PortoBioComp

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.

====== Manganese(III) - HHDHWa ======



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


----



===== 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_hhdhw_.png?120 |}}  |
|  OD1  |  D1  |  15.9994  | ::: |
|  NE2  |  NI  |  14.0067  | ::: |
|  NE2  |  NJ  |  14.0067  | ::: |
|  NE2  |  NK  |  14.0067  | ::: |
|  OW  |  W1  |  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  |  59.43  |  2.2457  | [[#references | [Neves, 2013]]] |
|  M1-NJ  |  75.35  |  2.1589  | ::: |
|  M1-NK  |  80.07  |  2.168  | ::: |
|  M1-D1  |  81.62  |  2.0542  | ::: |
|  M1-W1  |  38.02  |  2.2351  | ::: |
|  NI-CR  |  488  |  1.335  |
|  NI-CV  |  410  |  1.394  |
|  NJ-CR  |  488  |  1.335  |
|  NJ-CV  |  410  |  1.394  |
|  NK-CR  |  488  |  1.335  |
|  NK-CV  |  410  |  1.394  |
|  D1-C  |  656  |  1.25  |
|  W1-HM  |  553  |  0.9572  |


==== Angle Parameters ====

|  **ANGLE**  |  **K<sub>θ</sub>** / **kcal mol<sup>-1</sup> rad<sup>-2</sup>**  |  **θ / deg**  |  **REFERENCE**  |
|  NI-M1-NJ  |  48.40  |  95.4086  | [[#references | [Neves, 2013]]] |
|  NI-M1-NK  |  45.74  |  92.4322  | ::: |
|  NI-M1-D1  |  86.0  |  82.0242  | ::: |
|  NI-M1-W1  |  56.35  |  166.1284  | ::: |
|  NJ-M1-NK  |  37.87  |  139.1027  | ::: |
|  NJ-M1-D1  |  24.76  |  109.6451  | ::: |
|  NJ-M1-W1  |  46.58  |  90.8259  | ::: |
|  NK-M1-D1  |  23.465  |  111.182  | ::: |
|  NK-M1-W1  |  46.47  |  90.9222  | ::: |
|  D1-M1-W1  |  59.83  |  84.2125  | ::: |
|  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  |
|  HM-W1-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  |
|  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  |  2.05  |  2.04 ± 0.06  |  [1.982; 2.103]  |
|  M1-NI  |  2.10  |  2.25  |  2.26 ± 0.07  |  [2.192; 2.328]  |
|  M1-NJ  |  2.08  |  2.16  |  2.17 ± 0.06  |  [2.108; 2.234]  |
|  N1-NK  |  2.09  |  2.17  |  2.19 ± 0.06  |  [2.127; 2.246]  |
|  M1-W1  |  2.02  |  2.24  |  2.14 ± 0.09  |  [2.052; 2.232]  |


==== 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  |  95.4  |  96 ± 4  |  [88.7; 102.7]  |
|  NI-M1-NK  |  91.5  |  92.4  |  93 ± 3  |  [86.7; 100.2]  |
|  NI-M1-D1  |  82.4  |  82.0  |  82 ± 3  |  [77.2; 87.6]  |
|  NI-M1-W1  |  166.1  |  166.1  |  164 ± 3  |  [158.1; 169.9]  |
|  NJ-M1-NK  |  137.7  |  139.1  |  141 ± 4  |  [132.2; 149.1]  |
|  NJ-M1-D1  |  110.4  |  109.6  |  109 ± 5  |  [98.8; 119.0]  |
|  NJ-M1-W1  |  91.8  |  90.8  |  90 ± 4  |  [82.4; 97.5]  |
|  NK-M1-D1  |  106.4  |  111.2  |  110 ± 5  |  [99.9; 120.0]  |
|  NK-M1-W1  |  91.0  |  90.9  |  91 ± 4  |  [83.9; 98.4]  |
|  D1-M1-W1  |  83.9  |  84.2  |  82 ± 3  |  [76.4; 88.0]  |



===== Downloads =====

|  //Parameter File//  |  {{:mm:parameters:manganese:hhdhw-frcmod.zip| .frcmod}}  |
|  //Coordination Sphere Charges//  |  {{:mm:parameters:manganese:hhdhw_mn-iii.zip| .off}}  |
|  //Manganese Superoxide Dismutase’s PDB File (1N0J.pdb)\\ LEAPRC file//  |  {{:mm:parameters:manganese:mn_superoxide_dismutase.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
PortoBioComp

User Tools

Site Tools

Page Tools
