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mm:parameters:iron:ccc_c_2
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Table of Contents
Iron(III) - CC[C]2
| Coordination Sphere | Oxidation State: Fe(III) Spin Multiplicity: 1 |
| PATH TO IMAGE1 | PATH TO IMAGE2 1) |
Structure chosen to parameterize
| TEST PROTEIN | |
| Protein | Desulforedoxin |
| PDB Code | 1DXG |
| Crystallographic Resolution | 1.80 Å |
| Organism | Desulfovibrio gigas |
| [Archer, 1995] | |
Parameters Determined
Atom Types
| ATOM TYPE | NEW ATOM TYPE | MASS | STRUCTURE |
| FE | FE | 55.845 | IMAGE |
| SG | SF | 32.065 | |
| SG | SM | 32.065 |
Bond Parameters
| BOND | Kl / kcal mol-1 | l / angstrom | REFERENCE |
| FE-SF | 84.30 | 2.3100 | [Carvalho, 2013] |
| FE-SM | 74.1 | 2.3 | |
| CT-SF | 237.00 | 1.8100 | |
| SM-CT | 227.00 | 1.8100 |
Angle Parameters
| Angle | Ktheta / kcal mol-1 | theta / angstrom | REFERENCE |
| SF-FE-SM | 58.4 | 110.0 | [Carvalho, 2013] |
| FE-SF-CT | 68.5 | 102.0 | |
| FE-SM-CT | 57.3 | 107.0 | |
| SM-FE-SM | 58.4 | 110.0 | |
| SF-FE-SF | 33.2 | 110.0 | |
| SF-CT-H1 | 50.00 | 109.5000 | |
| SF-FE-SF | 33.15 | 109.8650 | |
| CT-CT-SF | 50.00 | 108.6000 | |
| SM-CT-H1 | 50.00 | 109.5000 | |
| CT-SM-CT | 62.00 | 98.9000 | |
| CT-CT-SM | 50.00 | 114.7000 |
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 | |
| SM | 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/ccc_c_2.1375710786.txt.gz · Last modified: 2013/08/05 14:53 by ruineves
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