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Abstract
Double decoupling absolute binding free energy simulations require an intermediate state at which the ligand is held solely by restraints in a position and orientation resembling the bound state. One possible choice consists of one distance, two angle and three dihedral angle restraints. Here, I demonstrate that in practically all cases, the analytical correction derived under the rigid rotator harmonic oscillator approximation is sufficient to account for the free energy of the restraint.
Supplementary materials
Title
Additional derivations and technical descriptions
Description
The PDF document (i) summarizes the expressions by Chen et al. [Chen2023] and lists the Mathematica commands by which they can be obtained, (ii) provides some hints on how to obtain the numerical results listed in Table 1 and to reproduce the results by Boresch et al. [Boresch2003], and (iii) outlines how to evaluate the configurational integral for the angle restraint exactly.
Actions
Supplementary weblinks
Title
Mathematica input to reproduce calculations
Description
Example input for Mathematica to derive the results and carry out the calculations reported here.
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