mm:parameters:manganese:hhdhwa_example_page
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| - | ====== Manganese(III) - HHDHWa ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 5 | | ||
| - | | {{ :mm:parameters:manganese:non-parameterized_hhdhw_.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// | Manganese Superoxide Dismutase | | ||
| - | | //PDB Code// | 1N0J | | ||
| - | | //Crystallographic Resolution// | 2.20 Å | | ||
| - | | //Organism// | Homo sapiens | | ||
| - | | [[http://www.sciencedirect.com/science/article/pii/009286749290270M | [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 | {{ :mm:parameters:manganese:parameterized_hhdhw_.png?120 |}} | | ||
| - | | OD1 | D1 | 15.9994 | ::: | | ||
| - | | NE2 | NI | 14.0067 | ::: | | ||
| - | | NE2 | NJ | 14.0067 | ::: | | ||
| - | | NE2 | NK | 14.0067 | ::: | | ||
| - | | OW | W1 | 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 | 59.43 | 2.2457 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-NJ | 75.35 | 2.1589 | ::: | | ||
| - | | M1-NK | 80.07 | 2.168 | ::: | | ||
| - | | M1-D1 | 81.62 | 2.0542 | ::: | | ||
| - | | M1-W1 | 38.02 | 2.2351 | ::: | | ||
| - | | NI-CR | 488 | 1.335 | | ||
| - | | NI-CV | 410 | 1.394 | | ||
| - | | NJ-CR | 488 | 1.335 | | ||
| - | | NJ-CV | 410 | 1.394 | | ||
| - | | NK-CR | 488 | 1.335 | | ||
| - | | NK-CV | 410 | 1.394 | | ||
| - | | D1-C | 656 | 1.25 | | ||
| - | | W1-HM | 553 | 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 | 48.40 | 95.4086 | [[#references | [Neves, 2013]]] | | ||
| - | | NI-M1-NK | 45.74 | 92.4322 | ::: | | ||
| - | | NI-M1-D1 | 86.0 | 82.0242 | ::: | | ||
| - | | NI-M1-W1 | 56.35 | 166.1284 | ::: | | ||
| - | | NJ-M1-NK | 37.87 | 139.1027 | ::: | | ||
| - | | NJ-M1-D1 | 24.76 | 109.6451 | ::: | | ||
| - | | NJ-M1-W1 | 46.58 | 90.8259 | ::: | | ||
| - | | NK-M1-D1 | 23.465 | 111.182 | ::: | | ||
| - | | NK-M1-W1 | 46.47 | 90.9222 | ::: | | ||
| - | | D1-M1-W1 | 59.83 | 84.2125 | ::: | | ||
| - | | 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 | | ||
| - | | HM-W1-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 | | ||
| - | | 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 | 2.05 | 2.04 ± 0.06 | [1.982; 2.103] | | ||
| - | | M1-NI | 2.10 | 2.25 | 2.26 ± 0.07 | [2.192; 2.328] | | ||
| - | | M1-NJ | 2.08 | 2.16 | 2.17 ± 0.06 | [2.108; 2.234] | | ||
| - | | N1-NK | 2.09 | 2.17 | 2.19 ± 0.06 | [2.127; 2.246] | | ||
| - | | M1-W1 | 2.02 | 2.24 | 2.14 ± 0.09 | [2.052; 2.232] | | ||
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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 | 95.4 | 96 ± 4 | [88.7; 102.7] | | ||
| - | | NI-M1-NK | 91.5 | 92.4 | 93 ± 3 | [86.7; 100.2] | | ||
| - | | NI-M1-D1 | 82.4 | 82.0 | 82 ± 3 | [77.2; 87.6] | | ||
| - | | NI-M1-W1 | 166.1 | 166.1 | 164 ± 3 | [158.1; 169.9] | | ||
| - | | NJ-M1-NK | 137.7 | 139.1 | 141 ± 4 | [132.2; 149.1] | | ||
| - | | NJ-M1-D1 | 110.4 | 109.6 | 109 ± 5 | [98.8; 119.0] | | ||
| - | | NJ-M1-W1 | 91.8 | 90.8 | 90 ± 4 | [82.4; 97.5] | | ||
| - | | NK-M1-D1 | 106.4 | 111.2 | 110 ± 5 | [99.9; 120.0] | | ||
| - | | NK-M1-W1 | 91.0 | 90.9 | 91 ± 4 | [83.9; 98.4] | | ||
| - | | D1-M1-W1 | 83.9 | 84.2 | 82 ± 3 | [76.4; 88.0] | | ||
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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/hhdhwa_example_page.1374846687.txt.gz · Last modified: 2013/07/26 14:51 by ruineves
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