mm:parameters:manganese:hhewawa_example_page
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mm:parameters:manganese:hhewawa_example_page [2013/07/25 17:28] ruineves |
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| - | ====== Manganese(II) - HHEWaWa ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 5 | | ||
| - | | {{ :mm:parameters:manganese:non-parameterized_hheww_.png?200 |}} | 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// | Homoprotocatechuate 2,3-Dioxygenase | | ||
| - | | //PDB Code// | 1F1U | | ||
| - | | //Crystallographic Resolution// | 1.50 Å | | ||
| - | | //Organism// | Arthrobacter globiformis | | ||
| - | | [[http://jb.asm.org/content/186/7/1945.long | [Vetting, 2004]]] || | ||
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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 | {{ :mm:parameters:manganese:parameterized_hheww_.png?120 |}} | | ||
| - | | OE1 | E1 | 15.9994 | ::: | | ||
| - | | NE2 | NI | 14.0067 | ::: | | ||
| - | | NE2 | NJ | 14.0067 | ::: | | ||
| - | | OW | W1 | 15.9994 | ::: | | ||
| - | | OW | W2 | 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 | 81.53 | 2.1862 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-NJ | 78.93 | 2.1763 | ::: | | ||
| - | | M1-E1 | 90.87 | 2.0648 | ::: | | ||
| - | | M1-W1 | 43.45 | 2.2506 | ::: | | ||
| - | | M1-W2 | 45.59 | 2.2237 | ::: | | ||
| - | | NI-CR | 488.0 | 1.335 | | ||
| - | | NI-CV | 410.0 | 1.394 | | ||
| - | | NJ-CR | 488.0 | 1.335 | | ||
| - | | NJ-CV | 410.0 | 1.394 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
| - | | W1-HM | 553.0 | 0.9572 | | ||
| - | | W2-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-NJ | 35.670 | 106.2009 | [[#references | [Neves, 2013]]] | | ||
| - | | NI-M1-E1 | 66.76 | 90.0029 | ::: | | ||
| - | | NI-M1-W1 | 27.91 | 89.1764 | ::: | | ||
| - | | NI-M1-W2 | 27.25 | 152.3584 | ::: | | ||
| - | | NJ-M1-E1 | 58.53 | 100.4401 | ::: | | ||
| - | | NJ-M1-W1 | 8.378 | 121.3184 | ::: | | ||
| - | | NJ-M1-W2 | 30.649 | 101.1859 | ::: | | ||
| - | | E1-M1-W1 | 8.825 | 136.6245 | ::: | | ||
| - | | E1-M1-W2 | 64.45 | 88.6732 | ::: | | ||
| - | | W1-M1-W2 | 41.88 | 73.2308 | ::: | | ||
| - | | M1-NI-CR | 46.273 | 126.3998 | ::: | | ||
| - | | M1-NI-CV | 46.273 | 126.3998 | ::: | | ||
| - | | M1-NJ-CR | 31.467 | 118.1041 | ::: | | ||
| - | | M1-NJ-CV | 31.467 | 118.1041 | ::: | | ||
| - | | M1-E1-C | 49.84 | 127.7223 | ::: | | ||
| - | | M1-W1-HM | 7.881 | 110.4316 | ::: | | ||
| - | | M1-W2-HM | 26.41 | 109.0419 | ::: | | ||
| - | | 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 | | ||
| - | | NJ-CR-NA | 70.0 | 120.0 | | ||
| - | | NJ-CR-H5 | 50.0 | 120.0 | | ||
| - | | NJ-CV-CC | 70.0 | 120.0 | | ||
| - | | CV-NJ-CR | 70.0 | 117.0 | | ||
| - | | H4-CV-NJ | 50.0 | 120.0 | | ||
| - | | 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 | | ||
| - | | HM-W1-HM | 100.0 | 104.52 | | ||
| - | | HM-W2-HM | 100.0 | 104.52 | | ||
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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 | | ||
| - | | NJ | 1.824 | 0.17 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
| - | | W1 | 1.7683 | 0.152 | | ||
| - | | W2 | 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 | 2.21 | 2.19 | 2.15 ± 0.06 | [2.086; 2.205] | | ||
| - | | M1-NJ | 2.03 | 2.18 | 2.15 ± 0.06 | [2.086; 2.212] | | ||
| - | | M1-E1 | 2.11 | 2.06 | 2.08 ± 0.06 | [2.017; 2.133] | | ||
| - | | M1-W1 | 2.38 | 2.25 | 2.18 ± 0.08 | [2.098; 2.266] | | ||
| - | | M1-W2 | 2.18 | 2.22 | 2.17 ± 0.08 | [2.095; 2.255] | | ||
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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-NJ | 95.6 | 106.2 | 110 ± 4 | [102.1; 117.0] | | ||
| - | | NI-M1-E1 | 86.7 | 90.0 | 94 ± 3 | [86.9; 100.5] | | ||
| - | | NI-M1-W1 | 91.4 | 89.2 | 80 ± 4 | [71.5; 89.3] | | ||
| - | | NI-M1-W2 | 151.4 | 152.4 | 152 ± 4 | [143.9; 159.7] | | ||
| - | | NJ-M1-E1 | 97.3 | 100.4 | 102 ± 4 | [93.6; 110.1] | | ||
| - | | NJ-M1-W1 | 93.4 | 121.3 | 122 ± 7 | [108.5; 135.2] | | ||
| - | | NJ-M1-W2 | 109.2 | 101.2 | 97 ± 4 | [88.6; 104.7] | | ||
| - | | E1-M1-W1 | 169.3 | 136.6 | 135 ± 7 | [121.3; 148.7] | | ||
| - | | E1-M1-W2 | 103.5 | 88.7 | 89 ± 4 | [82.0; 96.6] | | ||
| - | | W1-M1-W2 | 73.6 | 73.2 | 78 ± 4 | [69.5; 86.8] | | ||
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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/hhewawa_example_page.1374769733.txt.gz · Last modified: 2013/07/25 17:28 by ruineves
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