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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) | SDH |
Formula | None |
IUPAC InChI Key | None |
IUPAC InChI | None |
IUPAC Name | |
Common Name | |
Canonical SMILES (Daylight) | NULL |
Number of atoms | 12 |
Net Charge | 0 |
Forcefield | multiple |
Molecule ID | 17364 |
Tautomer Group ID | None |
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 |
---|---|---|---|---|---|---|---|
17339 | None | - | 18 | 0 | Manual | N/A | Compare with |
17309 | None | - | 25 | -1 | Manual | N/A | Compare with |
17341 | None | - | 23 | -2 | Manual | N/A | Compare with |
17311 | None | - | 25 | -1 | Manual | N/A | Compare with |
17313 | None | - | 32 | 0 | Manual | N/A | Compare with |
17283 | None | - | 23 | 0 | Manual | N/A | Compare with |
17315 | None | - | 32 | 0 | Manual | N/A | Compare with |
17285 | None | - | 17 | 0 | Manual | N/A | Compare with |
17317 | None | - | 24 | 0 | Manual | N/A | Compare with |
17287 | None | - | 17 | 0 | Manual | N/A | Compare with |
17319 | None | - | 24 | 0 | Manual | N/A | Compare with |
17289 | None | - | 28 | 0 | Manual | N/A | Compare with |
17321 | None | - | 18 | 0 | Manual | N/A | Compare with |
17291 | None | - | 28 | 0 | Manual | N/A | Compare with |
17323 | None | - | 18 | 0 | Manual | N/A | Compare with |
17293 | None | - | 9 | -1 | Manual | N/A | Compare with |
17325 | None | - | 25 | 0 | Manual | N/A | Compare with |
17295 | None | - | 9 | -1 | Manual | N/A | Compare with |
17327 | None | - | 25 | 0 | Manual | N/A | Compare with |
17297 | None | - | 18 | 0 | Manual | N/A | Compare with |
17329 | None | - | 17 | -2 | Manual | N/A | Compare with |
17299 | None | - | 18 | 0 | Manual | N/A | Compare with |
17331 | None | - | 17 | -2 | Manual | N/A | Compare with |
17301 | None | - | 25 | 0 | Manual | N/A | Compare with |
17333 | None | - | 30 | 1 | Manual | N/A | Compare with |
17303 | None | - | 25 | 0 | Manual | N/A | Compare with |
17335 | None | - | 30 | 1 | Manual | N/A | Compare with |
17305 | None | - | 23 | 0 | Manual | N/A | Compare with |
17337 | None | - | 18 | 0 | Manual | N/A | Compare with |
17307 | None | - | 23 | 0 | Manual | N/A | Compare with |
17400 | None | - | 21 | 0 | Manual | N/A | Compare with |
17370 | None | - | 18 | -1 | Manual | N/A | Compare with |
17372 | None | - | 18 | -1 | Manual | N/A | Compare with |
17374 | None | - | 30 | -1 | Manual | N/A | Compare with |
17343 | None | - | 23 | -2 | Manual | N/A | Compare with |
17376 | None | - | 30 | -1 | Manual | N/A | Compare with |
17345 | None | - | 20 | -2 | Manual | N/A | Compare with |
17378 | None | - | 28 | -1 | Manual | N/A | Compare with |
17347 | None | - | 20 | -2 | Manual | N/A | Compare with |
17380 | None | - | 28 | -1 | Manual | N/A | Compare with |
17349 | None | - | 15 | 0 | Manual | N/A | Compare with |
17382 | None | - | 23 | 0 | Manual | N/A | Compare with |
17351 | None | - | 15 | 0 | Manual | N/A | Compare with |
17384 | None | - | 23 | 0 | Manual | N/A | Compare with |
17353 | None | - | 23 | 0 | Manual | N/A | Compare with |
17386 | None | - | 20 | -2 | Manual | N/A | Compare with |
