Natural compounds continue to attract researchers' interest due to their rich biological activity. However, the series of enzymatic reactions that biosynthesize complex molecular skeletons of natural compounds is extremely difficult, and there are many reactions that cannot be envisaged in organic synthesis reaction theory. In this study, we focus on the secondary metabolic pathways of natural compounds and are working on the development of in silico tools to calculate the metabolic pathways appropriately. In this paper, we report the results of an attempt to reproduce in silico secondary metabolic pathways of natural compounds.