mm:parameters:manganese:dee_so2_example_page
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mm:parameters:manganese:dee_so2_example_page [2013/07/10 18:56] ruineves |
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| - | ====== Manganese(II) - DEE[SO2] ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | ||
| - | | IMAGE1 | IMAGE2 ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | ||
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| - | ---- | ||
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| - | ===== Structure chosen to parameterize ===== | ||
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| - | | **TEST PROTEIN** || | ||
| - | | //Protein// | PROTEIN NAME | | ||
| - | | //PDB Code// | PDB CODE | | ||
| - | | //Crystallographic Resolution// | RESOLUTION | | ||
| - | | //Organism// | ORGANISM | | ||
| - | | [[LINK OF THE PAPER OF THE STRUCTURE | [1ST AUTHOR, PUBL YEAR]]] || | ||
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| - | ===== Parameters Determined ===== | ||
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| - | ==== Atom Types ==== | ||
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| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | MN | M1 | 54.938 | IMAGE | | ||
| - | | OD2 | D1 | 15.9994 | ::: | | ||
| - | | OE2 | E1 | 15.9994 | ::: | | ||
| - | | OE1 | E2 | 15.9994 | ::: | | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | ||
| - | | M1-D1 | 33.32 | 2.2509 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-E1 | 47.15 | 2.1737 | ::: | | ||
| - | | M1-E2 | 49.51 | 2.2008 | ::: | | ||
| - | | M1-R1 | 41.81 | 2.1619 | ::: | | ||
| - | | M1-R2 | 45.80 | 2.1526 | ::: | | ||
| - | | D1-C | 656.0 | 1.25 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
| - | | E2-C | 656.0 | 1.25 | | ||
| - | | SO-R1 | 541.1 | 1.436 | | ||
| - | | SO-R2 | 541.1 | 1.436 | | ||
| - | | SO-O1 | 541.1 | 1.436 | | ||
| - | | SO-O2 | 541.1 | 1.436 | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **θ / deg** | **REFERENCE** | | ||
| - | | D1-M1-E1 | 45.46 | 92.3315 | [[#references | [Neves, 2013]]] | | ||
| - | | D1-M1-E2 | 25.03 | 123.0771 | ::: | | ||
| - | | D1-M1-R1 | 13.27 | 96.5510 | ::: | | ||
| - | | D1-M1-R2 | 4.321 | 121.0757 | ::: | | ||
| - | | E1-M1-E2 | 40.08 | 86.7147 | ::: | | ||
| - | | E1-M1-R1 | 19.90 | 160.9449 | ::: | | ||
| - | | E1-M1-R2 | 33.00 | 93.3926 | ::: | | ||
| - | | E2-M1-R1 | 8.95 | 102.2828 | ::: | | ||
| - | | E2-M1-R2 | 4.405 | 115.7857 | ::: | | ||
| - | | R1-M1-R2 | 291.6 | 67.5889 | ::: | | ||
| - | | M1-D1-C | 16.912 | 165.3084 | ::: | | ||
| - | | M1-E1-C | 22.912 | 145.6796 | ::: | | ||
| - | | M1-E2-C | 15.527 | 135.3597 | ::: | | ||
| - | | M1-R1-SO | 100.89 | 95.8499 | ::: | | ||
| - | | M1-R2-SO | 100.89 | 95.8499 | ::: | | ||
| - | | D1-C-CT | 70.0 | 117.0 | | ||
| - | | D1-C-O2 | 80.0 | 126.0 | | ||
| - | | E1-C-CT | 70.0 | 117.0 | | ||
| - | | E1-C-O2 | 80.0 | 126.0 | | ||
| - | | E2-C-CT | 70.0 | 117.0 | | ||
| - | | E2-C-O2 | 80.0 | 126.0 | | ||
| - | | R1-SO-O1 | 74.6 | 119.82 | | ||
| - | | R1-SO-O2 | 74.6 | 119.82 | | ||
| - | | R1-SO-R2 | 74.6 | 119.82 | | ||
