mm:parameters:manganese:hhdh_ho_example_page
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| - | ====== Manganese(III) - HHDH[HO] ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 5 | | ||
| - | | 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// | Manganese Superoxide Dismutase | | ||
| - | | //PDB Code// | 1N0J | | ||
| - | | //Crystallographic Resolution// | 2.20 | | ||
| - | | //Organism// | Homo sapiens | | ||
| - | | [[LINK OF THE PAPER OF THE STRUCTURE | [Borgstahl, 1992]]] || | ||
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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 | ::: | | ||
| - | | NE2 | NI | 14.0067 | ::: | | ||
| - | | NE2 | NJ | 14.0067 | ::: | | ||
| - | | NE2 | NK | 14.0067 | ::: | | ||
| - | | OW | W1 | 15.9994 | ::: | | ||
| - | | HO | 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 | 106.65 | 2.1265 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-NJ | 95.00 | 2.1147 | ::: | | ||
| - | | M1-NK | 81.69 | 2.1238 | ::: | | ||
| - | | M1-D1 | 129.13 | 1.9569 | ::: | | ||
| - | | M1-W1 | 247.2 | 1.7776 | ::: | | ||
| - | | NI-CR | 488.0 | 1.335 | | ||
| - | | NI-CV | 410.0 | 1.394 | | ||
| - | | NJ-CR | 488.0 | 1.335 | | ||
| - | | NJ-CV | 410.0 | 1.394 | | ||
| - | | NK-CR | 488.0 | 1.335 | | ||
| - | | NK-CV | 410.0 | 1.394 | | ||
| - | | D1-C | 656.0 | 1.25 | | ||
| - | | W1-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 | 88.01 | 91.6707 | [[#references | [Neves, 2013]]] | | ||
| - | | NI-M1-NK | 86.76 | 88.725 | ::: | | ||
| - | | NI-M1-D1 | 131.4 | 82.9759 | ::: | | ||
| - | | NI-M1-W1 | 75.8 | 176.7937 | ::: | | ||
| - | | NJ-M1-NK | 30.68 | 136.3174 | ::: | | ||
| - | | NJ-M1-D1 | 23.09 | 110.6038 | ::: | | ||
| - | | NJ-M1-W1 | 89.71 | 91.1769 | ::: | | ||
| - | | NK-M1-D1 | 20.64 | 112.8695 | ::: | | ||
| - | | NK-M1-W1 | 89.03 | 90.3375 | ::: | | ||
| - | | D1-M1-W1 | 100.0 | 94.5712 | ::: | | ||
| - | | M1-NI-CR | 53.671 | 126.4370 | ::: | | ||
| - | | M1-NI-CV | 53.671 | 126.4370 | ::: | | ||
| - | | M1-NJ-CR | 40.495 | 123.3813 | ::: | | ||
| - | | M1-NJ-CV | 40.495 | 123.3813 | ::: | | ||
| - | | M1-NK-CR | 31.220 | 112.3780 | ::: | | ||
| - | | M1-NK-CV | 31.220 | 112.3780 | ::: | | ||
| - | | M1-D1-C | 47.094 | 135.5495 | ::: | | ||
| - | | M1-W1-HM | 18.57 | 116.025 | ::: | | ||
| - | | 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 | | ||
| - | | NK-CR-NA | 70.0 | 120.0 | | ||
| - | | NK-CR-H5 | 50.0 | 120.0 | | ||
| - | | NK-CV-CC | 70.0 | 120.0 | | ||
| - | | CV-NK-CR | 70.0 | 117.0 | | ||
| - | | H4-CV-NK | 50.0 | 120.0 | | ||
| - | | D1-C-CT | 70.0 | 117.0 | | ||
| - | | D1-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 | | ||
| - | | NJ | 1.824 | 0.17 | | ||
| - | | NK | 1.824 | 0.17 | | ||
| - | | D1 | 1.6612 | 0.21 | | ||
| - | | W1 | 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 | 1.94 | 1.96 | 1.92 ± 0.05 | [1.875; 1.970] | | ||
| - | | M1-NI | 2.10 | 2.13 | 2.13 ± 0.05 | [2.075; 2.175] | | ||
| - | | M1-NJ | 2.08 | 2.12 | 2.11 ± 0.06 | [2.053; 2.163] | | ||
| - | | N1-NK | 2.09 | 2.12 | 2.14 ± 0.06 | [2.080; 2.197] | | ||
| - | | M1-W1 | 2.02 | 1.78 | 1.76 ± 0.04 | [1.722; 1.792] | | ||
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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 | 96.8 | 91.7 | 91 ± 3 | [86.1; 96.7] | | ||
| - | | NI-M1-NK | 91.5 | 88.7 | 91 ± 3 | [85.8; 96.0] | | ||
| - | | NI-M1-D1 | 82.4 | 83.0 | 83 ± 2 | [79.0; 87.6] | | ||
| - | | NI-M1-W1 | 166.1 | 176.8 | 174 ± 2 | [169.9; 179.1] | | ||
| - | | NJ-M1-NK | 137.7 | 136.4 | 138 ± 5 | [128.8; 146.9] | | ||
| - | | NJ-M1-D1 | 110.4 | 110.4 | 111 ± 5 | [100.1; 121.9] | | ||
| - | | NJ-M1-W1 | 91.8 | 91.1 | 91 ± 3 | [85.8; 96.4] | | ||
| - | | NK-M1-D1 | 106.4 | 112.9 | 111 ± 6 | [99.6; 122.2] | | ||
| - | | NK-M1-W1 | 91.0 | 90.3 | 90 ± 3 | [84.2; 95.1] | | ||
| - | | D1-M1-W1 | 83.9 | 94.6 | 93 ± 3 | [87.2; 97.8] | | ||
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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/hhdh_ho_example_page.1373528415.txt.gz · Last modified: 2013/07/11 08:40 by ruineves
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