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====== Manganese(II) - HHEWaWa ======

Homoprotocatechuate-2,3-deoxygenase is shown to have five ligands bonded to the iron(II) ion: a glutamate, two histidines and two waters in a square pyramidal geometry. The ligands in manganese(II) deoxygenases are likely to be the same.
Other studies show, however, that it might be hexacoordinated with three solvent molecules occupying ligand positions.


|  **Coordination Sphere**  |  **Oxidation State:** Mn(II)  \\  **Spin Multiplicity:** 5  |
|  {{ :mm:parameters:manganese:non-parameterized_hheww_.png?120 |}} | JMOL |


----



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


|  **TEST PROTEIN**  ||
|  //Protein//  |  Homoprotocatechuate 2,3-Dioxygenase  |
|  //PDB Code//  |  1F1U  |
|  //Crystallographic Resolution//  |  1.50 Å  |
|  //Organism//  |  Arthrobacter globiformis  |
|  [[http://jb.asm.org/content/186/7/1945.long | [Vetting, 2004]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_hheww_.png?120 |}}  |
|  OE1  |  E1  |  15.9994  | ::: |
|  NE2  |  NI  |  14.0067  | ::: |
|  NE2  |  NJ  |  14.0067  | ::: |
|  OW  |  W1  |  15.9994  | ::: |
|  OW  |  W2  |  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  |  81.53  |  2.1862  | [[#references | [Neves, 2013]]] |
|  M1-NJ  |  78.93  |  2.1763  | ::: |
|  M1-E1  |  90.87  |  2.0648  | ::: |
|  M1-W1  |  43.45  |  2.2506  | ::: |
|  M1-W2  |  45.59  |  2.2237  | ::: |
|  NI-CR  |  488.0  |  1.335  |
|  NI-CV  |  410.0  |  1.394  |
|  NJ-CR  |  488.0  |  1.335  |
|  NJ-CV  |  410.0  |  1.394  |
|  E1-C  |  656.0  |  1.25  |
|  W1-HM  |  553.0  |  0.9572  |
|  W2-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-NJ  |  35.670  |  106.2009  | [[#references | [Neves, 2013]]] |
|  NI-M1-E1  |  66.76  |  90.0029  | ::: |
|  NI-M1-W1  |  27.91  |  89.1764  | ::: |
|  NI-M1-W2  |  27.25  |  152.3584  | ::: |
|  NJ-M1-E1  |  58.53  |  100.4401  | ::: |
|  NJ-M1-W1  |  8.378  |  121.3184  | ::: |
|  NJ-M1-W2  |  30.649  |  101.1859  | ::: |
|  E1-M1-W1  |  8.825  |  136.6245  | ::: |
|  E1-M1-W2  |  64.45  |  88.6732  | ::: |
|  W1-M1-W2  |  41.88  |  73.2308  | ::: |
|  M1-NI-CR  |  46.273  |  126.3998  | ::: |
|  M1-NI-CV  |  46.273  |  126.3998  | ::: |
|  M1-NJ-CR  |  31.467  |  118.1041  | ::: |
|  M1-NJ-CV  |  31.467  |  118.1041  | ::: |
|  M1-E1-C  |  49.84  |  127.7223  | ::: |
|  M1-W1-HM  |  7.881  |  110.4316  | ::: |
|  M1-W2-HM  |  26.41  |  109.0419  | ::: |
|  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  |
|  E1-C-CT  |  70.0  |  117.0  |
|  E1-C-O2  |  80.0  |  126.0  |
|  HM-W1-HM  |  100.0  |  104.52  |
|  HM-W2-HM  |  100.0  |  104.52  |


==== 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  |
|  NJ  |  1.824  |  0.17  |
|  E1  |  1.6612  |  0.21  |
|  W1  |  1.7683  |  0.152  |
|  W2  |  1.7683  |  0.152  |
|  HM  |  0.6000  |  0.0157  |  [[http://pubs.acs.org/doi/abs/10.1021/ja00124a002 | [Cornell, 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  |  2.21  |  2.19  |  2.15 ± 0.06  |  [2.086; 2.205]  |
|  M1-NJ  |  2.03  |  2.18  |  2.15 ± 0.06  |  [2.086; 2.212]  |
|  M1-E1  |  2.11  |  2.06  |  2.08 ± 0.06  |  [2.017; 2.133]  |
|  M1-W1  |  2.38  |  2.25  |  2.18 ± 0.08  |  [2.098; 2.266]  |
|  M1-W2  |  2.18  |  2.22  |  2.17 ± 0.08  |  [2.095; 2.255]  |


==== 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-NJ  |  95.6  |  106.2  |  110 ± 4  |  [102.1; 117.0]  |
|  NI-M1-E1  |  86.7  |  90.0  |  94 ± 3  |  [86.9; 100.5]  |
|  NI-M1-W1  |  91.4  |  89.2  |  80 ± 4  |  [71.5; 89.3]  |
|  NI-M1-W2  |  151.4  |  152.4  |  152 ± 4  |  [143.9; 159.7]  |
|  NJ-M1-E1  |  97.3  |  100.4  |  102 ± 4  |  [93.6; 110.1]  |
|  NJ-M1-W1  |  93.4  |  121.3  |  122 ± 7  |  [108.5; 135.2]  |
|  NJ-M1-W2  |  109.2  |  101.2  |  97 ± 4  |  [88.6; 104.7]  |
|  E1-M1-W1  |  169.3  |  136.6  |  135 ± 7  |  [121.3; 148.7]  |
|  E1-M1-W2  |  103.5  |  88.7  |  89 ± 4  |  [82.0; 96.6]  |
|  W1-M1-W2  |  73.6  |  73.2  |  78 ± 4  |  [69.5; 86.8]  |



===== Downloads =====

|  //Parameter File//  |  {{:mm:parameters:manganese:hheww-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:hheww_mn-ii.zip| .off}}  |
|  //Homoprotocatechuate-2,3-dioxygenase’s PDB File (1F1U.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:homoprotocatechuate-2,3-dioxygenase.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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