Building an interpretable and large-scale protein-compound interactions model is an very important subject. A new chemical interpretable model to cover the protein-compound interactions was proposed. The core idea of the model is based on the hypothesis that a protein-compound interaction can be decomposed as protein fragments and compound fragments interactions, so composing the fragments interactions brings about a protein-compound interaction. Firstly, amino acid oligomer clusters and compound substructures were applied to describe protein and compound respectively. And then the protein fragments and the compound fragments were viewed as the two parts of a bipartite graph, fragments interactions as the edges. Based on the hypothesis, the protein-compound interaction is determined by the summation of protein fragments and compound fragments interactions. The experiment demonstrates that the model prediction accuracy achieves 97% and has the very good explanatory.