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mm:parameters:iron:cccc

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Iron(III) - CCCC

Coordination Sphere Oxidation State: Fe(III)
Spin Multiplicity: 1
PATH TO IMAGE2 1)

Structure chosen to parameterize

TEST PROTEIN
Protein Rubredoxin
PDB Code 1IRO
Crystallographic Resolution 1.10 Å
Organism Clostridium pasteurianum
[Dauter, 1996]

Parameters Determined

Atom Types

ATOM TYPE NEW ATOM TYPE MASS STRUCTURE
FE FE 55.845
SG SF 32.065

Bond Parameters

BOND Kl / kcal mol-1 l / angstrom REFERENCE
FE-SF 80.75 2.3170 [Carvalho, 2013]
CT-SF 237.00 1.8100

Angle Parameters

Angle Ktheta / kcal mol-1 theta / angstrom REFERENCE
SF-FE-SF 33.15 109.8650 [Carvalho, 2013]
CT-SF-FE 27.60 100.9150
SF-CT-H1 50.00 109.5000
CT-CT-SF 50.00 108.6000

Van der Waals Parameters

ATOM TYPE Ri / angstrom epsiloni / kcal mol-1 REFERENCE
FE 2.6500 0.0450 [Giammona, 1984]
SF 2.0000 0.2500

Downloads

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

References

A.T.P. Carvalho, A.F.S. Teixeira, MJ.Ramos. Parameters for Molecular Dynamics Simulations of Iron-Sulfur Proteins. J. Comput. Chem., 2013, 34, 1540-1548

D. A. Giammona, Ph.D. Thesis; University of California: Davis, 1984

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/iron/cccc.1375721738.txt.gz · Last modified: 2013/08/05 17:55 by ruineves