Covalent organic frameworks (COFs) have attracted much interest due to their utility as functional materials. Unfortunately, experimental synthesis struggles with low single crystallinity of COFs. We have theoretically investigated isomer structures of a representative two-dimensional COF for both monolayer and three-dimensional stacking orders. We show that rotations of p-phenylene rings are common in monolayers, however, affect the global stacking order substantially. We also discuss the discrepancy between powder X-ray diffraction patterns corresponding to the structures predicted by our calculations and those experimentally observed. The discrepancy demonstrates the importance of dynamics in the self-assembly process of COF organic components. (C) 2016 Elsevier B.V. All rights reserved.