mm:parameters:manganese:ded_cl_example_page
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| - | ====== Manganese(II) - DED[CL] ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | ||
| - | | {{ :mm:parameters:manganese:non-parameterized_dedcl_.png?200 |}} | {{ :mm:parameters:manganese:tetrahedral_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.)) | | ||
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| - | ---- | ||
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| - | ===== Structure chosen to parameterize ===== | ||
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| - | | **TEST PROTEIN** || | ||
| - | | //Protein// | Chloromuconate Cycloisomerase | | ||
| - | | //PDB Code// | 2CHR | | ||
| - | | //Crystallographic Resolution// | 3.00 Å | | ||
| - | | //Organism// | Cupriavidus necator | | ||
| - | | [[http://www.ncbi.nlm.nih.gov/pubmed/15299651?dopt=Abstract | [Kleywegt, 1996]]] || | ||
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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_dedcl_.png?120 |}} | | ||
| - | | OD2 | D1 | 15.9994 | ::: | | ||
| - | | OD2 | D2 | 15.9994 | ::: | | ||
| - | | OE2 | E1 | 15.9994 | ::: | | ||
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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-D1 | 86.71 | 2.0770 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-D2 | 72.61 | 2.0834 | ::: | | ||
| - | | M1-E1 | 75.79 | 2.0710 | ::: | | ||
| - | | M1-R1 | 69.25 | 2.4005 | ::: | | ||
| - | | D1-C | 656.0 | 1.25 | | ||
| - | | D2-C | 656.0 | 1.25 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
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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** | | ||
| - | | D1-M1-D2 | 18.812 | 124.2299 | [[#references | [Neves, 2013]]] | | ||
| - | | D1-M1-E1 | 35.39 | 100.9790 | ::: | | ||
| - | | D1-M1-R1 | 23.76 | 106.7074 | ::: | | ||
| - | | D2-M1-E1 | 38.51 | 102.8186 | ::: | | ||
| - | | D2-M1-R1 | 23.73 | 108.1030 | ::: | | ||
| - | | E1-M1-R1 | 19.27 | 113.6328 | ::: | | ||
| - | | M1-D1-C | 10.075 | 144.1664 | ::: | | ||
| - | | M1-D2-C | 45.967 | 141.6861 | ::: | | ||
| - | | M1-E1-C | 20.462 | 135.2443 | ::: | | ||
| - | | D1-C-CT | 70.0 | 117.0 | | ||
| - | | D1-C-O2 | 80.0 | 126.0 | | ||
| - | | D2-C-CT | 70.0 | 117.0 | | ||
| - | | D2-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]]] | | ||
| - | | D1 | 1.6612 | 0.21 | | ||
| - | | D2 | 1.6612 | 0.21 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
| - | | R1 | 1.948 | 0.265 | | ||
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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 | 3.08 | 2.08 | 2.10 ± 0.06 | [2.042; 2.161] | | ||
| - | | M1-D2 | 2.10 | 2.08 | 2.08 ± 0.07 | [2.016; 2.148] | | ||
| - | | M1-E1 | 2.05 | 2.07 | 2.07 ± 0.06 | [2.011; 2.137] | | ||
| - | | M1-R1 | 2.95 | 2.40 | 2.38 ± 0.07 | [2.316; 2.451] | | ||
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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)** | | ||
| - | | D1-M1-D2 | 173.5 | 124.2 | 138 ± 5 | [127.1; 148.5] | | ||
| - | | D1-M1-E1 | 80.0 | 101.0 | 107 ± 5 | [96.8; 116.8] | | ||
| - | | D1-M1-R1 | 87.2 | 106.7 | 80 ± 7 | [66.5; 93.4] | | ||
| - | | D2-M1-E1 | 99.4 | 102.8 | 105 ± 5 | [95.9; 114.8] | | ||
| - | | D2-M1-R1 | 87.1 | 108.1 | 79 ± 6 | [65.8; 91.4] | | ||
| - | | E1-M1-R1 | 112.9 | 113.6 | 85 ± 7 | [71.7; 98.4] | | ||
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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/ded_cl_example_page.1374846669.txt.gz · Last modified: 2013/07/26 14:51 by ruineves
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