mm:parameters:manganese:dedwawawa_example_page
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mm:parameters:manganese:dedwawawa_example_page [2013/07/11 09:04] ruineves |
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| - | ====== Manganese(II) - DEDWaWaWa ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | ||
| - | | PATH TO IMAGE1 | {{ :mm:parameters:manganese:octahedral_highspin_d5.png?400|}} ((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// | Muconate Cycloisomerase | | ||
| - | | //PDB Code// | 3CT2 | | ||
| - | | //Crystallographic Resolution// | 1.80 | | ||
| - | | //Organism// | Pseudomonas protegens Pf-5 | | ||
| - | | [[http://pubs.acs.org/doi/abs/10.1021/bi802277h | [Sakai, 2009]]] || | ||
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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 | ::: | | ||
| - | | OD2 | D2 | 15.9994 | ::: | | ||
| - | | OE2 | E1 | 15.9994 | ::: | | ||
| - | | OW | W1 | 15.9994 | ::: | | ||
| - | | OW | W2 | 15.9994 | ::: | | ||
| - | | OW | W3 | 15.9994 | ::: | | ||
| - | | HW | HM | 1.00794 | ::: | | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | | ||
| - | | M1-D1 | 87.24 | 2.1060 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-D2 | 67.69 | 2.1358 | ::: | | ||
| - | | M1-E1 | 64.66 | 2.1182 | ::: | | ||
| - | | M1-W1 | 37.55 | 2.2668 | ::: | | ||
| - | | M1-W2 | 21.70 | 2.3891 | ::: | | ||
| - | | M1-W3 | 26.88 | 2.3509 | ::: | | ||
| - | | D1-C | 656.0 | 1.25 | | ||
| - | | D2-C | 656.0 | 1.25 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
| - | | W1-HM | 553.0 | 0.9572 | | ||
| - | | W2-HM | 553.0 | 0.9572 | | ||
| - | | W3-HM | 553.0 | 0.9572 | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | | ||
| - | | D1-M1-D2 | 34.80 | 166.2571 | [[#references | [Neves, 2013]]] | | ||
| - | | D1-M1-E1 | 36.67 | 98.6591 | ::: | | ||
| - | | D1-M1-W1 | 64.83 | 84.6089 | ::: | | ||
| - | | D1-M1-W2 | 28.655 | 100.2850 | ::: | | ||
| - | | D1-M1-W3 | 12.63 | 104.2522 | ::: | | ||
| - | | D2-M1-E1 | 52.68 | 94.9867 | ::: | | ||
| - | | D2-M1-W1 | 51.096 | 88.2121 | ::: | | ||
| - | | D2-M1-W2 | 70.4 | 68.8061 | ::: | | ||
| - | | D2-M1-W3 | 15.15 | 83.2134 | ::: | | ||
| - | | E1-M1-W1 | 28.47 | 108.9767 | ::: | | ||
| - | | E1-M1-W2 | 27.038 | 151.2138 | ::: | | ||
| - | | E1-M1-W3 | 78.1 | 70.7310 | ::: | | ||
| - | | W1-M1-W2 | 22.205 | 95.5613 | ::: | | ||
| - | | W1-M1-W3 | 11.62 | 171.1984 | ::: | | ||
| - | | W2-M1-W3 | 24.74 | 84.5113 | ::: | | ||
| - | | M1-D1-C | 42.921 | 132.3478 | ::: | | ||
| - | | M1-D2-C | 38.71 | 134.0663 | ::: | | ||
| - | | M1-E1-C | 14.90 | 132.1818 | ::: | | ||
| - | | M1-W1-HM | 19.45 | 110.5423 | ::: | | ||
| - | | M1-W2-HM | 13.29 | 96.8796 | ::: | | ||
| - | | M1-W3-HM | 14.52 | 88.2507 | ::: | | ||
