Hydrogen bonds in the top scoring pose of the 3 molecules are listed in Table Geometrically the molecules fit into the X-shaped Mpro cavity differently. Nirmatrelvir and 48:32 share 2 of the X-legs and the surface tunnel. Molecule 74:19 occupies all 3 X-legs and the tunnel. This partly results in the overlaps of different hydrogen bonds of the 3 molecules and also explains the presence of 6 hydrogen bond contacts in molecule 74:16. None of the amino acids with these bonds are in a helix, but rather in strands.