mm:parameters:iron:cc_fe2_ss_fe2_cc
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| - | ====== Iron(III) - CC[FE2]SS[FE2]CC ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Fe(III) \\ **Spin Multiplicity:** 1 | | ||
| - | | PATH TO IMAGE1 | 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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| - | ---- | ||
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| - | ===== Structure chosen to parameterize ===== | ||
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| - | | **TEST PROTEIN** || | ||
| - | | //Protein// | [2Fe-2S] Ferrodoxin | | ||
| - | | //PDB Code// | 4FXC | | ||
| - | | //Crystallographic Resolution// | 2.50 Å | | ||
| - | | //Organism// | Spirulina platensis | | ||
| - | | [[http://jb.oxfordjournals.org/content/117/5/1017.long | [Fukuyama, 1995]]] || | ||
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| - | ===== Parameters Determined ===== | ||
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| - | ==== Atom Types ==== | ||
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| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | FE | FE | 55.845 | IMAGE | | ||
| - | | SG | SX | 32.065 | ::: | | ||
| - | | S | S | 32.065 | ::: | | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | ||
| - | | FE-S | 93.4 | 2.17 | [[#references | [Carvalho, 2013]]] | | ||
| - | | FE-SX | 82.6 | 2.23 | ::: | | ||
| - | | CT-SX | 237.00 | 1.8100 | | ||
| - | | SX-CT | 227.00 | 1.8100 | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | ||
| - | | S-FE-S | 17.3 | 102.84 | [[#references | [Carvalho, 2013]]] | | ||
| - | | SX-FE-S | 17.3 | 102.84 | ::: | | ||
| - | | FE-S-FE | 18.0 | 77.200 | ::: | | ||
| - | | SX-FE-SX | 65.5 | 108.44 | ::: | | ||
| - | | FE-SX-CT | 65.5 | 108.44 | ::: | | ||
| - | | HS-SX-FE | 65.5 | 108.44 | ::: | | ||
| - | | SX-CT-H1 | 50.00 | 109.5000 | | ||
| - | | SX-FE-SX | 33.15 | 109.8650 | ::: | | ||
| - | | CT-CT-SX | 50.00 | 108.6000 | | ||
| - | | CT-SX-CT | 62.00 | 98.9000 | | ||
| - | | CT-CT-SX | 50.00 | 114.7000 | | ||
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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** | | ||
| - | | FE | 2.6500 | 0.0450 | [[#references | [Giammona, 1984]]] | | ||
| - | | S | 2.0000 | 0.2500 | | ||
| - | | SX | 2.0000 | 0.2500 | | ||
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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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| - | 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 | ||
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| - | D. A. Giammona, //Ph.D. Thesis//; University of California: Davis, **1984** | ||
mm/parameters/iron/cc_fe2_ss_fe2_cc.1375699403.txt.gz · Last modified: 2013/08/05 11:43 by ruineves
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