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mm:parameters:manganese:ed_py2_wawa_example_page

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Table of Contents

Manganese(II) - DEE[SO2]

Coordination Sphere Oxidation State: Mn(II)
Spin Multiplicity: 6
IMAGE1 IMAGE2 1)

Structure chosen to parameterize

TEST PROTEIN
Protein PROTEIN NAME
PDB Code PDB CODE
Crystallographic Resolution RESOLUTION
Organism ORGANISM
[1ST AUTHOR, PUBL YEAR]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938 IMAGE
OD2 D1 15.9994
OE2 E1 15.9994
OE1 E2 15.9994

Bond Parameters

BOND Kl / kcal mol-1 l / angstrom REFERENCE
M1-D1 33.32 2.2509 [Neves, 2013]
M1-E1 47.15 2.1737
M1-E2 49.51 2.2008
M1-R1 41.81 2.1619
M1-R2 45.80 2.1526
D1-C 656.0 1.25
E1-C 656.0 1.25
E2-C 656.0 1.25
SO-R1 541.1 1.436
SO-R2 541.1 1.436
SO-O1 541.1 1.436
SO-O2 541.1 1.436

Angle Parameters

Angle Ktheta / kcal mol-1 theta / angstrom REFERENCE
D1-M1-E1 45.46 92.3315 [Neves, 2013]
D1-M1-E2 25.03 123.0771
D1-M1-R1 13.27 96.5510
D1-M1-R2 4.321 121.0757
E1-M1-E2 40.08 86.7147
E1-M1-R1 19.90 160.9449
E1-M1-R2 33.00 93.3926
E2-M1-R1 8.95 102.2828
E2-M1-R2 4.405 115.7857
R1-M1-R2 291.6 67.5889
M1-D1-C 16.912 165.3084
M1-E1-C 22.912 145.6796
M1-E2-C 15.527 135.3597
M1-R1-SO 100.89 95.8499
M1-R2-SO 100.89 95.8499
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
E2-C-CT 70.0 117.0
E2-C-O2 80.0 126.0
R1-SO-O1 74.6 119.82
R1-SO-O2 74.6 119.82
R1-SO-R2 74.6 119.82
R2-SO-O1 74.6 119.82
R2-SO-O2 74.6 119.82
O1-SO-O2 74.6 119.82

Van der Waals Parameters

ATOM TYPE Ri / angstrom epsiloni / kcal mol-1 REFERENCE
M1 1.4544 0.03 [Babu, 2006]
D1 1.6612 0.21
E1 1.6612 0.21
E2 1.6612 0.21
R1 1.6612 0.2100
R2 1.6612 0.2100
O1 1.6612 0.2100
O2 1.6612 0.2100
SO 2.0000 0.2500

Validation of Parameters from MD Simulations

Bond Parameters

BOND l0 crystal l0 opt <l>MD ± sigma(l) <l>MD ± 2sigma(l)
M1-D1 2.03 2.25 2.41 ± 0.09 [2.318; 2.506]
M1-E1 2.15 2.17 2.28 ± 0.08 [2.200; 2.359]
M1-E2 1.95 2.20 2.27 ± 0.08 [2.193; 2.347]
M1-R2 3.54 2.16 2.18 ± 0.06 [2.114; 2.238]
M1-R2 2.20 2.15 2.17 ± 0.06 [2.113; 2.232]

Angle Parameters

ANGLE theta0 crystal theta0 QM <theta>MD ± sigma(theta) <θ>MD ± 2sigma(theta)
D1-M1-E1 87.7 92.3 89 ± 4 [80.5; 97.0]
D1-M1-E2 170.0 123.1 127 ± 5 [117.4; 137.5]
D1-M1-R1 85.6 96.6 91 ± 6 [78.7; 103.7]
D1-M1-R2 94.6 121.1 99 ± 8 [82.2; 115.1]
E1-M1-E2 88.0 86.7 87 ± 5 [78.0; 96.9]
E1-M1-R1 129.4 160.9 156 ± 4 [147.4; 163.8]
E1-M1-R2 92.1 93.4 92 ± 4 [83.3; 100.7]
E2-M1-R1 104.1 102.3 111 ± 6 [97.8; 123.6]
E2-M1-R2 94.6 115.8 133 ± 9 [115.9; 150.5]
R1-M1-R2 39.0 67.6 66 ± 1 [63.1; 69.0]

Downloads

Parameter File .frcmod
Coordination Sphere Charges .off
ENZYME’s PDB File (PDB_CODE.pdb)\ LEAPRC file .pdb, leaprc

References

Neves, R.P.P.; Sousa, S.F.; Fernandes, P.A.; Ramos, M.J.. Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins . J. Chem. Theory Comput., 2013, 9 (6), 2718–2732

1) The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.
mm/parameters/manganese/ed_py2_wawa_example_page.1373478349.txt.gz · Last modified: 2013/07/10 18:45 by ruineves

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