In this contribution we report on a study of conformation transitions in a cyclohexane in the temperature range from –100° to 1200°С. The bond charge molecular dynamics was used. To explain the results obtained, we have developed a method with the help of which the theory of electron pairs repulsion can be enlarged and be applied to cyclic molecules. The approach created reveals a hidden symmetry of spatial electronic structure which, in general, does not coincide with the symmetry of a visible atomic structure. However this spatial electronic structure presets an atomic structure and explains why a cyclohexane molecule has so unusual conformations as a boat and a chair.