In the initialization, atomic number z i is passed to the embedding layer and summed with the positional embedding ζ i to compute the initial node embedding h 0 i . The distance d t ij of t-th edge between node i and j is expanded via a set of radial basis functions (RBF) and transformed by linear layers and Softplus activation function to obtain the edge embedding e t ij . The message passing phase follows an edge-wise attention mechanism . In the l-th (0 ≤ l ≤ L) attention layer, edge-wise attention weights α t ij and message m t ij of t-th edge between node i and j are calculated based on h l i , h l j and e t ij according to