Fig. 7: Penicillin (used here as the source molecule) and its analogs where a nitrogen atom (N) is replaced with an oxygen atom (O), phosphorus atom (P), and arsenic atom (As), respectively.
From: Exhaustive local chemical space exploration using a transformer model
The area enclosed within the orange circles in the lower part of the figure contains the atoms that differ from the penicillin. The molecular similarity, denoted with S in the figure, between Penicillin and the modified analogs are the same, while their corresponding NLLs (negative log-likelihoods or precedence) are different. The molecular transformation from penicillin to the analog with an arsenic atom has lower precedence (higher NLL) than transforming penicillin to the analog with phosphorus and oxygen, respectively. The derivative with an oxygen atom has the highest precedence after penicillin. The Tanimoto similarity is denoted with the letter S on top of the penicillin analogs in the lower part of the figure.
