mm:parameters:manganese:ddwawawawa_example_page
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| - | ====== Manganese (II) - DDWaWaWa ====== | ||
| - | The avian viral S integrase shows preference by manganese(II) over magnesium. In both cases the metal atom is bonded to two aspartates and four water molecules. | ||
| - | |||
| - | | **Coordination Sphere** | **Oxidation state:** Mn(II) \\ **Spin multiplicity:** 6 | | ||
| - | | {{ :mm:parameters:manganese:non-parameterized_ddwwww_.png?200 |}} | {{ :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.)) | | ||
| - | |||
| - | |||
| - | ---- | ||
| - | |||
| - | ===== Structure chosen to parameterize ===== | ||
| - | |||
| - | | **TEST PROTEIN** || | ||
| - | | //Protein// | Integrase | | ||
| - | | //PDB Code// | 1A5V | | ||
| - | | //Crystallographic Resolution// | 1.90 Å | | ||
| - | | //Organism// | Rous Sarcoma Virus | | ||
| - | | [[http://www.pnas.org/content/95/9/4831.long | [Lubkowski, 1998]]] || | ||
| - | |||
| - | |||
| - | ===== Parameters Determined ===== | ||
| - | |||
| - | ==== Atom Types ==== | ||
| - | |||
| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | MN | M1 | 54.938 | {{ :mm:parameters:manganese:parameterized_ddwwww_.png?120 |}} | | ||
| - | | OD1 | D1 | 15.9994 | ::: | | ||
| - | | OD2 | D2 | 15.9994 | ::: | | ||
| - | | OW | W1 | 15.9994 | ::: | | ||
| - | | OW | W2 | 15.9994 | ::: | | ||
| - | | OW | W3 | 15.9994 | ::: | | ||
| - | | OW | W4 | 15.9994 | ::: | | ||
| - | | HW | HM | 1.00794 | ::: | | ||
| - | |||
| - | ==== Bond Parameters ==== | ||
| - | |||
| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | | ||
| - | | M1-D1 | 86.69 | 2.0912 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-D2 | 73.44 | 2.1278 | ::: | | ||
| - | | M1-W1 | 41.1 | 2.2458 | ::: | | ||
| - | | M1-W2 | 58.63 | 2.1786 | ::: | | ||
| - | | M1-W3 | 34.55 | 2.3171 | ::: | | ||
| - | | M1-W4 | 25.05 | 2.3835 | ::: | | ||
| - | | D1-C | 656 | 1.25 | | ||
| - | | D2-C | 656 | 1.25 | | ||
| - | | W1-HM | 553 | 0.9572 | | ||
| - | | W2-HM | 553 | 0.9572 | | ||
| - | | W3-HM | 553 | 0.9572 | | ||
| - | | W4-HM | 553 | 0.9572 | | ||
| - | |||
| - | |||
| - | ==== Angles Parameters ==== | ||
| - | |||
| - | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | | ||
| - | | D1-M1-D2 | 38.782 | 108.3864 | [[#references | [Neves, 2013]]] | | ||
| - | | D1-M1-W1 | 52.48 | 86.0095 | ::: | | ||
| - | | D1-M1-W2 | 40.523 | 93.9632 | ::: | | ||
| - | | D1-M1-W3 | 14.18 | 90.4522 | ::: | | ||
| - | | D1-M1-W4 | 22.791 | 173.2496 | ::: | | ||
| - | | D2-M1-W1 | 26.46 | 97.5246 | ::: | | ||
| - | | D2-M1-W2 | 55.17 | 91.2115 | ::: | | ||
| - | | D2-M1-W3 | 14.57 | 157.0825 | ::: | | ||
| - | | D2-M1-W4 | 49.51 | 85.9497 | ::: | | ||
| - | | W1-M1-W2 | 22.81 | 165.2888 | ::: | | ||
| - | | W1-M1-W3 | 21.4 | 75.017 | ::: | | ||
| - | | W1-M1-W4 | 30.33 | 100.0581 | ::: | | ||
| - | | W2-M1-W3 | 16.61 | 92.3995 | ::: | | ||
| - | | W2-M1-W4 | 21.06 | 84.0447 | ::: | | ||
