Energy-filtered quantitative electron diffraction at liquid nitrogen temperature has been used to examine the atomic structure and bonding of metastable alpha-Cu phthalocyanine crystals. Three theoretical methods (kinematic, kinematic with excitation errors and Bloch wave) were employed for the intensity calculations. The Bloch-wave method was found to account for dynamical effects by greatly reducing the residual factor between experimental and simulated results. A new method for calculating electron scattering factors for partially charged ions is proposed and the sensitivity of electron diffraction to charge transfer is discussed. The atomic charge states were analyzed for alpha-Cu phthalocyanine using a charge cloud model in which the Gaussian bond charge is positioned along the bonds. Spot patterns were collected in the Kohler mode at two beam energies to reduce error. Using the best-fitting model, a deformation charge-density map is produced and compared to the neutral-atom model. From this, the main features of atomic charge transfer in the alpha-Cu phthalocyanine structure can be seen in the (010) plane.