| - | | HM-W1-HM | 100.0 | 104.52 | | ||
| - | | HM-W2-HM | 100.0 | 104.52 | | ||
| - | | HM-W3-HM | 100.0 | 104.52 | | ||
| - | | D1-C-CT | 70.0 | 117.0 | | ||
| - | | D1-C-O2 | 80.0 | 126.0 | | ||
| - | | D2-C-CT | 70.0 | 117.0 | | ||
| - | | D2-C-O2 | 80.0 | 126.0 | | ||
| - | | E1-C-CT | 70.0 | 117.0 | | ||
| - | | E1-C-O2 | 80.0 | 126.0 | | ||
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| - | ==== Van der Waals Parameters ==== | ||
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| - | | **ATOM TYPE** | **R<sub>i</sub> / Å** | **ε<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 | | ||
| - | | D2 | 1.6612 | 0.21 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
| - | | W1 | 1.7683 | 0.152 | | ||
| - | | W2 | 1.7683 | 0.152 | | ||
| - | | W3 | 1.7683 | 0.152 | | ||
| - | | HM | 0.6000 | 0.0157 | [[LINK | [Cornel, 1995]]] | | ||
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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> ± σ(l)** | **‹l›<sub>MD</sub> ± 2σ(l)** | | ||
| - | | M1-D1 | 2.10 | 2.11 | 2.22 ± 0.06 | [2.162; 2.279] | | ||
| - | | M1-D2 | 2.16 | 2.14 | 2.26 ± 0.06 | [2.194; 2.324] | | ||
| - | | M1-E1 | 2.00 | 2.12 | 2.14 ± 0.07 | [2.076; 2.212] | | ||
| - | | M1-W1 | 2.03 | 2.27 | 2.28 ± 0.09 | [2.184; 2.370] | | ||
| - | | M1-W2 | 1.94 | 2.39 | 2.4 ± 0.1 | [2.295; 2.536] | | ||
| - | | M1-W3 | 1.97 | 2.35 | 2.3 ± 0.1 | [2.225; 2.443] | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **ANGLE** | **θ<sub>0 crystal</sub>** | **θ<sub>0 QM</sub>** | **‹θ›<sub>MD</sub> ± σ(θ)** | **‹θ›<sub>MD</sub> ± 2σ(θ)** | | ||
| - | | D1-M1-D2 | 175.3 | 166.3 | 168 ± 4 | [160.5; 174.6] | | ||
| - | | D1-M1-E1 | 89.4 | 98.7 | 98 ± 4 | [90.0; 106.0] | | ||
| - | | D1-M1-W1 | 93.4 | 84.6 | 87 ± 4 | [78.7; 95.2] | | ||
| - | | D1-M1-W2 | 94.1 | 100.3 | 103 ± 5 | [93.4; 112.2] | | ||
| - | | D1-M1-W3 | 89.6 | 104.3 | 106 ± 6 | [94.1; 118.1] | | ||
| - | | D2-M1-E1 | 94.2 | 95.0 | 93 ± 4 | [85.3; 100.0] | | ||
| - | | D2-M1-W1 | 88.8 | 88.2 | 88 ± 4 | [80.4; 96.5] | | ||
| - | | D2-M1-W2 | 81.9 | 68.8 | 68 ± 3 | [61.3; 74.6] | | ||
| - | | D2-M1-W3 | 86.6 | 83.2 | 78 ± 5 | [67.5; 88.9] | | ||
| - | | E1-M1-W1 | 102.9 | 109.0 | 112 ± 5 | [102.6; 121.9] | | ||
| - | | E1-M1-W2 | 169.8 | 151.2 | 146 ± 4 | [138.1; 153.5] | | ||
| - | | E1-M1-W3 | 102.8 | 70.7 | 69 ± 3 | [62.4; 75.8] | | ||
| - | | W1-M1-W2 | 86.5 | 94.6 | 95 ± 5 | [85.4; 104.9] | | ||
| - | | W1-M1-W3 | 154.2 | 171.2 | 165 ± 5 | [155.6; 175.3] | | ||
| - | | W2-M1-W3 | 67.7 | 84.5 | 80 ± 5 | [70.5; 89.0] | | ||
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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/dedwawawa_example_page.1373529883.txt.gz · Last modified: 2013/07/11 09:04 by ruineves
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