mm:parameters:manganese:hdewawawa_example_page
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| - | ====== Manganese(II) - HDEWaWaWa ====== | ||
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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// | Citochrome //c// Oxidase | | ||
| - | | //PDB Code// | 3HB3 | | ||
| - | | //Crystallographic Resolution// | 2.25 | | ||
| - | | //Organism// | Paracoccus denitrificans | | ||
| - | | [[LINK OF THE PAPER OF THE STRUCTURE | [Koepke, 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 | | ||
| - | | OD1 | D1 | 15.9994 | ::: | | ||
| - | | OE1 | E1 | 15.9994 | ::: | | ||
| - | | NE2 | NI | 14.0067 | ::: | | ||
| - | | 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-NI | 63.17 | 2.242 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-D1 | 77.67 | 2.141 | ::: | | ||
| - | | M1-E1 | 68.41 | 2.147 | ::: | | ||
| - | | M1-W1 | 31.5 | 2.3664 | ::: | | ||
| - | | M1-W2 | 31.4 | 2.325 | ::: | | ||
| - | | M1-W3 | 64.37 | 2.1601 | ::: | | ||
| - | | NI-CR | 488.0 | 1.335 | | ||
| - | | NI-CV | 410.0 | 1.394 | | ||
| - | | D1-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** | | ||
| - | | NI-M1-D1 | 55.1 | 90.0153 | [[#references | [Neves, 2013]]] | | ||
| - | | NI-M1-E1 | 41.458 | 159.9206 | ::: | | ||
| - | | NI-M1-W1 | 24.19 | 94.3889 | ::: | | ||
| - | | NI-M1-W2 | 31.3 | 89.0778 | ::: | | ||
| - | | NI-M1-W3 | 34.86 | 98.8181 | ::: | | ||
| - | | D1-M1-E1 | 50.26 | 103.9094 | ::: | | ||
| - | | D1-M1-W1 | 42.6 | 73.0866 | ::: | | ||
| - | | D1-M1-W2 | 12.075 | 162.4957 | ::: | | ||
| - | | D1-M1-W3 | 56.22 | 90.7127 | ::: | | ||
| - | | E1-M1-W1 | 37.25 | 76.4231 | ::: | | ||
| - | | E1-M1-W2 | 54.4 | 73.2795 | ::: | | ||
| - | | E1-M1-W3 | 37.25 | 95.45 | ::: | | ||
| - | | W1-M1-W2 | 12.36 | 89.5541 | ::: | | ||
| - | | W1-M1-W3 | 32.47 | 159.1053 | ::: | | ||
| - | | W2-M1-W3 | 11.975 | 106.6994 | ::: | | ||
| - | | M1-NI-CR | 34.139 | 123.4259 | ::: | | ||
| - | | M1-NI-CV | 34.139 | 123.4259 | ::: | | ||
| - | | M1-D1-C | 46.237 | 123.2712 | ::: | | ||
| - | | M1-E1-C | 44.53 | 121.9953 | ::: | | ||
| - | | M1-W1-HM | 8.322 | 99.514 | ::: | | ||
| - | | M1-W2-HM | 9.174 | 99.3627 | ::: | | ||
| - | | M1-W3-HM | 33.538 | 97.246 | ::: | | ||
| - | | NI-CR-NA | 70.0 | 120.0 | | ||
| - | | NI-CR-H5 | 50.0 | 120.0 | | ||
| - | | NI-CV-CC | 70.0 | 120.0 | | ||
| - | | CV-NI-CR | 70.0 | 117.0 | | ||
| - | | H4-CV-NI | 50.0 | 120.0 | | ||
| - | | 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 | | ||
| - | | 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]]] | | ||
| - | | NI | 1.824 | 0.17 | | ||
| - | | D1 | 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-NI | 1.98 | 2.24 | 2.17 ± 0.06 | [2.111; 2.238] | | ||
| - | | M1-D1 | 2.17 | 2.14 | 2.18 ± 0.06 | [2.117; 2.245] | | ||
| - | | M1-E1 | 2.19 | 2.15 | 2.18 ± 0.07 | [2.112; 2.245] | | ||
| - | | M1-W1 | 2.20 | 2.37 | 2.3 ± 0.1 | [2.189; 2.383] | | ||
| - | | M1-W2 | 2.14 | 2.33 | 2.3 ± 0.1 | [2.170; 2.371] | | ||
| - | | M1-W3 | 2.11 | 2.16 | 2.14 ± 0.07 | [2.070; 2.215] | | ||
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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)** | | ||
| - | | NI-M1-D1 | 74.7 | 90.0 | 84 ± 4 | [76.5; 90.8] | | ||
| - | | NI-M1-E1 | 171.1 | 159.9 | 159 ± 3 | [151.8; 165.4] | | ||
| - | | NI-M1-W1 | 87.0 | 94.4 | 88 ± 4 | [81.0; 95.7] | | ||
| - | | NI-M1-W2 | 99.9 | 89.1 | 82 ± 4 | [73.3; 90.8] | | ||
| - | | NI-M1-W3 | 98.0 | 98.8 | 96 ± 5 | [86.6; 105.4] | | ||
| - | | D1-M1-E1 | 113.6 | 103.9 | 100 ± 4 | [92.0; 107.2] | | ||
| - | | D1-M1-W1 | 72.3 | 73.1 | 76 ± 4 | [68.2; 83.2] | | ||
| - | | D1-M1-W2 | 166.7 | 162.5 | 135 ± 6 | [123.2; 146.7] | | ||
| - | | D1-M1-W3 | 86.4 | 90.7 | 84 ± 4 | [76.2; 91.5] | | ||
| - | | E1-M1-W1 | 86.4 | 76.4 | 73 ± 4 | [64.6; 81.0] | | ||
| - | | E1-M1-W2 | 71.3 | 73.3 | 81 ± 4 | [73.5; 89.0] | | ||
| - | | E1-M1-W3 | 79.7 | 95.5 | 105 ± 5 | [95.1; 114.4] | | ||
| - | | W1-M1-W2 | 120.1 | 89.6 | 62 ± 6 | [50.6; 72.9] | | ||
| - | | W1-M1-W3 | 156.1 | 159.1 | 158 ± 4 | [149.5; 166.0] | | ||
| - | | W2-M1-W3 | 82.2 | 106.7 | 139 ± 6 | [127.5; 151.4] | | ||
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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/hdewawawa_example_page.1373528623.txt.gz · Last modified: 2013/07/11 08:43 by ruineves
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