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====== Manganese(II) - HHE[D2] ======



|  **Coordination Sphere**  |  **Oxidation State:** Mn(II)  \\  **Spin Multiplicity:** 6  |
|  {{ :mm:parameters:manganese:non-parameterized_hhed2_.png?200 |}} | 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//  |  Pneumococcal Surface Antigen Adhesin A  |
|  //PDB Code//  |  1PSZ  |
|  //Crystallographic Resolution//  |  2.00 Å  |
|  //Organism//  |  Streptococcus pneumoniae  |
|  [[http://www.cell.com/structure/abstract/S0969-2126(98)00153-1 | [Lawrence, 1998]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_hhed2_.png?120 |}}  |
|  OE1  |  E1  |  15.9994  | ::: |
|  NE2  |  NI  |  14.0067  | ::: |
|  NE2  |  NJ  |  14.0067  | ::: |


==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  M1-NI  |  70.46  |  2.1984  | [[#references | [Neves, 2013]]] |
|  M1-NJ  |  74.91  |  2.1938  | ::: |
|  M1-D1  |  19.70  |  2.3425  | ::: |
|  M1-D2  |  44.64  |  2.1299  | ::: |
|  M1-E1  |  88.82  |  2.0723  | ::: |
|  NI-CR  |  488.0  |  1.335  |
|  NI-CV  |  410.0  |  1.394  |
|  NJ-CR  |  488.0  |  1.335  |
|  NJ-CV  |  410.0  |  1.394  |
|  D1-C  |  656.0  |  1.25  |
|  D2-C  |  656.0  |  1.25  |
|  E1-C  |  656.0  |  1.25  |
|  D1-C  |  D2  |  80.0  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>?</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **? / deg**  |  **REFERENCE**  |
|  NI-M1-NJ  |  34.37  |  107.8506  | [[#references | [Neves, 2013]]] |
|  NI-M1-D1  |  18.529  |  105.7841  | ::: |
|  NI-M1-D2  |  17.70  |  103.3854  | ::: |
|  NI-M1-E1  |  30.53  |  99.0461  | ::: |
|  NJ-M1-D1  |  56.3  |  86.6415  | ::: |
|  NJ-M1-D2  |  26.03  |  138.8515  | ::: |
|  NJ-M1-E1  |  41.44  |  94.4727  | ::: |
|  D1-M1-D2  |  269.0  |  59.1658  | ::: |
|  D1-M1-E1  |  15.58  |  153.5286  | ::: |
|  D2-M1-E1  |  32.59  |  106.4565  | ::: |
|  M1-NI-CR  |  38.80  |  124.8643  | ::: |
|  M1-NI-CV  |  38.80  |  124.8643  | ::: |
|  M1-NJ-CR  |  44.269  |  126.5684  | ::: |
|  M1-NJ-CV  |  44.269  |  126.5684  | ::: |
|  M1-D1-C  |  52.84  |  89.6886  | ::: |
|  M1-D2-C  |  52.84  |  89.6886  | ::: |
|  M1-E1-C  |  22.930  |  129.8278  | ::: |
|  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  |
|  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**  |  **?<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  |
|  D1  |  1.6612  |  0.21  |
|  D2  |  1.6612  |  0.21  |
|  E1  |  1.6612  |  0.21  |



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


==== Bond Parameters ====

|  **BOND**  |  **l<sub>0 crystal</sub>**  |  **l<sub>0 opt</sub>**  |  **‹l›<sub>MD</sub> ± ?(l)**  |  **‹l›<sub>MD</sub> ± 2?(l)**   |
|  M1-NI  |  2.00  |  2.20  |  2.12 ± 0.07  |  [2.059; 2.190]  |
|  M1-NJ  |  2.01  |  2.19  |  2.17 ± 0.06  |  [2.105; 2.229]  |
|  M1-D1  |  2.03  |  2.34  |  2.24 ± 0.08  |  [2.160; 2.317]  |
|  M1-D2  |  2.84  |  2.13  |  2.19 ± 0.06  |  [2.128; 2.255]  |
|  M1-E1  |  2.05  |  2.07  |  2.09 ± 0.06  |  [2.028; 2.148]  |


==== Angle Parameters ====

|  **ANGLE**  |  **?<sub>0 crystal</sub>**  |  **?<sub>0 QM</sub>**  |  **‹?›<sub>MD</sub> ± ?(?)**  |  **‹?›<sub>MD</sub> ± 2?(?)**  |
|  NI-M1-NJ  |  106.9  |  107.9  |  105 ± 5  |  [95.1; 114.6]  |
|  NI-M1-D1  |  109.9  |  105.8  |  102 ± 6  |  [90.7; 113.6]  |
|  NI-M1-D2  |  101.1  |  103.4  |  92 ± 5  |  [81.6; 103.0]  |
|  NI-M1-E1  |  122.5  |  99.0  |  95 ± 5  |  [85.2; 105.3]  |
|  NJ-M1-D1  |  82.8  |  86.6  |  85 ± 3  |  [78.8; 90.3]  |
|  NJ-M1-D2  |  131.3  |  138.9  |  142 ± 3  |  [135.5; 147.8]  |
|  NJ-M1-E1  |  103.8  |  94.5  |  98 ± 4  |  [89.8; 106.4]  |
|  D1-M1-D2  |  50.1  |  59.2  |  59 ± 1  |  [56.0; 61.8]  |
|  D1-M1-E1  |  121.3  |  153.5  |  160 ± 6  |  [148.6; 172.0]  |
|  D2-M1-E1  |  93.1  |  106.5  |  114 ± 5  |  [104.3; 122.8]  |



===== 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
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