The study of key molecular mechanisms of mitochondrial dysfunctions, which are responsible for neurodegenerative diseases, is a critical step to assist for the diagnosis and therapy success. In this regard, we suggest an alternative of treatment on neurodegenerative disorders-based on Single-Walled Carbon Nanotubes (SWCNT) as potential mito protective -(Phe)-F0-ATPase targeting nanoparticles toward Precision Molecular Nanomedicine against pathological ATP-hydrolysis conditions. Herein, we used ab initio computational simulation to analyze the structural and electronic properties from SWCNT-family with zigzag topologies (n, m - Hamada indices n > 0; m = 0) like: SWCNT-pristine, SWCNT-COOH, SWCNT-OH, SWCNT-monovacancy interacting with the critical (Phe)-residues of the mitochondrial F0-ATPase and using oligomycin A (specific Phe-F0-ATPase inhibitor) as reference control. Then, we show that the SWCNT-family can be potentially used to selectively inhibit the (Phe)-F0-ATPase activity liked to pathological mitochondrial ATP-hydrolysis associated to human neurodegenerative disorders by using DFT-ab initio simulation. The in-silico results suggest the formation of more stable complexes of interaction following the order: SWCNT-COOH/F0-ATPase complex (1.79 eV) > SWCNT-OH/F0-ATPase complex (0.61 eV) > SWCNT/F0-ATPase complex (0.45 eV) > SWCNT-monovacancy/F0-ATPase complex (0.43 eV) based on the strength of the chemisorption interactions. These theoretical evidences open new horizons towards mito-target precision nanomedicine.