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====== Manganese(III) - HHDH[HO] ======
###
The coordination sphere of Manganese Superoxide Dismutase is located in a hydrophobic pocket formed by two subunits. In the resting state the manganese coordination geometry presents distorted trigonal bipyramidal geometry with two histidine and an aspartate equatorial ligands and a histidine and water/hydroxide in axial positions.
###
|  **COORDINATION SPHERE**  ||
|  {{ :mm:parameters:manganese:non-parameterized_hhdhho_.png?120 |}} |  \\ **Oxidation State:** Mn(III)  \\  **Spin Multiplicity:** 5  |


----



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


|  **TEST PROTEIN**  ||
|  //Protein//  |  Manganese Superoxide Dismutase  |
|  //PDB Code//  |  1N0J  |
|  //Crystallographic Resolution//  |  2.20 Å  |
|  //Organism//  |  Homo sapiens  |
|  [[http://www.sciencedirect.com/science/article/pii/009286749290270M | [Borgstahl, 1992]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_hhdhho_.png?120 |}}  |
|  OD1  |  D1  |  15.9994  | ::: |
|  NE2  |  NI  |  14.0067  | ::: |
|  NE2  |  NJ  |  14.0067  | ::: |
|  NE2  |  NK  |  14.0067  | ::: |
|  OW  |  W1  |  15.9994  | ::: |
|  HO  |  HM  |  1.00794  | ::: |


==== Bond Parameters ====

|  **BOND**  |  **K<sub>l</sub>** / **kcal mol<sup>-1</sup> Å<sup>-2</sup>**  |  **l / Å**  |  **REFERENCE**  |
|  M1-NI  |  106.65  |  2.1265  | [[#references | [Neves, 2013]]] |
|  M1-NJ  |  95.00  |  2.1147  | ::: |
|  M1-NK  |  81.69  |  2.1238  | ::: |
|  M1-D1  |  129.13  |  1.9569  | ::: |
|  M1-W1  |  247.2  |  1.7776  | ::: |
|  NI-CR  |  488.0  |  1.335  |
|  NI-CV  |  410.0  |  1.394  |
|  NJ-CR  |  488.0  |  1.335  |
|  NJ-CV  |  410.0  |  1.394  |
|  NK-CR  |  488.0  |  1.335  |
|  NK-CV  |  410.0  |  1.394  |
|  D1-C  |  656.0  |  1.25  |
|  W1-HM  |  553.0  |  0.9572  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>?</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  NI-M1-NJ  |  88.01  |  91.6707  | [[#references | [Neves, 2013]]] |
|  NI-M1-NK  |  86.76  |  88.725  | ::: |
|  NI-M1-D1  |  131.4  |  82.9759  | ::: |
|  NI-M1-W1  |  75.8  |  176.7937  | ::: |
|  NJ-M1-NK  |  30.68  |  136.3174  | ::: |
|  NJ-M1-D1  |  23.09  |  110.6038  | ::: |
|  NJ-M1-W1  |  89.71  |  91.1769  | ::: |
|  NK-M1-D1  |  20.64  |  112.8695  | ::: |
|  NK-M1-W1  |  89.03  |  90.3375  | ::: |
|  D1-M1-W1  |  100.0  |  94.5712  | ::: |
|  M1-NI-CR  |  53.671  |  126.4370  | ::: |
|  M1-NI-CV  |  53.671  |  126.4370  | ::: |
|  M1-NJ-CR  |  40.495  |  123.3813  | ::: |
|  M1-NJ-CV  |  40.495  |  123.3813  | ::: |
|  M1-NK-CR  |  31.220  |  112.3780  | ::: |
|  M1-NK-CV  |  31.220  |  112.3780  | ::: |
|  M1-D1-C  |  47.094  |  135.5495  | ::: |
|  M1-W1-HM  |  18.57  |  116.025  | ::: |
|  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  |
|  NK-CR-NA  |  70.0  |  120.0  |
|  NK-CR-H5  |  50.0  |  120.0  |
|  NK-CV-CC  |  70.0  |  120.0  |
|  CV-NK-CR  |  70.0  |  117.0  |
|  H4-CV-NK  |  50.0  |  120.0  |
|  D1-C-CT  |  70.0  |  117.0  |
|  D1-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  |
|  NJ  |  1.824  |  0.17  |
|  NK  |  1.824  |  0.17  |
|  D1  |  1.6612  |  0.21  |
|  W1  |  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-D1  |  1.94  |  1.96  |  1.92 ± 0.05  |  [1.875; 1.970]  |
|  M1-NI  |  2.10  |  2.13  |  2.13 ± 0.05  |  [2.075; 2.175]  |
|  M1-NJ  |  2.08  |  2.12  |  2.11 ± 0.06  |  [2.053; 2.163]  |
|  N1-NK  |  2.09  |  2.12  |  2.14 ± 0.06  |  [2.080; 2.197]  |
|  M1-W1  |  2.02  |  1.78  |  1.76 ± 0.04  |  [1.722; 1.792]  |


==== 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  |  96.8  |  91.7  |  91 ± 3  |  [86.1; 96.7]  |
|  NI-M1-NK  |  91.5  |  88.7  |  91 ± 3  |  [85.8; 96.0]  |
|  NI-M1-D1  |  82.4  |  83.0  |  83 ± 2  |  [79.0; 87.6]  |
|  NI-M1-W1  |  166.1  |  176.8  |  174 ± 2  |  [169.9; 179.1]  |
|  NJ-M1-NK  |  137.7  |  136.4  |  138 ± 5  |  [128.8; 146.9]  |
|  NJ-M1-D1  |  110.4  |  110.4  |  111 ± 5  |  [100.1; 121.9]  |
|  NJ-M1-W1  |  91.8  |  91.1  |  91 ± 3  |  [85.8; 96.4]  |
|  NK-M1-D1  |  106.4  |  112.9  |  111 ± 6  |  [99.6; 122.2]  |
|  NK-M1-W1  |  91.0  |  90.3  |  90 ± 3  |  [84.2; 95.1]  |
|  D1-M1-W1  |  83.9  |  94.6  |  93 ± 3  |  [87.2; 97.8]  |




===== Downloads =====

|  //Parameter File//  |  {{:mm:parameters:manganese:hhdh_ho-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:hhdh[ho]_mn-iii.zip| .off}}  |
|  //Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:mn_superoxide_dismutase-oh.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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