To construct an accurate and general molecular and bimolecular representation for organic functional materials, we employ atomic numbers and pairwise distances as the initial repre-sentation to encode both atomic and 3D spatial information of the molecular or bimolecular system. Then, we employ the self-attention mechanism in Transformer architecture to couple and update the initial atomic and pair representations, thereby obtaining representations that accurately capture the complex interactions within the molecules or bimolecules. Similar to using the CLS token as a sequence representation aggregator for 1D sequence tasks in the BERT model, we choose the geometric centers of the molecules or bimolecules as the CLS atoms to aggregate atomic features, thereby reflecting the overall structural characteristics of the molecules or bimolecules. We denote the initial atomic representation as: