Unbound structures were used both for the receptor, EIN (chain A from PDB entry 1ZYM) and for the ligand, HPr (chain P from PDB entry 2JEL). Encounter complexes were generated using Fast Fourier transform (FFT) based sampling. (A) Cartoon of the specific complex formed by EIN and HPr, shown in grey and yellow, respectively. The locations of the paramagnetic tags E5C-EDTA-Mn+ and E32C-EDTA-Mn2+ on HPr are encircled and are shown in red and blue, respectively. (B) Centers of HPr structures in the encounter complex ensemble. Colors indicate classification as follows (8): blue, Class I (i.e., overlapping with the specific complex); magenta, patch 1 of Class II (i.e., non-overlapping) positions; red, patch 2 of Class II positions; and pink, additional Class II position outside the main patches. (C) Ligand IRMSD vs PIPER energy score. (D) Two representative HPr poses, colored light blue and dark blue, from Class I. (E) Two representative HPr poses (in different shades of magenta) from Patch 1 of Class II. (F) View of the EIN–HPr complex and the centers of HPr poses after rotating 180° around the vertical axis (the bound HPr is now on the left side, almost completely hidden by EIN). (G) Representative HPr poses (in different shades of red) from Patch 2 of Class II, shown in the rotated view.