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mm:parameters:manganese:dedwawawa_example_page

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Table of Contents

Manganese(II) - DEDWaWaWa

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

Structure chosen to parameterize

TEST PROTEIN
Protein Muconate Cycloisomerase
PDB Code 3CT2
Crystallographic Resolution 1.80
Organism Pseudomonas protegens Pf-5
[Sakai, 2009]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
MN M1 54.938 IMAGE
OD2 D1 15.9994
OD2 D2 15.9994
OE2 E1 15.9994
OW W1 15.9994
OW W2 15.9994
OW W3 15.9994
HW HM 1.00794

Bond Parameters

BOND Kl / kcal mol-1 Å-2 l / Å REFERENCE
M1-D1 87.24 2.1060 [Neves, 2013]
M1-D2 67.69 2.1358
M1-E1 64.66 2.1182
M1-W1 37.55 2.2668
M1-W2 21.70 2.3891
M1-W3 26.88 2.3509
D1-C 656.0 1.25
D2-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 Kθ / kcal mol-1 rad-2 θ / deg REFERENCE
D1-M1-D2 34.80 166.2571 [Neves, 2013]
D1-M1-E1 36.67 98.6591
D1-M1-W1 64.83 84.6089
D1-M1-W2 28.655 100.2850
D1-M1-W3 12.63 104.2522
D2-M1-E1 52.68 94.9867
D2-M1-W1 51.096 88.2121
D2-M1-W2 70.4 68.8061
D2-M1-W3 15.15 83.2134
E1-M1-W1 28.47 108.9767
E1-M1-W2 27.038 151.2138
E1-M1-W3 78.1 70.7310
W1-M1-W2 22.205 95.5613
W1-M1-W3 11.62 171.1984
W2-M1-W3 24.74 84.5113
M1-D1-C 42.921 132.3478
M1-D2-C 38.71 134.0663
M1-E1-C 14.90 132.1818
M1-W1-HM 19.45 110.5423
M1-W2-HM 13.29 96.8796
M1-W3-HM 14.52 88.2507
HM-W1-HM 100.0 104.52
HM-W2-HM 100.0 104.52
HM-W3-HM 100.0 104.52
D1-C-CT 70.0 117.0
D1-C-O2 80.0 126.0
D2-C-CT 70.0 117.0
D2-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 Ri / Å εi / kcal mol-1 REFERENCE
M1 1.4544 0.03 [Babu, 2006]
D1 1.6612 0.21
D2 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 [Cornel, 1995]

Validation of Parameters from MD Simulations

Bond Parameters

BOND l0 crystal l0 opt ‹l›MD ± σ(l) ‹l›MD ± 2σ(l)
M1-D1 2.10 2.11 2.22 ± 0.06 [2.162; 2.279]
M1-D2 2.16 2.14 2.26 ± 0.06 [2.194; 2.324]
M1-E1 2.00 2.12 2.14 ± 0.07 [2.076; 2.212]
M1-W1 2.03 2.27 2.28 ± 0.09 [2.184; 2.370]
M1-W2 1.94 2.39 2.4 ± 0.1 [2.295; 2.536]
M1-W3 1.97 2.35 2.3 ± 0.1 [2.225; 2.443]

Angle Parameters

ANGLE θ0 crystal θ0 QM ‹θ›MD ± σ(θ) ‹θ›MD ± 2σ(θ)
D1-M1-D2 175.3 166.3 168 ± 4 [160.5; 174.6]
D1-M1-E1 89.4 98.7 98 ± 4 [90.0; 106.0]
D1-M1-W1 93.4 84.6 87 ± 4 [78.7; 95.2]
D1-M1-W2 94.1 100.3 103 ± 5 [93.4; 112.2]
D1-M1-W3 89.6 104.3 106 ± 6 [94.1; 118.1]
D2-M1-E1 94.2 95.0 93 ± 4 [85.3; 100.0]
D2-M1-W1 88.8 88.2 88 ± 4 [80.4; 96.5]
D2-M1-W2 81.9 68.8 68 ± 3 [61.3; 74.6]
D2-M1-W3 86.6 83.2 78 ± 5 [67.5; 88.9]
E1-M1-W1 102.9 109.0 112 ± 5 [102.6; 121.9]
E1-M1-W2 169.8 151.2 146 ± 4 [138.1; 153.5]
E1-M1-W3 102.8 70.7 69 ± 3 [62.4; 75.8]
W1-M1-W2 86.5 94.6 95 ± 5 [85.4; 104.9]
W1-M1-W3 154.2 171.2 165 ± 5 [155.6; 175.3]
W2-M1-W3 67.7 84.5 80 ± 5 [70.5; 89.0]

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/dedwawawa_example_page.1373529883.txt.gz · Last modified: 2013/07/11 09:04 by ruineves

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