k θ , θ, and θ 0 are an angle parameter, angle, and equilibrium angle. The fifth term is the dihedral potential between four atoms. k χ , η, and δ are dihedral angle parameters, and χ is a dihedral angle. Note again that we treat atom i as a density while other atoms are treated as points in the equation (7). The explicit forms of differentials, that is, -∇ϕ are described in supplemental information 3. Then, we calculate coordinates of each atom by Gaussian fitting as shown above.