Supramolecular cages benchmark datasets

Two benchmark datasets, comprising 22 well-known supramolecular cages, have been selected from the supramolecular chemistry literature to evaluate cavity detection and volume characterization.

All supramolecular cage structures were prepared in the following way: the original CIF files were downloaded from the Cambridge Structural Database (CSD) and atoms and molecular fragments, that are not part of the cage-framework, were removed from the structures, using Diamond Crystal and Molecular Structure Visualization software and saved in a PDB format.

• Benchmark dataset 1: host-guest pairs

For benchmark dataset 1, the guest structures were obtained, from the corresponding CIF files, by removing the supramolecular cage and other molecular fragments that are not part of the guest.  

Benchmark dataset 2: topologically and morphologically distinct supramolecular cages

The single resorcin[4]arene ligand (O2) was prepared from the corresponding resorcin[4]arene-cage (A1) by removing 5 ligands. In the cyclotricatechylene cage (C1), the outward-pointing phenyl groups (that do not affect the cavity calculations) were removed.