mm:parameters:iron:cc_fe2_ss_fe2_cc
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| - | ====== Iron(III) - CC[Fe2]SS[Fe2]CC ====== | ||
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| - | | **Coordination Sphere** | **Oxidation State:** Fe(III) \\ **Spin Multiplicity:** 1 | | ||
| - | | PATH TO IMAGE1 | PATH TO IMAGE2 ((The schemes represent geometrical dispositions for crystal lattices. These should be roughly similar to the corresponding distorted geometries in enzymatic coordination spheres.)) | | ||
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| - | ---- | ||
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| - | ===== Structure chosen to parameterize ===== | ||
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| - | | **TEST PROTEIN** || | ||
| - | | //Protein// | PROTEIN NAME | | ||
| - | | //PDB Code// | PDB CODE | | ||
| - | | //Crystallographic Resolution// | RESOLUTION | | ||
| - | | //Organism// | ORGANISM | | ||
| - | | [[LINK OF THE PAPER OF THE STRUCTURE | [1ST AUTHOR, PUBL YEAR]]] || | ||
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| - | ===== Parameters Determined ===== | ||
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| - | ==== Atom Types ==== | ||
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| - | | **ATOM TYPE** | **NEW ATOM TYPE** | **MASS** | **STRUCTURE** | | ||
| - | | FE | FE | 55.845 | IMAGE | | ||
| - | | SG | SX | 32.065 | ::: | | ||
| - | | OG | SX | 32.065 | ::: | | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **K<sub>l</sub>** / **kcal mol<sup>-1</sup>** | **l / angstrom** | **REFERENCE** | | ||
| - | | FE-S | 93.4 | 2.17 | | ||
| - | | FE-SX | 82.6 | 2.23 | | ||
| - | | CT-SX | 237.00 | 1.8100 | | ||
| - | | SX-CT | 227.00 | 1.8100 | | ||
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| - | ==== Angle Parameters ==== | ||
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| - | | **Angle** | **K<sub>theta</sub>** / **kcal mol<sup>-1</sup>** | **theta / angstrom** | **REFERENCE** | | ||
| - | | S-FE-S | 17.3 | 102.84 | | ||
| - | | SX-FE-S | 17.3 | 102.84 | | ||
| - | | FE-S-FE | 18.0 | 77.200 | | ||
| - | | SX-FE-SX | 65.5 | 108.44 | | ||
| - | | FE-SX-CT | 65.5 | 108.44 | | ||
| - | | HS-SX-FE | 65.5 | 108.44 | | ||
| - | | SX-CT-H1 | 50.00 | 109.5000 | | ||
| - | | SX-FE-SX | 33.15 | 109.8650 | | ||
| - | | CT-CT-SX | 50.00 | 108.6000 | | ||
| - | | CT-SX-CT | 62.00 | 98.9000 | | ||
| - | | CT-CT-SX | 50.00 | 114.7000 | | ||
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| - | ==== Van der Waals Parameters ==== | ||
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| - | | **ATOM TYPE** | **R<sub>i</sub> / angstrom** | **epsilon<sub>i</sub> / kcal mol<sup>-1</sup>** | **REFERENCE** | | ||
| - | | FE | 2.6500 | 0.0450 | [[http://pubs.acs.org/doi/abs/10.1021/jp054177x | [Giammona, 1984]]] | | ||
| - | | S | 2.0000 | 0.2500 | | ||
| - | | SX | 2.0000 | 0.2500 | | ||
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| - | ===== Validation of Parameters from MD Simulations ===== | ||
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| - | ==== Bond Parameters ==== | ||
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| - | | **BOND** | **l<sub>0 crystal</sub>** | **l<sub>0 opt</sub>** | **<l><sub>MD</sub> ± sigma(l)** | **<l><sub>MD</sub> ± 2sigma(l)** | | ||
mm/parameters/iron/cc_fe2_ss_fe2_cc.1375694429.txt.gz · Last modified: 2013/08/05 10:20 by ruineves
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