Input files (meshes, pqr, cavities) for binding energy calculations in the manuscript "Coupling finite and boundary element methods to solve the Poisson--Boltzmann equation for electrostatics in molecular solvation" (preprint at https://arxiv.org/abs/2305.11886). This data set of molecular structures was originally proposed by Harris, R.C., Boschtisch, A.H., and Fenley, M.O., JCTC 9 (8) (2013) (https://doi.org/10.1021/ct300765w). Scripts to generate results are available in https://github.com/MichalBosy/FEM_BEM_coupling/.