====== Iron(III) - CCCC ======
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Rubredoxin is a mononuclear iron tetrahedral metal center coordinated with four cysteines that are not directly connected in the backbone of the protein.
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|  **COORDINATION SPHERE**  ||
|  {{ :mm:parameters:iron:cccc_non-parameterized.png?120|}} |  \\ **Oxidation State:** Fe(III)  \\  **Spin Multiplicity:** 6  |


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===== Structure chosen to parameterize =====


|  **TEST PROTEIN**  ||
|  //Protein//  |  Rubredoxin  |
|  //PDB Code//  |  1IRO  |
|  //Crystallographic Resolution//  |  1.10 Å  |
|  //Organism//  |  Clostridium pasteurianum  |
|  [[http://www.pnas.org/content/93/17/8836.long | [Dauter, 1996]]]  ||



===== Parameters Determined =====



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  FE  |  FE  |  55.845  |  {{ :mm:parameters:iron:cccc_parameterized.png?120|}}  |
|  SG  |  SF  |  32.065  | ::: |


==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  FE-SF  |  80.75  |  2.3170  | [[#references | [Carvalho, 2013]]] |
|  CT-SF  |  237.00  |  1.8100  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  SF-FE-SF  |  33.15  |  109.8650  | [[#references | [Carvalho, 2013]]] |
|  CT-SF-FE  |  27.60  |  100.9150  | ::: |
|  SF-CT-H1  |  50.00  |  109.5000  |
|  CT-CT-SF  |  50.00  |  108.6000  |


==== Van der Waals Parameters ====

|  **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]]]  |
|  SF  |  2.0000  |  0.2500  |  [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 1995]]]  |



===== Downloads =====

|  //Parameter File//  |  {{mm:parameters:iron:cccc-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{mm:parameters:iron:cccc_fe-iii.zip| .off}}  |
|  //Rubredoxin’s PDB File (1IRO.pdb)\ LEAPRC file//  |  {{mm:parameters:iron:rubredoxin.zip| .pdb, leaprc}}  |




===== 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**
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