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====== Manganese (II) - DDWaWaWa ======

The avian viral S integrase shows preference by manganese(II) over magnesium. In both cases the metal atom is bonded to two aspartates and four water molecules.

|  **Coordination Sphere**  |  **Oxidation state:** Mn(II) \\  **Spin multiplicity:** 6  |
|  {{ :mm:parameters:manganese:non-parameterized_ddwwww_.png?120 |}} | JMOL |


----

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

|  **TEST PROTEIN**  ||
|  //Protein//  |  Integrase  |
|  //PDB Code//  |  1A5V  |
|  //Crystallographic Resolution//  |  1.90 Å  |
|  //Organism//  |  Rous Sarcoma Virus  |
|  [[http://www.pnas.org/content/95/9/4831.long | [Lubkowski, 1998]]]  ||


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

==== Atom Types ====

|  **ATOM TYPE**  |  **NEW ATOM TYPE**  |  **MASS**  |  **STRUCTURE**  |
|  MN  |  M1  |  54.938  |  {{ :mm:parameters:manganese:parameterized_ddwwww_.png?120 |}}  |
|  OD1  |  D1  |  15.9994  | ::: |
|  OD2  |  D2  |  15.9994  | ::: |
|  OW  |  W1  |  15.9994  | ::: |
|  OW  |  W2  |  15.9994  | ::: |
|  OW  |  W3  |  15.9994  | ::: |
|  OW  |  W4  |  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-D1  |  86.69  |  2.0912  |  [[#references | [Neves, 2013]]]  |
|  M1-D2  |  73.44  |  2.1278  | ::: |
|  M1-W1  |  41.1  |  2.2458  | ::: |
|  M1-W2  |  58.63  |  2.1786  | ::: |
|  M1-W3  |  34.55  |  2.3171  | ::: |
|  M1-W4  |  25.05  |  2.3835  | ::: |
|  D1-C  |  656  |  1.25  |
|  D2-C  |  656  |  1.25  |
|  W1-HM  |  553  |  0.9572  |
|  W2-HM  |  553  |  0.9572  |
|  W3-HM  |  553  |  0.9572  |
|  W4-HM  |  553  |  0.9572  |


==== Angles Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  D1-M1-D2  |  38.782  |  108.3864  |  [[#references | [Neves, 2013]]]  |
|  D1-M1-W1  |  52.48  |  86.0095  | ::: |
|  D1-M1-W2  |  40.523  |  93.9632  | ::: |
|  D1-M1-W3  |  14.18  |  90.4522  | ::: |
|  D1-M1-W4  |  22.791  |  173.2496  | ::: |
|  D2-M1-W1  |  26.46  |  97.5246  | ::: |
|  D2-M1-W2  |  55.17  |  91.2115  | ::: |
|  D2-M1-W3  |  14.57  |  157.0825  | ::: |
|  D2-M1-W4  |  49.51  |  85.9497  | ::: |
|  W1-M1-W2  |  22.81  |  165.2888  | ::: |
|  W1-M1-W3  |  21.4  |  75.017  | ::: |
|  W1-M1-W4  |  30.33  |  100.0581  | ::: |
|  W2-M1-W3  |  16.61  |  92.3995  | ::: |
|  W2-M1-W4  |  21.06  |  84.0447  | ::: |
|  W3-M1-W4  |  16.8  |  84.2736  | ::: |
|  M1-D1-C  |  52.071  |  128.7239  | ::: |
|  M1-D2-C  |  46.53  |  125.6353  | ::: |
|  M1-W1-HM  |  24.91  |  107.2734  | ::: |
|  M1-W2-HM  |  24.17  |  105.0104  | ::: |
|  M1-W3-HM  |  7.36  |  101.1843  | ::: |
|  M1-W4-HM  |  7.764  |  101.9263  | ::: |
|  HM-W1-HM  |  100  |  104.52  |
|  HM-W2-HM  |  100  |  104.52  |
|  HM-W3-HM  |  100  |  104.52  |
|  HM-W4-HM  |  100  |  104.52  |
|  D1-C-CT  |  70  |  117  |
|  D1-C-O2  |  80  |  126  |
|  D2-C-CT  |  70  |  117  |
|  D2-C-O2  |  80  |  126  |

==== 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]]]  |
|  HM  |  0.6  |  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  |  2.22  |  2.09  |  2.25 ± 0.06  |  [2.13; 2.37]  | 
|  M1-D2  |  2.23  |  2.13  |  2.18 ± 0.07  |  [2.04; 2.31]  |
|  M1-W1  |  2.10  |  2.25  |  2.23 ± 0.09  |  [2.05; 2.40]  |
|  M1-W2  |  2.18  |  2.18  |  2.16 ± 0.08  |  [2.01; 2.31]  |
|  M1-W3  |  2.17  |  2.32  |  2.3 ± 0.1  |  [2.1; 2.5]  |
|  M1-W4  |  2.51  |  2.38  |  2.4 ± 0.1  |  [2.1; 2.6]  | 

==== 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-D2  |  90.6  |  108.4  |  105 ± 5  |  [95; 116]  |
|  D1-M1-W1  |  87.3  |  86.0  |  85 ± 4  |  [76; 94]  |
|  D1-M1-W2  |  94.2  |  94.0  |  104 ± 6  |  [92; 117]  |
|  D1-M1-W3  |  84.5  |  90.5  |  99 ± 7  |  [85; 114]  |
|  D1-M1-W4  |  171.9  |  173.2  |  171 ± 4  |  [162; 179]  |
|  D2-M1-W1  |  89.9  |  97.5  |  96 ± 7  |  [83; 109]  |
|  D2-M1-W2  |  90.2  |  91.2  |  88 ± 5  |  [79; 98]  |
|  D2-M1-W3  |  179.0  |  157.1  |  149 ± 7  |  [136; 163]  |
|  D2-M1-W4  |  97.4  |  85.9  |  80 ± 5  |  [71; 89]  |
|  W1-M1-W2  |  178.6  |  165.3  |  164 ± 5  |  [153; 175]  |
|  W1-M1-W3  |  90.9  |  75.0  |  70 ± 7  |  [56; 84]  |
|  W1-M1-W4  |  94.2  |  100.1  |  94 ± 6  |  [83; 106]  |
|  W2-M1-W3  |  89.1  |  92.4  |  101 ± 10  |  [82; 120]  |
|  W2-M1-W4  |  84.4  |  84.0  |  75 ± 9  |  [57; 93]  |
|  W3-M1-W4  |  87.5  |  84.3  |  76 ± 7  |  [62; 89]  |

===== Downloads =====
|  //Parameter File//  |  {{:mm:parameters:manganese:ddwwww-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:ddwwww_mn-ii.zip| .off}}  |
|  //Integrase’s PDB File (1A5V.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:integrase.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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