mm:parameters:manganese:denwawawa_example_page
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| - | ====== Manganese(II) - DENWaWaWa ====== | ||
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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 | | ||
| - | | OD2 | D1 | 15.9994 | ::: | | ||
| - | | OE2 | E1 | 15.9994 | ::: | | ||
| - | | OD1 | NW | 15.9994 | ::: | | ||
| - | | OW | W1 | 15.9994 | ::: | | ||
| - | | OW | W2 | 15.9994 | ::: | | ||
| - | | OW | W3 | 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>** | **l / angstrom** | **REFERENCE** | | ||
| - | | M1-NW | 35.45 | 2.2737 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-D1 | 67.93 | 2.1478 | ::: | | ||
| - | | M1-E1 | 92.09 | 2.0644 | ::: | | ||
| - | | M1-W1 | 50.25 | 2.2190 | ::: | | ||
| - | | M1-W2 | 33.63 | 2.3313 | ::: | | ||
| - | | M1-W3 | 41.73 | 2.2662 | ::: | | ||
| - | | NW-C | 570.0 | 1.229 | | ||
| - | | D1-C | 656.0 | 1.25 | | ||
| - | | E1-C | 656.0 | 1.25 | | ||
| - | | W1-HM | 553.0 | 0.9572 | | ||
| - | | W2-HM | 553.0 | 0.9572 | | ||
| - | | W3-HM | 553.0 | 0.9572 | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | ||
| - | | NW-M1-D1 | 50.31 | 168.8916 | [[#references | [Neves, 2013]]] | | ||
| - | | NW-M1-E1 | 36.14 | 92.7969 | ::: | | ||
| - | | NW-M1-W1 | 38.04 | 100.6537 | ::: | | ||
| - | | NW-M1-W2 | 30.57 | 95.9566 | ::: | | ||
| - | | NW-M1-W3 | 33.91 | 78.7883 | ::: | | ||
| - | | D1-M1-E1 | 35.463 | 100.5525 | ::: | | ||
| - | | D1-M1-W1 | 64.49 | 85.2832 | ::: | | ||
| - | | D1-M1-W2 | 48.3 | 73.9644 | ::: | | ||
| - | | D1-M1-W3 | 32.46 | 94.4909 | ::: | | ||
| - | | E1-M1-W1 | 27.16 | 94.9567 | ::: | | ||
| - | | E1-M1-W2 | 16.85 | 166.1705 | ::: | | ||
| - | | E1-M1-W3 | 44.90 | 89.8914 | ::: | | ||
| - | | W1-M1-W2 | 13.16 | 97.1854 | ::: | | ||
| - | | W1-M1-W3 | 26.160 | 175.1204 | ::: | | ||
| - | | W2-M1-W3 | 23.22 | 78.0892 | ::: | | ||
| - | | M1-NW-C | 10.785 | 144.0557 | ::: | | ||
| - | | M1-D1-C | 47.557 | 125.7501 | ::: | | ||
| - | | M1-E1-C | 36.476 | 122.3574 | ::: | | ||
| - | | M1-W1-HM | 24.67 | 106.0283 | ::: | | ||
| - | | M1-W2-HM | 9.470 | 89.9559 | ::: | | ||
| - | | M1-W3-HM | 23.78 | 97.5290 | ::: | | ||
| - | | HM-W1-HM | 100.0 | 104.52 | | ||
| - | | HM-W2-HM | 100.0 | 104.52 | | ||
| - | | HM-W3-HM | 100.0 | 104.52 | | ||
| - | | NW-C-CT | 80.0 | 120.40 | | ||
| - | | NW-C-N | 80.0 | 122.90 | | ||
| - | | 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 | | ||
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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]]] | | ||
| - | | NW | 1.6612 | 0.21 | | ||
| - | | D1 | 1.6612 | 0.21 | | ||
| - | | E1 | 1.6612 | 0.21 | | ||
| - | | W1 | 1.7683 | 0.152 | | ||
| - | | W2 | 1.7683 | 0.152 | | ||
| - | | W3 | 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> ± sigma(l)** | **<l><sub>MD</sub> ± 2sigma(l)** | | ||
| - | | M1-D1 | 2.28 | 2.15 | 2.16 ± 0.06 | [2.095; 2.224] | | ||
| - | | M1-E1 | 2.45 | 2.06 | 2.13 ± 0.06 | [2.066; 2.186] | | ||
| - | | M1-NW | 2.40 | 2.27 | 2.29 ± 0.09 | [2.195; 2.383] | | ||
| - | | M1-W1 | 2.26 | 2.22 | 2.21 ± 0.08 | [2.127; 2.290] | | ||
| - | | M1-W2 | 2.51 | 2.33 | 2.3 ± 0.1 | [2.222; 2.416] | | ||
| - | | M1-W3 | 2.47 | 2.27 | 2.25 ± 0.09 | [2.165; 2.341] | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **ANGLE** | **theta<sub>0 crystal</sub>** | **theta<sub>0 QM</sub>** | **<theta><sub>MD</sub> ± sigma(theta)** | **<θ><sub>MD</sub> ± 2sigma(theta)** | | ||
| - | | D1-M1-E1 | 100.8 | 100.6 | 98 ± 4 | [89.3; 106.1] | | ||
| - | | D1-M1-NW | 154.1 | 168.9 | 165 ± 3 | [158.6; 172.1] | | ||
| - | | D1-M1-W1 | 84.5 | 85.3 | 85 ± 4 | [78.1; 92.1] | | ||
| - | | D1-M1-W2 | 93.4 | 73.9 | 70 ± 4 | [61.8; 77.6] | | ||
| - | | D1-M1-W3 | 80.9 | 94.5 | 91 ± 4 | [82.4; 100.0] | | ||
| - | | E1-M1-NW | 66.7 | 88.4 | 94 ± 4 | [85.9; 102.0] | | ||
| - | | E1-M1-W1 | 113.1 | 94.9 | 96 ± 5 | [86.4; 104.6] | | ||
| - | | E1-M1-W2 | 160.1 | 166.2 | 157 ± 5 | [148.0; 166.1] | | ||
| - | | E1-M1-W3 | 95.6 | 89.9 | 88 ± 5 | [78.7; 97.4] | | ||
| - | | NW-M1-W1 | 95.7 | 100.7 | 101 ± 4 | [92.7; 109.3] | | ||
| - | | NW-M1-W2 | 86.6 | 95.9 | 97 ± 4 | [88.2; 105.4] | | ||
| - | | NW-M1-W3 | 98.7 | 78.8 | 82 ± 4 | [73.2; 90.6] | | ||
| - | | W1-M1-W2 | 107.8 | 97.2 | 101 ± 5 | [91.3; 111.6] | | ||
| - | | W1-M1-W3 | 149.8 | 175.1 | 172 ± 4 | [164.7; 179.6] | | ||
| - | | W2-M1-W3 | 69.2 | 78.1 | 74 ± 6 | [62.6; 85.8] | | ||
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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/denwawawa_example_page.1373478303.txt.gz · Last modified: 2013/07/10 18:45 by ruineves
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