Although these initial structures should be slightly different from the optimal trigonal structure of (M)SubPc-3Cl(α), molecules can move and change their configurations during simulation from the initial structure. MD simulations can provide the total energy of the resultant assemblies as well as the magnitude of molecular fluctuations as the B-factor (temperature factor or Debye-Waller factor) used for color coding. B-factor is commonly used to represent the thermal fluctuations of atoms in the MD simulations of proteins, where blue and red indicate less and larger fluctuation, respectively. As shown in Figure , the fluctuation (red parts) of SubPc for the experimentally "NOT"-obtained structures becomes unevenly large with increasing temperature, which indicates that the assembly structure is distorted and not a stable packing. The total energy of the assembled structures confirms the higher stability of the experimentally obtained crystal structure (Table ). Although the total energy of structures indicates their stability, the B-factor allows us to understand the reason intuitively. Furthermore, the simulation results of rSubPc-3Cl(α), (M)SubPc-3Br(α), and rSubPc-3Br(α) (Figures 5b, S38a, and S38b) all well reproduced the experimental results. Thus, at a minimum computational cost, molecular design guidelines can accurately predict three-dimensional assembly structures (trigonal or P212121).