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====== Manganese(II) - HDEWaWaWa ======



|  **Coordination Sphere**  |  **Oxidation State:** Mn(II)  \\  **Spin Multiplicity:** 6  |
|  IMAGE1 | 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//  |  Citochrome //c// Oxidase  |
|  //PDB Code//  |  3HB3  |
|  //Crystallographic Resolution//  |  2.25  |
|  //Organism//  |  Paracoccus denitrificans  |
|  [[LINK OF THE PAPER OF THE STRUCTURE | [Koepke, 2009]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  IMAGE  |
|  OD1  |  D1  |  15.9994  | ::: |
|  OE1  |  E1  |  15.9994  | ::: |
|  NE2  |  NI  |  14.0067  | ::: |
|  OW  |  W1  |  15.9994  | ::: |
|  OW  |  W2  |  15.9994  | ::: |
|  OW  |  W3  |  15.9994  | ::: |
|  HW  |  HM  |  1.00794  | ::: |


==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  M1-NI  |  63.17  |  2.242  | [[#references | [Neves, 2013]]] |
|  M1-D1  |  77.67  |  2.141  | ::: |
|  M1-E1  |  68.41  |  2.147  | ::: |
|  M1-W1  |  31.5  |  2.3664  | ::: |
|  M1-W2  |  31.4  |  2.325  | ::: |
|  M1-W3  |  64.37  |  2.1601  | ::: |
|  NI-CR  |  488.0  |  1.335  |
|  NI-CV  |  410.0  |  1.394  |
|  D1-C  |  656.0  |  1.25  |
|  E1-C  |  656.0  |  1.25  |
|  W1-HM  |  553.0  |  0.9572  |
|  W2-HM  |  553.0  |  0.9572  |
|  W3-HM  |  553.0  |  0.9572  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  NI-M1-D1  |  55.1  |  90.0153  | [[#references | [Neves, 2013]]] |
|  NI-M1-E1  |  41.458  |  159.9206  | ::: |
|  NI-M1-W1  |  24.19  |  94.3889  | ::: |
|  NI-M1-W2  |  31.3  |  89.0778  | ::: |
|  NI-M1-W3  |  34.86  |  98.8181  | ::: |
|  D1-M1-E1  |  50.26  |  103.9094  | ::: |
|  D1-M1-W1  |  42.6  |  73.0866  | ::: |
|  D1-M1-W2  |  12.075  |  162.4957  | ::: |
|  D1-M1-W3  |  56.22  |  90.7127  | ::: |
|  E1-M1-W1  |  37.25  |  76.4231  | ::: |
|  E1-M1-W2  |  54.4  |  73.2795  | ::: |
|  E1-M1-W3  |  37.25  |  95.45  | ::: |
|  W1-M1-W2  |  12.36  |  89.5541  | ::: |
|  W1-M1-W3  |  32.47  |  159.1053  | ::: |
|  W2-M1-W3  |  11.975  |  106.6994  | ::: |
|  M1-NI-CR  |  34.139  |  123.4259  | ::: |
|  M1-NI-CV  |  34.139  |  123.4259  | ::: |
|  M1-D1-C  |  46.237  |  123.2712  | ::: |
|  M1-E1-C  |  44.53  |  121.9953  | ::: |
|  M1-W1-HM  |  8.322  |  99.514  | ::: |
|  M1-W2-HM  |  9.174  |  99.3627  | ::: |
|  M1-W3-HM  |  33.538  |  97.246  | ::: |
|  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  |
|  HM-W1-HM  |  100.0  |  104.52  |
|  HM-W2-HM  |  100.0  |  104.52  |
|  HM-W3-HM  |  100.0  |  104.52  |
|  D1-C-CT  |  70.0  |  117.0  |
|  D1-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]]]  |
|  NI  |  1.824  |  0.17  |
|  D1  |  1.6612  |  0.21  |
|  E1  |  1.6612  |  0.21  |
|  W1  |  1.7683  |  0.152  |
|  W2  |  1.7683  |  0.152  |
|  W3  |  1.7683  |  0.152  |
|  HM  |  0.6000  |  0.0157  |  [[LINK | [Cornel, 1995]]]  |



===== 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-NI  |  1.98  |  2.24  |  2.17 ± 0.06  |  [2.111; 2.238]  |
|  M1-D1  |  2.17  |  2.14  |  2.18 ± 0.06  |  [2.117; 2.245]  |
|  M1-E1  |  2.19  |  2.15  |  2.18 ± 0.07  |  [2.112; 2.245]  |
|  M1-W1  |  2.20  |  2.37  |  2.3 ± 0.1  |  [2.189; 2.383]  |
|  M1-W2  |  2.14  |  2.33  |  2.3 ± 0.1  |  [2.170; 2.371]  |
|  M1-W3  |  2.11  |  2.16  |  2.14 ± 0.07  |  [2.070; 2.215]  |


==== 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)**  |
|  NI-M1-D1  |  74.7  |  90.0  |  84 ± 4  |  [76.5; 90.8]  |
|  NI-M1-E1  |  171.1  |  159.9  |  159 ± 3  |  [151.8; 165.4]  |
|  NI-M1-W1  |  87.0  |  94.4  |  88 ± 4  |  [81.0; 95.7]  |
|  NI-M1-W2  |  99.9  |  89.1  |  82 ± 4  |  [73.3; 90.8]  |
|  NI-M1-W3  |  98.0  |  98.8  |  96 ± 5  |  [86.6; 105.4]  |
|  D1-M1-E1  |  113.6  |  103.9  |  100 ± 4  |  [92.0; 107.2]  |
|  D1-M1-W1  |  72.3  |  73.1  |  76 ± 4  |  [68.2; 83.2]  |
|  D1-M1-W2  |  166.7  |  162.5  |  135 ± 6  |  [123.2; 146.7]  |
|  D1-M1-W3  |  86.4  |  90.7  |  84 ± 4  |  [76.2; 91.5]  |
|  E1-M1-W1  |  86.4  |  76.4  |  73 ± 4  |  [64.6; 81.0]  |
|  E1-M1-W2  |  71.3  |  73.3  |  81 ± 4  |  [73.5; 89.0]  |
|  E1-M1-W3  |  79.7  |  95.5  |  105 ± 5  |  [95.1; 114.4]  |
|  W1-M1-W2  |  120.1  |  89.6  |  62 ± 6  |  [50.6; 72.9]  |
|  W1-M1-W3  |  156.1  |  159.1  |  158 ± 4  |  [149.5; 166.0]  |
|  W2-M1-W3  |  82.2  |  106.7  |  139 ± 6  |  [127.5; 151.4]  |



===== 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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