mm:parameters:manganese:hhe_d2_example_page
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| - | ====== Manganese(II) - HHE[D2] ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Mn(II) \\ **Spin Multiplicity:** 6 | | ||
| - | | 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// | PROTEIN NAME | | ||
| - | | //PDB Code// | PDB CODE | | ||
| - | | //Crystallographic Resolution// | RESOLUTION | | ||
| - | | //Organism// | ORGANISM | | ||
| - | | [[LINK OF THE PAPER OF THE STRUCTURE | [1ST AUTHOR, PUBL YEAR]]] || | ||
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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 | | ||
| - | | OE1 | E1 | 15.9994 | ::: | | ||
| - | | NE2 | NI | 14.0067 | ::: | | ||
| - | | NE2 | NJ | 14.0067 | ::: | | ||
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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 | 70.46 | 2.1984 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-NJ | 74.91 | 2.1938 | ::: | | ||
| - | | M1-D1 | 19.70 | 2.3425 | ::: | | ||
| - | | M1-D2 | 44.64 | 2.1299 | ::: | | ||
| - | | M1-E1 | 88.82 | 2.0723 | ::: | | ||
| - | | NI-CR | 488.0 | 1.335 | | ||
| - | | NI-CV | 410.0 | 1.394 | | ||
| - | | NJ-CR | 488.0 | 1.335 | | ||
| - | | NJ-CV | 410.0 | 1.394 | | ||
| - | | D1-C | 656.0 | 1.25 | | ||
| - | | D2-C | 656.0 | 1.25 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
| - | | D1-C | D2 | 80.0 | | ||
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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 | 34.37 | 107.8506 | [[#references | [Neves, 2013]]] | | ||
| - | | NI-M1-D1 | 18.529 | 105.7841 | ::: | | ||
| - | | NI-M1-D2 | 17.70 | 103.3854 | ::: | | ||
| - | | NI-M1-E1 | 30.53 | 99.0461 | ::: | | ||
| - | | NJ-M1-D1 | 56.3 | 86.6415 | ::: | | ||
| - | | NJ-M1-D2 | 26.03 | 138.8515 | ::: | | ||
| - | | NJ-M1-E1 | 41.44 | 94.4727 | ::: | | ||
| - | | D1-M1-D2 | 269.0 | 59.1658 | ::: | | ||
| - | | D1-M1-E1 | 15.58 | 153.5286 | ::: | | ||
| - | | D2-M1-E1 | 32.59 | 106.4565 | ::: | | ||
| - | | M1-NI-CR | 38.80 | 124.8643 | ::: | | ||
| - | | M1-NI-CV | 38.80 | 124.8643 | ::: | | ||
| - | | M1-NJ-CR | 44.269 | 126.5684 | ::: | | ||
| - | | M1-NJ-CV | 44.269 | 126.5684 | ::: | | ||
| - | | M1-D1-C | 52.84 | 89.6886 | ::: | | ||
| - | | M1-D2-C | 52.84 | 89.6886 | ::: | | ||
| - | | M1-E1-C | 22.930 | 129.8278 | ::: | | ||
| - | | 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 | | ||
| - | | 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> / angstrom** | **epsilon<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 | | ||
| - | | D1 | 1.6612 | 0.21 | | ||
| - | | D2 | 1.6612 | 0.21 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
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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> ± sigma(l)** | **<l><sub>MD</sub> ± 2sigma(l)** | | ||
| - | | M1-NI | 2.00 | 2.20 | 2.12 ± 0.07 | [2.059; 2.190] | | ||
| - | | M1-NJ | 2.01 | 2.19 | 2.17 ± 0.06 | [2.105; 2.229] | | ||
| - | | M1-D1 | 2.03 | 2.34 | 2.24 ± 0.08 | [2.160; 2.317] | | ||
| - | | M1-D2 | 2.84 | 2.13 | 2.19 ± 0.06 | [2.128; 2.255] | | ||
| - | | M1-E1 | 2.05 | 2.07 | 2.09 ± 0.06 | [2.028; 2.148] | | ||
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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 | 106.9 | 107.9 | 105 ± 5 | [95.1; 114.6] | | ||
| - | | NI-M1-D1 | 109.9 | 105.8 | 102 ± 6 | [90.7; 113.6] | | ||
| - | | NI-M1-D2 | 101.1 | 103.4 | 92 ± 5 | [81.6; 103.0] | | ||
| - | | NI-M1-E1 | 122.5 | 99.0 | 95 ± 5 | [85.2; 105.3] | | ||
| - | | NJ-M1-D1 | 82.8 | 86.6 | 85 ± 3 | [78.8; 90.3] | | ||
| - | | NJ-M1-D2 | 131.3 | 138.9 | 142 ± 3 | [135.5; 147.8] | | ||
| - | | NJ-M1-E1 | 103.8 | 94.5 | 98 ± 4 | [89.8; 106.4] | | ||
| - | | D1-M1-D2 | 50.1 | 59.2 | 59 ± 1 | [56.0; 61.8] | | ||
| - | | D1-M1-E1 | 121.3 | 153.5 | 160 ± 6 | [148.6; 172.0] | | ||
| - | | D2-M1-E1 | 93.1 | 106.5 | 114 ± 5 | [104.3; 122.8] | | ||
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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/hhe_d2_example_page.1373479618.txt.gz · Last modified: 2013/07/10 19:06 by ruineves
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