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====== Manganese(II) - DENWaWaWa ======
###
D-Glutarate Dehydratase is analogous to mandelate racemase and enolase.
The manganese coordination sphere has a manganese(II) atom bonded to a glutamate, an aspartate and an asparagine from the same subunit.
###

|  **COORDINATION SPHERE**  ||
|  {{ :mm:parameters:manganese:non-parameterized_denwww_.png?120 |}} |  \\ **Oxidation State:** Mn(II)  \\  **Spin Multiplicity:** 6  |


----



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


|  **TEST PROTEIN**  ||
|  //Protein//  |  D-Glucarate Dehydratase  |
|  //PDB Code//  |  3NXL  |
|  //Crystallographic Resolution//  |  1.89 Å  |
|  //Organism//  |  Burkholderia sp. 383  |
|  [[LINK OF THE PAPER OF THE STRUCTURE | [Fedorov, 2010]]]  ||



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



==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_denwww_.png?120 |}}  |
|  OD2  |  D1  |  15.9994  | ::: |
|  OE2  |  E1  |  15.9994  | ::: |
|  OD1  |  NW  |  15.9994  | ::: |
|  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-NW  |  35.45  |  2.2737  | [[#references | [Neves, 2013]]] |
|  M1-D1  |  67.93  |  2.1478  | ::: |
|  M1-E1  |  92.09  |  2.0644  | ::: |
|  M1-W1  |  50.25  |  2.2190  | ::: |
|  M1-W2  |  33.63  |  2.3313  | ::: |
|  M1-W3  |  41.73  |  2.2662  | ::: |
|  NW-C  |  570.0  |  1.229  |
|  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**  |
|  NW-M1-D1  |  50.31  |  168.8916  | [[#references | [Neves, 2013]]] |
|  NW-M1-E1  |  36.14  |  92.7969  | ::: |
|  NW-M1-W1  |  38.04  |  100.6537  | ::: |
|  NW-M1-W2  |  30.57  |  95.9566  | ::: |
|  NW-M1-W3  |  33.91  |  78.7883  | ::: |
|  D1-M1-E1  |  35.463  |  100.5525  | ::: |
|  D1-M1-W1  |  64.49  |  85.2832  | ::: |
|  D1-M1-W2  |  48.3  |  73.9644  | ::: |
|  D1-M1-W3  |  32.46  |  94.4909  | ::: |
|  E1-M1-W1  |  27.16  |  94.9567  | ::: |
|  E1-M1-W2  |  16.85  |  166.1705  | ::: |
|  E1-M1-W3  |  44.90  |  89.8914  | ::: |
|  W1-M1-W2  |  13.16  |  97.1854  | ::: |
|  W1-M1-W3  |  26.160  |  175.1204  | ::: |
|  W2-M1-W3  |  23.22  |  78.0892  | ::: |
|  M1-NW-C  |  10.785  |  144.0557  | ::: |
|  M1-D1-C  |  47.557  |  125.7501  | ::: |
|  M1-E1-C  |  36.476  |  122.3574  | ::: |
|  M1-W1-HM  |  24.67  |  106.0283  | ::: |
|  M1-W2-HM  |  9.470  |  89.9559  | ::: |
|  M1-W3-HM  |  23.78  |  97.5290  | ::: |
|  HM-W1-HM  |  100.0  |  104.52  |
|  HM-W2-HM  |  100.0  |  104.52  |
|  HM-W3-HM  |  100.0  |  104.52  |
|  NW-C-CT  |  80.0  |  120.40  |
|  NW-C-N  |  80.0  |  122.90  |
|  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]]]  |
|  NW  |  1.6612  |  0.21  |
|  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  |  [[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  |  2.28  |  2.15  |  2.16 ± 0.06  |  [2.095; 2.224]  |
|  M1-E1  |  2.45  |  2.06  |  2.13 ± 0.06  |  [2.066; 2.186]  |
|  M1-NW  |  2.40  |  2.27  |  2.29 ± 0.09  |  [2.195; 2.383]  |
|  M1-W1  |  2.26  |  2.22  |  2.21 ± 0.08  |  [2.127; 2.290]  |
|  M1-W2  |  2.51  |  2.33  |  2.3 ± 0.1  |  [2.222; 2.416]  |
|  M1-W3  |  2.47  |  2.27  |  2.25 ± 0.09  |  [2.165; 2.341]  |


==== 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-E1  |  100.8  |  100.6  |  98 ± 4  |  [89.3; 106.1]  |
|  D1-M1-NW  |  154.1  |  168.9  |  165 ± 3  |  [158.6; 172.1]  |
|  D1-M1-W1  |  84.5  |  85.3  |  85 ± 4  |  [78.1; 92.1]  |
|  D1-M1-W2  |  93.4  |  73.9  |  70 ± 4  |  [61.8; 77.6]  |
|  D1-M1-W3  |  80.9  |  94.5  |  91 ± 4  |  [82.4; 100.0]  |
|  E1-M1-NW  |  66.7  |  88.4  |  94 ± 4  |  [85.9; 102.0]  |
|  E1-M1-W1  |  113.1  |  94.9  |  96 ± 5  |  [86.4; 104.6]  |
|  E1-M1-W2  |  160.1  |  166.2  |  157 ± 5  |  [148.0; 166.1]  |
|  E1-M1-W3  |  95.6  |  89.9  |  88 ± 5  |  [78.7; 97.4]  |
|  NW-M1-W1  |  95.7  |  100.7  |  101 ± 4  |  [92.7; 109.3]  |
|  NW-M1-W2  |  86.6  |  95.9  |  97 ± 4  |  [88.2; 105.4]  |
|  NW-M1-W3  |  98.7  |  78.8  |  82 ± 4  |  [73.2; 90.6]  |
|  W1-M1-W2  |  107.8  |  97.2  |  101 ± 5  |  [91.3; 111.6]  |
|  W1-M1-W3  |  149.8  |  175.1  |  172 ± 4  |  [164.7; 179.6]  |
|  W2-M1-W3  |  69.2  |  78.1  |  74 ± 6  |  [62.6; 85.8]  |



===== Downloads =====
|  //Parameter File//  |  {{:mm:parameters:manganese:denwww-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:denwww_mn-ii.zip| .off}}  |
|  //D-Glutarate Dehydratase’s PDB File (3NXL.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:d-glutarate_dehydratase.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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