mm:parameters:iron:cc_c_2
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mm:parameters:iron:cc_c_2 [2013/08/05 17:56] ruineves |
mm:parameters:iron:cc_c_2 [2013/10/03 18:59] (current) ruineves |
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| ====== Iron(III) - CC[C]2 ====== | ====== Iron(III) - CC[C]2 ====== | ||
| + | ### | ||
| + | Desulforedoxin is a mononuclear iron tetrahedral metal center coordinated with two directly linked cysteines and and two cysteines that are not linked. | ||
| + | ### | ||
| - | + | | **COORDINATION SPHERE** || | |
| - | + | | {{ :mm:parameters:iron:cc[c]2_non-parameterized.png?120|}} | \\ **Oxidation State:** Fe(III) \\ **Spin Multiplicity:** 6 | | |
| - | | **Coordination Sphere** | **Oxidation State:** Fe(III) \\ **Spin Multiplicity:** 1 | | + | |
| - | | {{ :mm:parameters:iron:cc[c]2_non-parameterized.png?200|}} | PATH TO 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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| | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | FE | FE | 55.845 | {{ :mm:parameters:iron:cc[c]2_parameterized.png?200|}} | | + | | FE | FE | 55.845 | {{ :mm:parameters:iron:cc[c]2_parameterized.png?120|}} | |
| | SG | SF | 32.065 | ::: | | | SG | SF | 32.065 | ::: | | ||
| | SG | SM | 32.065 | ::: | | | SG | SM | 32.065 | ::: | | ||
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| ==== Bond Parameters ==== | ==== Bond Parameters ==== | ||
| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | + | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>** | **l / Å** | **REFERENCE** | |
| | FE-SF | 84.30 | 2.3100 | [[#references | [Carvalho, 2013]]] | | | FE-SF | 84.30 | 2.3100 | [[#references | [Carvalho, 2013]]] | | ||
| | FE-SM | 74.1 | 2.3 | ::: | | | FE-SM | 74.1 | 2.3 | ::: | | ||
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| ==== Angle Parameters ==== | ==== Angle Parameters ==== | ||
| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | + | | **ANGLE** | **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>** | **θ / deg** | **REFERENCE** | |
| | SF-FE-SM | 58.4 | 110.0 | [[#references | [Carvalho, 2013]]] | | | SF-FE-SM | 58.4 | 110.0 | [[#references | [Carvalho, 2013]]] | | ||
| | FE-SF-CT | 68.5 | 102.0 | ::: | | | FE-SF-CT | 68.5 | 102.0 | ::: | | ||
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| ==== Van der Waals Parameters ==== | ==== Van der Waals Parameters ==== | ||
| - | | **ATOM TYPE** | **R<sub>i</sub> / angstrom** | **epsilon<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | + | | **ATOM TYPE** | **R<sub>i</sub> / Å** | **ε<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | |
| | FE | 2.6500 | 0.0450 | [[#references | [Giammona, 1984]]] | | | FE | 2.6500 | 0.0450 | [[#references | [Giammona, 1984]]] | | ||
| - | | SF | 2.0000 | 0.2500 | | + | | SF | 2.0000 | 0.2500 | [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]] | |
| - | | SM | 2.0000 | 0.2500 | | + | | SM | 2.0000 | 0.2500 | ::: | |
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| ===== Downloads ===== | ===== Downloads ===== | ||
| - | | //Parameter File// | {{PATH TO FRCMOD FILE| .frcmod}} | | + | | //Parameter File// | {{mm:parameters:iron:cc_c_2-frcmod.zip| .frcmod}} | |
| - | | //Coordination Sphere Charges// | {{PATH TO CHARGE FILES| .off}} | | + | | //Coordination Sphere Charges// | {{mm:parameters:iron:cc_c_2_fe-iii.zip| .off}} | |
| - | | //ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file// | {{PATH TO PDB AND LEAPRC FILES| .pdb, leaprc}} | | + | | //Desulforedoxin’s PDB File (1DXG.pdb)\ LEAPRC file// | {{mm:parameters:iron:desulforedoxin.zip| .pdb, leaprc}} | |
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| ===== References ===== | ===== References ===== | ||
| + | ### | ||
| A.T.P. Carvalho, A.F.S. Teixeira, MJ.Ramos. [[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23287/abstract;jsessionid=415EECAA000727C4BCBA82544438C428.d03t02 | Parameters for Molecular Dynamics Simulations of Iron-Sulfur Proteins]]. //J. Comput. Chem.//, **2013**, 34, 1540-1548 | A.T.P. Carvalho, A.F.S. Teixeira, MJ.Ramos. [[http://onlinelibrary.wiley.com/doi/10.1002/jcc.23287/abstract;jsessionid=415EECAA000727C4BCBA82544438C428.d03t02 | Parameters for Molecular Dynamics Simulations of Iron-Sulfur Proteins]]. //J. Comput. Chem.//, **2013**, 34, 1540-1548 | ||
| + | ### | ||
| + | ### | ||
| D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984** | D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984** | ||
| + | ### | ||
mm/parameters/iron/cc_c_2.1375721777.txt.gz · Last modified: 2013/08/05 17:56 by ruineves
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