17355 | None | - | 23 | 0 | Manual | N/A | Compare with |
17388 | None | - | 20 | -2 | Manual | N/A | Compare with |
17357 | None | - | 30 | 0 | Manual | N/A | Compare with |
17390 | None | - | 18 | 0 | Manual | N/A | Compare with |
17359 | None | - | 30 | 0 | Manual | N/A | Compare with |
17392 | None | - | 18 | 0 | Manual | N/A | Compare with |
17361 | None | - | 12 | 0 | Manual | N/A | Compare with |
17394 | None | - | 24 | -1 | Manual | N/A | Compare with |
17363 | None | - | 12 | 0 | Manual | N/A | Compare with |
17396 | None | - | 24 | -1 | Manual | N/A | Compare with |
17366 | None | - | 29 | 0 | Manual | N/A | Compare with |
17398 | None | - | 21 | 0 | Manual | N/A | Compare with |
17368 | None | - | 29 | 0 | Manual | N/A | Compare with |
17430 | None | - | 15 | 0 | Manual | N/A | Compare with |
584 | None | - | 15 | 0 | Manual* | N/A | Compare with |
206 | None | - | 25 | 1 | Manual* | N/A | Compare with |
17432 | None | - | 15 | 0 | Manual | N/A | Compare with |
17402 | None | - | 16 | -1 | Manual | N/A | Compare with |
1502 | None | - | 106 | 0 | Manual* | N/A | Compare with |
208 | None | - | 23 | 0 | Manual* | N/A | Compare with |
17434 | None | - | 21 | -1 | Manual | N/A | Compare with |
17404 | None | - | 16 | -1 | Manual | N/A | Compare with |
1505 | None | - | 130 | 0 | Manual* | N/A | Compare with |
211 | None | - | 14 | 0 | Manual* | N/A | Compare with |
17436 | None | - | 21 | -1 | Manual | N/A | Compare with |
17406 | None | - | 28 | -1 | Manual | N/A | Compare with |
1507 | None | - | 138 | 0 | Manual* | N/A | Compare with |
213 | None | - | 27 | 0 | Manual* | N/A | Compare with |
17438 | None | - | 25 | 0 | Manual | N/A | Compare with |
17408 | None | - | 28 | -1 | Manual | N/A | Compare with |
1511 | None | - | 131 | 0 | Manual* | N/A | Compare with |
215 | None | - | 19 | 0 | Manual* | N/A | Compare with |
17440 | None | - | 25 | 0 | Manual | N/A | Compare with |
17410 | None | - | 18 | 0 | Manual | N/A | Compare with |
562 | None | - | 9 | 0 | Manual* | N/A | Compare with |
17442 | None | - | 28 | 1 | Manual | N/A | Compare with |
17412 | None | - | 18 | 0 | Manual | N/A | Compare with |
565 | None | - | 9 | 0 | Manual* | N/A | Compare with |
164 | None | - | 27 | 1 | Manual* | N/A | Compare with |
17444 | None | - | 28 | 1 | Manual | N/A | Compare with |
17414 | None | - | 24 | 1 | Manual | N/A | Compare with |
567 | None | - | 10 | 0 | Manual* | N/A | Compare with |
166 | None | - | 17 | 0 | Manual* | N/A | Compare with |
17446 | None | - | 28 | 0 | Manual | N/A | Compare with |
17416 | None | - | 24 | 1 | Manual | N/A | Compare with |
569 | None | - | 8 | 0 | Manual* | N/A | Compare with |
168 | None | - | 15 | 0 | Manual* | N/A | Compare with |
17448 | None | - | 28 | 0 | Manual | N/A | Compare with |
17418 | None | - | 21 | 0 | Manual | N/A | Compare with |
571 | None | - | 14 | 0 | Manual* | N/A | Compare with |
170 | None | - | 14 | 0 | Manual* | N/A | Compare with |
17450 | None | - | 23 | 0 | Manual | N/A | Compare with |
17420 | None | - | 21 | 0 | Manual | N/A | Compare with |
573 | 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.