Ligand 3D

When R is the reactivity of the atom i in the appropriate reaction mechanism, it represents the activation energy required to produce the reactive intermediate. It depends on the ligand 3D structure and on the mechanism of reaction. Therefore, R, is a score proportional to the reactivity of the ligand atom i in a specific reaction mechanism. 

AllChem 12 Tripos Hour 100 Tripos Discovery Research (TDR) 1.00E+20 3D/2D ligand 3D Topomer... 

Figure 11.3 Diagrammatic representation of metal-ligand bonds, (a)

Figure 9. Ligand-ligand 3D similarity Total and common (overlap) multiple 4-point potential 3-D pharmacophores for two potent endothelin antagonists.

The accessibility component, represents the recognition between the specific CYP-protein and the ligand when the ligand is positioned in the CYP-protein and exposes the atom i to the heme. It depends on the ligand 3D structure, conformation, chirality, and on the 3D structure and sidechain flexibility of the CYP-enzyme. Thus the score is proportional to the exposure of the ligand atom i to the heme group of a specific CYP-enzyme. 

The ligand 3D coordinates were converted to a SMILES string using an in-house translation algorithm, as described previously. An alternative SMILES string was generated using the lookup table available from the M S D web site [4] that converts the... 

Isolating the less thermodynamically stable of two interconvertible forms of the same composition (whether it be coordination compounds, allotropes of elements, or any other chemical composition) can be done only if the rate of reaching equilibrium is so slow as to render the conversion of the metastable isomer to the stable one very protracted. This is a form of Ostwald s law of metastable intermediates. Such rates are slow (minutes < ti/2 < years) for the equilibrations of coordinated cobalt(III), chromium(III), a few (spin-paired) d ferrous compounds, such as salts of the ferroin 22a, tris-l,10-phenanthrolineiron(II) cation, and a few octahedral nickel(II) species with strong field ligands (3d, e.g., the tris-l,10-phenanthrolinenickel(II) ion 22b). 

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