, where l is the number of ligands. In LigandDiff, before passing through the neural network 𝜙 , the noise is added to only the coordinates and the atom types which belong to the diffused ligand, while the ligand-group embeddings are unchanged. Although the whole atomic embeddings 𝑥 = [𝑟, ℎ, ℎ . ] are updated through the neural network, we only consider the predicted coordinates and the predicted atom type features.