| - | | W3-M1-W4 | 16.8 | 84.2736 | ::: | | ||
| - | | M1-D1-C | 52.071 | 128.7239 | ::: | | ||
| - | | M1-D2-C | 46.53 | 125.6353 | ::: | | ||
| - | | M1-W1-HM | 24.91 | 107.2734 | ::: | | ||
| - | | M1-W2-HM | 24.17 | 105.0104 | ::: | | ||
| - | | M1-W3-HM | 7.36 | 101.1843 | ::: | | ||
| - | | M1-W4-HM | 7.764 | 101.9263 | ::: | | ||
| - | | HM-W1-HM | 100 | 104.52 | | ||
| - | | HM-W2-HM | 100 | 104.52 | | ||
| - | | HM-W3-HM | 100 | 104.52 | | ||
| - | | HM-W4-HM | 100 | 104.52 | | ||
| - | | D1-C-CT | 70 | 117 | | ||
| - | | D1-C-O2 | 80 | 126 | | ||
| - | | D2-C-CT | 70 | 117 | | ||
| - | | D2-C-O2 | 80 | 126 | | ||
| - | |||
| - | ==== Van der Waals Parameters ==== | ||
| - | |||
| - | | **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]]] | | ||
| - | | HM | 0.6 | 0.0157 | | | ||
| - | |||
| - | |||
| - | ===== Validation of Parameters from MD Simulations ===== | ||
| - | |||
| - | ==== Bond Parameters ==== | ||
| - | |||
| - | | **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 | 2.22 | 2.09 | 2.25 ± 0.06 | [2.13; 2.37] | | ||
| - | | M1-D2 | 2.23 | 2.13 | 2.18 ± 0.07 | [2.04; 2.31] | | ||
| - | | M1-W1 | 2.10 | 2.25 | 2.23 ± 0.09 | [2.05; 2.40] | | ||
| - | | M1-W2 | 2.18 | 2.18 | 2.16 ± 0.08 | [2.01; 2.31] | | ||
| - | | M1-W3 | 2.17 | 2.32 | 2.3 ± 0.1 | [2.1; 2.5] | | ||
| - | | M1-W4 | 2.51 | 2.38 | 2.4 ± 0.1 | [2.1; 2.6] | | ||
| - | |||
| - | ==== Angle Parameters ==== | ||
| - | |||
| - | | **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 | 90.6 | 108.4 | 105 ± 5 | [95; 116] | | ||
| - | | D1-M1-W1 | 87.3 | 86.0 | 85 ± 4 | [76; 94] | | ||
| - | | D1-M1-W2 | 94.2 | 94.0 | 104 ± 6 | [92; 117] | | ||
| - | | D1-M1-W3 | 84.5 | 90.5 | 99 ± 7 | [85; 114] | | ||
| - | | D1-M1-W4 | 171.9 | 173.2 | 171 ± 4 | [162; 179] | | ||
| - | | D2-M1-W1 | 89.9 | 97.5 | 96 ± 7 | [83; 109] | | ||
| - | | D2-M1-W2 | 90.2 | 91.2 | 88 ± 5 | [79; 98] | | ||
| - | | D2-M1-W3 | 179.0 | 157.1 | 149 ± 7 | [136; 163] | | ||
| - | | D2-M1-W4 | 97.4 | 85.9 | 80 ± 5 | [71; 89] | | ||
| - | | W1-M1-W2 | 178.6 | 165.3 | 164 ± 5 | [153; 175] | | ||
| - | | W1-M1-W3 | 90.9 | 75.0 | 70 ± 7 | [56; 84] | | ||
| - | | W1-M1-W4 | 94.2 | 100.1 | 94 ± 6 | [83; 106] | | ||
| - | | W2-M1-W3 | 89.1 | 92.4 | 101 ± 10 | [82; 120] | | ||
| - | | W2-M1-W4 | 84.4 | 84.0 | 75 ± 9 | [57; 93] | | ||
| - | | W3-M1-W4 | 87.5 | 84.3 | 76 ± 7 | [62; 89] | | ||
| - | |||
| - | ===== Downloads ===== | ||
| - | | //Parameter File// | {{:mm:parameters:manganese:frcmod.zip| .frcmod}} | | ||
| - | | //Coordination Sphere Charges// | {{:mm:parameters:manganese:ddwwww_mn-ii.zip| .off}} | | ||
| - | | //Integrase’s PDB File (1A5V.pdb)\\ LEAPRC file// | {{:mm:parameters:manganese:integrase.zip| .pdb, leaprc}} | | ||
| - | |||
| - | ===== References ===== | ||
| - | 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/ddwawawawa_example_page.1374768868.txt.gz · Last modified: 2013/07/25 17:14 by ruineves
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