The elements of the design matrix block that defines the reference ligands, 𝐴 Δ𝐺 𝑖𝑗 , are either 0 or a value of 1 at the column of the reference ligand row in 𝚫𝐆 𝐓𝐫𝐮𝐞 . The elements of the design matrix block for the relative free energy calculations, 𝐴 ΔΔ𝐺