| - | | R2-SO-O1 | 74.6 | 119.82 | | ||
| - | | R2-SO-O2 | 74.6 | 119.82 | | ||
| - | | O1-SO-O2 | 74.6 | 119.82 | | ||
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| - | ==== Van der Waals Parameters ==== | ||
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| - | | **ATOM TYPE** | **R<sub>i</sub> / angstrom** | **epsilon<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | ||
| - | | M1 | 1.4544 | 0.03 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Babu, 2006]]] | | ||
| - | | D1 | 1.6612 | 0.21 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
| - | | E2 | 1.6612 | 0.21 | | ||
| - | | R1 | 1.6612 | 0.2100 | | ||
| - | | R2 | 1.6612 | 0.2100 | | ||
| - | | O1 | 1.6612 | 0.2100 | | ||
| - | | O2 | 1.6612 | 0.2100 | | ||
| - | | SO | 2.0000 | 0.2500 | | ||
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| - | ===== Validation of Parameters from MD Simulations ===== | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **<l><sub>MD</sub> ± sigma(l)** | **<l><sub>MD</sub> ± 2sigma(l)** | | ||
| - | | M1-D1 | 2.03 | 2.25 | 2.41 ± 0.09 | [2.318; 2.506] | | ||
| - | | M1-E1 | 2.15 | 2.17 | 2.28 ± 0.08 | [2.200; 2.359] | | ||
| - | | M1-E2 | 1.95 | 2.20 | 2.27 ± 0.08 | [2.193; 2.347] | | ||
| - | | M1-R2 | 3.54 | 2.16 | 2.18 ± 0.06 | [2.114; 2.238] | | ||
| - | | M1-R2 | 2.20 | 2.15 | 2.17 ± 0.06 | [2.113; 2.232] | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **ANGLE** | **theta<sub>0 crystal</sub>** | **theta<sub>0 QM</sub>** | **<theta><sub>MD</sub> ± sigma(theta)** | **<θ><sub>MD</sub> ± 2sigma(theta)** | | ||
| - | | D1-M1-E1 | 87.7 | 92.3 | 89 ± 4 | [80.5; 97.0] | | ||
| - | | D1-M1-E2 | 170.0 | 123.1 | 127 ± 5 | [117.4; 137.5] | | ||
| - | | D1-M1-R1 | 85.6 | 96.6 | 91 ± 6 | [78.7; 103.7] | | ||
| - | | D1-M1-R2 | 94.6 | 121.1 | 99 ± 8 | [82.2; 115.1] | | ||
| - | | E1-M1-E2 | 88.0 | 86.7 | 87 ± 5 | [78.0; 96.9] | | ||
| - | | E1-M1-R1 | 129.4 | 160.9 | 156 ± 4 | [147.4; 163.8] | | ||
| - | | E1-M1-R2 | 92.1 | 93.4 | 92 ± 4 | [83.3; 100.7] | | ||
| - | | E2-M1-R1 | 104.1 | 102.3 | 111 ± 6 | [97.8; 123.6] | | ||
| - | | E2-M1-R2 | 94.6 | 115.8 | 133 ± 9 | [115.9; 150.5] | | ||
| - | | R1-M1-R2 | 39.0 | 67.6 | 66 ± 1 | [63.1; 69.0] | | ||
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| - | ===== Downloads ===== | ||
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| - | | //Parameter File// | {{PATH TO FRCMOD FILE| .frcmod}} | | ||
| - | | //Coordination Sphere Charges// | {{PATH TO CHARGE FILES| .off}} | | ||
| - | | //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file// | {{PATH TO PDB AND LEAPRC FILES| .pdb, leaprc}} | | ||
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| - | ===== References ===== | ||
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| - | Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. [[http://pubs.acs.org/doi/abs/10.1021/ct400055v | Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins]] . //J. Chem. Theory Comput.//, **2013**, 9 (6), 2718–2732 | ||
mm/parameters/manganese/dee_so2_example_page.1373479008.txt.gz · Last modified: 2013/07/10 18:56 by ruineves
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