• Microscopic 3D Structure Generation. Generating microscopic 3D structures involves creating irregular 3D geometry, along with graph-based structures for molecules and sequencebased structures for peptide chains, making it significantly more challenging than generating common 3D structures, such as 3D point clouds. Moreover, most existing methods rely on unconditional generation, where a large number of microscopic structures are first generated without specific constraints, and then another method is applied to filter out potentially useful structures. Directly generating microscopic structures based on given conditions would be highly beneficial for drug and material design .