Nanoparticle surfaces are passivated by surface-bound ligands, and their adsorption on synthesized nanoparticles is complicated because of intricate and low-symmetry surface structures. Thus, it is challenging to precisely investigate ligand adsorption on synthesized nanoparticles. Here, we applied a machine-learning-accelerated ab-initio calculation into experimentally resolved 3D atomic structures of Pt nanoparticles to analyze the complex adsorption behavior of polyvinylpyrrolidone (PVP) ligands on synthesized nanoparticles. Different angular configurations of the large-sized ligands are thoroughly investigated to understand adsorption behaviors onto the various surface-exposed atoms with intrinsic low-symmetry. It is revealed that long-range van der Waals interaction (EvdW) shows weak negative relationship against generalized coordination number (-CN-), in contrast to the positive relationship in short-range direct bonding (Ebind), which attenuates the correlation between ligand binding energy (Eads) and -CN-. In addition, the PVP ligands favor to adsorb at which the long-range vdW interaction with surrounding surface structure is maximized. Our results highlight the significant contribution of vdW interactions and importance of local geometry of surface atoms to adsorption behavior of large-sized ligands on synthesized nanoparticle surfaces.