We present isomerism in a few supramolecular adducts of atomically precise nanoparticles, [Ag29(BDT)12∩(CD) n]3- ( n = 1-6), abbreviated as I where BDT and CD are 1,3-benzenedithiol and cyclodextrins (α, β and γ), respectively; ∩ 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 (α, β and γ) encapsulate a pair of BDT ligands protecting the Ag29 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.