I am using this to compare with X-ray crystallography experiment. Indeed with an independent atom approach, the partial charge cannot be deduced unless atomistic forcefield is used, like AMBER and CHARMM.

@jezzo for your suggestion. I have just updated my inquiry to specify my interest.

Thank you Karsten. I am exploring Phenix and fmodel generates structure factor from pdb. However, I fail to find a way to turn structure factor into electron density. Although I can take its square norm of its fourier transform as electron density, my result will be off by some normalization constant. Do you happen to know the exact command/function?