Abstract The inclusion complexes of AQ and CQ with the different native cyclodextrins (α, β and γ-CD) have been analyzed by using molecular docking with the help of Patch-Dock server. The guest molecules such as AQ and CQ along with different native CDs as the host has been organized by AM1 method. An interaction has been proposed in virtual state based on the data obtained through docking outcome. According to geometric shape complementarity score, approximate interface area size of the complex and atomic contact energy for the obtained supramolecular complexes of the chosen guest with three different native CDs, the structure has been provided and compared with each other for the applications such as anti-bacterial activity and so on.