This dataset contains tabulated potentials of mean force (PMFs) and associated adsorption (binding) free energies for interactions of amino acids side chain analogues and lipid fragments (LF) with a range of materials: titanium dioxide, iron oxide, amorphous silica, quartz, and a range of carbon-based materials including amorphous carbon, graphene and carbon nanotubes both in a pristine form and functionalized by certain chemical groups. All data were computed from atomistic molecular dynamics simulations as a part of the SmartNanoTox project 2016-2020. Version 2 of the dataset includes additional materials: zink oxide, zink sulfate in pristine and PMMA-coated forms computed within NanoSolveIt project (2019-2023). The data are intended to be used in coarse-grained models describing interactions of nanomaterials with nanoparticles, for the prediction of the binding affinity of proteins and lipids to nanoparticles, and as biological "fingerprints" of nanomaterials characterizing behavior of the nanomaterials in biological environments.