The performance of our APAN models learning on 2D molecular graphs has been shown in Table . In MoleculeNet database, ligand 3D conformations are included in QM7, QM8 and QM9 datasets besides 2D molecule graphs. One interesting question would be if using 3D conformation will be beneficial for improving model performance. Previous work demonstrated that pre-trained 3D models performed very well for molecular property prediction. As illustrated in the 3D ligand workflow described in the method section, the Euclidean distance matrix between atom pairs can be incorporated in the atom pairing layer (as shown in Fig. ). Here, we would like to compare the performance between APAN model using 2D graph and the model using 3D information.