mm:parameters:manganese:hhdh_ho_o_example_page
Differences
This shows you the differences between two versions of the page.
|
mm:parameters:manganese:hhdh_ho_o_example_page [2013/07/10 18:48] ruineves created |
— (current) | ||
|---|---|---|---|
| Line 1: | Line 1: | ||
| - | ====== Manganese(III) - HHDH[HO]O ====== | ||
| - | |||
| - | |||
| - | |||
| - | | **Coordination Sphere** | **Oxidation State:** Mn(III) \\ **Spin Multiplicity:** 4 | | ||
| - | | IMAGE1 | IMAGE2 ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | ||
| - | |||
| - | |||
| - | ---- | ||
| - | |||
| - | |||
| - | |||
| - | ===== Structure chosen to parameterize ===== | ||
| - | |||
| - | |||
| - | | **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]]] || | ||
| - | |||
| - | |||
| - | |||
| - | ===== Parameters Determined ===== | ||
| - | |||
| - | |||
| - | |||
| - | ==== Atom Types ==== | ||
| - | |||
| - | | **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 | ::: | | ||
| - | |||
| - | |||
| - | ==== Bond Parameters ==== | ||
| - | |||
| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | ||
| - | | M1-NI | 82.11 | 2.1879 | [[#references | [Neves, 2013]]] | | ||
| - | | M1-NJ | 123.46 | 2.0161 | ::: | | ||
| - | | M1-NK | 138.95 | 2.0175 | ::: | | ||
| - | | M1-D1 | 111.54 | 2.0630 | ::: | | ||
| - | | M1-R1 | 96.51 | 1.9361 | ::: | | ||
| - | | M1-W1 | 227.9 | 1.7993 | ::: | | ||
| - | | 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 | | ||
| - | | R1-O | 384.3 | 1.430 | | ||
| - | | W1-HM | 553.0 | 0.9572 | | ||
| - | |||
| - | |||
| - | ==== Angle Parameters ==== | ||
| - | |||
| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | ||
| - | | NI-M1-NJ | 93.41 | 91.0663 | [[#references | [Neves, 2013]]] | | ||
| - | | NI-M1-NK | 96.11 | 86.5034 | ::: | | ||
| - | | NI-M1-D1 | 118.5 | 82.0566 | ::: | | ||
| - | | NI-M1-W1 | 77.66 | 176.5931 | ::: | | ||
| - | | NI-M1-R1 | 83.7 | 84.2181 | ::: | | ||
| - | | NJ-M1-NK | 97.22 | 172.0561 | ::: | | ||
| - | | NJ-M1-D1 | 74.40 | 93.5533 | ::: | | ||
| - | | NJ-M1-W1 | 96.31 | 90.3808 | ::: | | ||
| - | | NJ-M1-R1 | 95.80 | 86.9561 | ::: | | ||
| - | | NK-M1-D1 | 75.579 | 93.5990 | ::: | | ||
| - | | NK-M1-W1 | 92.14 | 92.4642 | ::: | | ||
| - | | NK-M1-R1 | 99.09 | 85.2759 | ::: | | ||
| - | | D1-M1-W1 | 83.35 | 94.7758 | ::: | | ||
| - | | D1-M1-R1 | 70.04 | 166.2720 | ::: | | ||
| - | | W1-M1-R1 | 61.59 | 98.9401 | ::: | | ||
| - | | 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 | 36.67 | 106.2284 | ::: | | ||
| - | | M1-R1-O | 41.32 | 118.4913 | ::: | | ||
| - | | 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 | | ||
| - | |||
| - | |||
| - | ==== Van der Waals Parameters ==== | ||
| - | |||
| - | | **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 | | ||
| - | | NK | 1.824 | 0.17 | | ||
| - | | D1 | 1.6612 | 0.21 | | ||
| - | | R1 | 1.6612 | 0.2100 | | ||
| - | | O | 1.6612 | 0.2100 | | ||
| - | | W1 | 1.7210 | 0.2104 | | ||
| - | | HM | 0.6000 | 0.0157 | [[LINK | [Cornel, 1995]]] | | ||
| - | |||
| - | |||
| - | |||
| - | ===== Validation of Parameters from MD Simulations ===== | ||
| - | |||
| - | |||
| - | ==== Bond Parameters ==== | ||
| - | |||
| - | | **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 | 1.80 | 2.06 | 2.09 ± 0.05 | [2.038; 2.142] | | ||
| - | | M1-NI | 2.15 | 2.19 | 2.20 ± 0.06 | [2.141; 2.254] | | ||
| - | | M1-NJ | 2.12 | 2.02 | 2.02 ± 0.05 | [1.969; 2.063] | | ||
| - | | M1-NK | 2.16 | 2.02 | 2.05 ± 0.05 | [2.003; 2.094] | | ||
| - | | M1-W1 | 2.07 | 1.80 | 1.79 ± 0.04 | [1.752; 1.825] | | ||
| - | | M1-R1 | 2.68 | 1.94 | 1.93 ± 0.06 | [1.872; 1.984] | | ||
| - | |||
| - | |||
| - | ==== Angle Parameters ==== | ||
| - | |||
| - | | **ANGLE** | **theta<sub>0 crystal</sub>** | **theta<sub>0 QM</sub>** | **<theta><sub>MD</sub> ± sigma(theta)** | **<θ><sub>MD</sub> ± 2sigma(theta)** | | ||
| - | | NI-M1-NJ | 92.4 | 91.1 | 92 ± 2 | [86.9; 96.6] | | ||
| - | | NI-M1-NK | 90.3 | 86.5 | 89 ± 2 | [84.3; 93.7] | | ||
| - | | NI-M1-D1 | 89.1 | 82.1 | 82 ± 2 | [77.6; 87.0] | | ||
| - | | NI-M1-W1 | 175.5 | 176.6 | 176 ± 2 | [172.3; 179.7] | | ||
| - | | NI-M1-R1 | 97.6 | 84.2 | 86 ± 2 | [80.8; 90.8] | | ||
| - | | NJ-M1-NK | 130.8 | 172.1 | 170 ± 2 | [165.7; 174.9] | | ||
| - | | NJ-M1-D1 | 110.1 | 93.6 | 93 ± 3 | [87.0; 98.6] | | ||
| - | | NJ-M1-W1 | 90.0 | 90.4 | 87 ± 2 | [82.6; 92.4] | | ||
| - | | NJ-M1-R1 | 66.4 | 87.0 | 85 ± 3 | [80.4; 90.5] | | ||
| - | | NK-M1-D1 | 119.2 | 93.6 | 97 ± 3 | [90.9; 102.1] | | ||
| - | | NK-M1-W1 | 91.0 | 92.5 | 92 ± 3 | [86.9; 97.1] | | ||
| - | | NK-M1-R1 | 64.6 | 85.3 | 85 ± 2 | [80.5; 90.2] | | ||
| - | | D1-M1-W1 | 86.5 | 94.8 | 96 ± 3 | [90.5; 101.8] | | ||
| - | | D1-M1-R1 | 172.4 | 166.3 | 167 ± 3 | [162.3; 172.5] | | ||
| - | | W1-M1-R1 | 86.8 | 98.9 | 96 ± 3 | [90.1; 101.3] | | ||
| - | |||
| - | |||
| - | |||
| - | ===== Downloads ===== | ||
| - | |||
| - | | //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}} | | ||
| - | |||
| - | |||
| - | |||
| - | |||
| - | ===== References ===== | ||
| - | |||
| - | 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_o_example_page.1373478481.txt.gz · Last modified: 2013/07/10 18:48 by ruineves
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 3.0 Unported
