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====== Manganese(II) - DED[CL] ======



|  **Coordination Sphere**  |  **Oxidation State:** Mn(II)  \\  **Spin Multiplicity:** 6  |
|  {{ :mm:parameters:manganese:non-parameterized_dedcl_.png?200 |}} | {{ :mm:parameters:manganese:tetrahedral_highspin_d5.png?400 |}}  ((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//  |  Chloromuconate Cycloisomerase  |
|  //PDB Code//  |  2CHR  |
|  //Crystallographic Resolution//  |  3.00 Å  |
|  //Organism//  |  Cupriavidus necator  |
|  [[http://www.ncbi.nlm.nih.gov/pubmed/15299651?dopt=Abstract | [Kleywegt, 1996]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_dedcl_.png?120 |}}  |
|  OD2  |  D1  |  15.9994  | ::: |
|  OD2  |  D2  |  15.9994  | ::: |
|  OE2  |  E1  |  15.9994  | ::: |


==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  M1-D1  |  86.71  |  2.0770  | [[#references | [Neves, 2013]]] |
|  M1-D2  |  72.61  |  2.0834  | ::: |
|  M1-E1  |  75.79  |  2.0710  | ::: |
|  M1-R1  |  69.25  |  2.4005  | ::: |
|  D1-C  |  656.0  |  1.25  |
|  D2-C  |  656.0  |  1.25  |
|  E1-C  |  656.0  |  1.25  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  D1-M1-D2  |  18.812  |  124.2299  | [[#references | [Neves, 2013]]] |
|  D1-M1-E1  |  35.39  |  100.9790  | ::: |
|  D1-M1-R1  |  23.76  |  106.7074  | ::: |
|  D2-M1-E1  |  38.51  |  102.8186  | ::: |
|  D2-M1-R1  |  23.73  |  108.1030  | ::: |
|  E1-M1-R1  |  19.27  |  113.6328  | ::: |
|  M1-D1-C  |  10.075  |  144.1664  | ::: |
|  M1-D2-C  |  45.967  |  141.6861  | ::: |
|  M1-E1-C  |  20.462  |  135.2443  | ::: |
|  D1-C-CT  |  70.0  |  117.0  |
|  D1-C-O2  |  80.0  |  126.0  |
|  D2-C-CT  |  70.0  |  117.0  |
|  D2-C-O2  |  80.0  |  126.0  |
|  E1-C-CT  |  70.0  |  117.0  |
|  E1-C-O2  |  80.0  |  126.0  |


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

|  **ATOM TYPE**  |  **R<sub>i</sub> / Å**  |  **ε<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]]]  |
|  D1  |  1.6612  |  0.21  |
|  D2  |  1.6612  |  0.21  |
|  E1  |  1.6612  |  0.21  |
|  R1  |  1.948  |  0.265  |



===== Validation of Parameters from MD Simulations =====


==== Bond Parameters ====

|  **BOND**  |  **l<sub>0 crystal</sub>**  |  **l<sub>0 opt</sub>**  |  **‹l›<sub>MD</sub> ± σ(l)**  |  **‹l›<sub>MD</sub> ± 2σ(l)**   |
|  M1-D1  |  3.08  |  2.08  |  2.10 ± 0.06  |  [2.042; 2.161]  |
|  M1-D2  |  2.10  |  2.08  |  2.08 ± 0.07  |  [2.016; 2.148]  |
|  M1-E1  |  2.05  |  2.07  |  2.07 ± 0.06  |  [2.011; 2.137]  |
|  M1-R1  |  2.95  |  2.40  |  2.38 ± 0.07  |  [2.316; 2.451]  |


==== Angle Parameters ====

|  **ANGLE**  |  **θ<sub>0 crystal</sub>**  |  **θ<sub>0 QM</sub>**  |  **‹θ›<sub>MD</sub> ± σ(θ)**  |  **‹θ›<sub>MD</sub> ± 2σ(θ)**  |
|  D1-M1-D2  |  173.5  |  124.2  |  138 ± 5  |  [127.1; 148.5]  |
|  D1-M1-E1  |  80.0  |  101.0  |  107 ± 5  |  [96.8; 116.8]  |
|  D1-M1-R1  |  87.2  |  106.7  |  80 ± 7  |  [66.5; 93.4]  |
|  D2-M1-E1  |  99.4  |  102.8  |  105 ± 5  |  [95.9; 114.8]  |
|  D2-M1-R1  |  87.1  |  108.1  |  79 ± 6  |  [65.8; 91.4]  |
|  E1-M1-R1  |  112.9  |  113.6  |  85 ± 7  |  [71.7; 98.4]  |



===== Downloads =====
|  //Parameter File//  |  {{:mm:parameters:manganese:ded_cl-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:ded[cl]_mn-ii.zip| .off}}  |
|  //Integrase’s PDB File (2CHR.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:chloromuconate_cycloisomerase.zip| .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
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