The calculation of the relative distance matrix is straightforward, but the computation of the bond angle matrix requires careful design. As shown in Fig. and, we calculate and organize the angles formed between a central atom and its surrounding atoms based on their distances. Starting from the closest neighbors, we sort the surrounding atoms by their distance to the central atom. For each neighbor, we progressively calculate the angles between its vector and the vectors of other, more distant neighbors. This approach results in a structured matrix of angles, ordered by distance, which captures the spatial relationships around the central atom.