We apply a model for analyzing the importance of variations conformational charge flux to 11 molecules with the R-(CH2)(n) -R structure (R = Cl, F, OH, SH, COOH, CONH2, and NH2 and n = 4-6). Atomic charges were obtained by fitting to results from density functional theory calculations using the HLY procedure, and their geometry dependence is decomposed into contributions from changes in bond lengths, bond angles, and torsional angles. The torsional degrees of freedom are the main contribution to the conformational dependence of atomic charges and molecular dipole moments, but indirect effects due to changes in bond distances and angles account for similar to 15% of the variations. While the magnitude of charge flux and geometry effects have been found to be independent of the number of internal degrees of freedom, the nature of the R- group has a moderate influence. The indirect effects are comparable for all of the R-groups and are approximately one-half the magnitude of the corresponding effects in peptide models. However, the magnitudes are different, yet the relative importance of geometry and charge flux effects are completely similar to those of the peptide models, which suggests that modeling the charge flux effects for changes in bond lengths, bond angles, and torsional angles should be considered for developing improved force fields.