Despite the fact that protein chemistry occurs in solution, studying the structure of desolvated proteins in mass spectrometry vacuum conditions allows one to study biological molecules in complete isolation. The electrospray ionization process results in charged protein conformers for which the charge locations distribution and the corresponding structure are not known. In this paper, we explore the influence of different charge distributions on the structure of conformers of ubiquitin 6+ in the vacuum conditions of mass spectrometry. Using the Tinker implementation of the AMBER99FF force field, the atomistic lowest-energy structures for those charge distributions were calculated by the DEEPSAM algorithm. Differences among the calculated structures are analyzed and discussed in terms of the relation to experimentally observable ion mobility mass spectrometry cross sections. They also are compared to the neutral ubiquitin's native structure and to the nearly linear structure of the ubiquitin 13+ ion. In general, different charge distributions lead to substantially different structures and ion mobility cross sections. In this study, however, it was found that this is not always the case. Our conclusion is that measurements of ion mobility cross sections cannot be used to help determine a unique charge distribution because different charge distributions lead to structures that approximately agree in terms of experimental cross sections.