Evaluation of shape complementarity

The grid values «¡i m, n for the static molecule at node I, m, n are given by

The two grids can then be superimposed and the movable grid (B) translated by shifts a, ft, y (see Figure 8.3). The value of where p is negative (we use —15, see below). For the second molecule (B) the grid values

1 for the molecule 0 for outside the molecule.

1 for the molecule 0 for outside the molecule.

gives the extent of shape complementarity for grid point I, m, n of the grid of molecule A. A value of 1 for the product indicates that the cell from molecule B is superimposed on the surface of A which is favorable shape complementarity. A value of p indicates a steric clash with the cell from B superimposed on the core of A. The value of p is chosen so as to penalise but not totally prevent steric clashes. A value of zero means that there is no overlap between the two molecules. Thus the total shape complementarity for the two superimposed grids ca, p, y is evaluated from

Continue reading here: Use of discrete Fourier transforms

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