Hi - I’ve written up some code that searched through all pairings of covalent and non-covalent fragments, and saved the pairings that have a planar overlap in 3D space. I’ve defined ‘planar overlap’ as one fragment having 4 or more atoms within 0.8 angstroms of another 4 or more atoms in fragment B.
.csv of fragment pairs (as well as code to change the above parameters) can be found in this git repo:
https://github.com/wjm41/covid-frag-analysis/blob/master/data/overlapping_fragments.csv
Hopefully this is useful for people looking for fragments to merge!