We present isomerism in a few supra molecular adducts of atomically precise nanoparticles, [Ag-29(BDT)(12)boolean AND(CD)(n)](3-) (n = 1-6), abbreviated as I where BDT and CD are 1,3-benzenedithiol and cyclodextrins (alpha, beta and gamma), respectively; boolean AND symbolizes an inclusion complex. The different host-guest complexes of I were characterized in the solution state as well as in the gas phase. The CDs (alpha, beta and gamma) encapsulate a pair of BDT ligands protecting the Ag-29 core. This unique geometry of the supramolecular adducts makes the system similar to octahedral complexes of transition metals, which manifest various isomers. These isomers of I (n = 2-4) were separated by ion mobility mass spectrometry (IM MS). We proposed structures of all the inclusion complexes with the help of IM MS measurements and molecular docking, density functional theory (DFT), and collision cross section (CCS) calculations.