A | Compare with |
1646 | None | - | 3 | 0 | Manual* | N/A | Compare with |
1572 | None | - | 153 | 0 | Manual* | N/A | Compare with |
17499 | None | - | 25 | 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.