Head-Mounted Displays (HMDs) based Virtual Reality (VR) has shown promising results in training and education. We present ATOM, an HMD-VR interface to educate students about atoms, atomic structures and historical research experiments conducted in understanding atomic structures. ATOM is designed to complement the classroom learning for grade 9 students through an interactive and practice-based learning experience. Preliminary evaluation with 10 students revealed higher interest, increase engagement and playfulness. The students also pointed out a few difficult user interactions. © 2020 Owner/Author.