where r is the atom coordinates 𝑟 = (𝑟 ) , … , 𝑟 / ) ∈ ℝ /×1 and h is the one-hot representations of atom type ℎ = (ℎ ) , … , ℎ / ) ∈ ℝ /×2 , N is the total number of atoms, m is the number of atom types. ℎ . is a one-hot embedding to decode the ligand group information, i.e., for a given atom, it belongs to which ligand;