Yes, many of the places that are featured in Persona 5 are real locations from our world. Unlike the past games that were either based on a real place or something completely fictional, Persona 5 is largely based on the real-world city of Tokyo. As such, many of the places that you visit in the game are also really like Shibuya, Akihabara, and many more wards and cities that you visit in that game. Even the train station and some of the streets that you go on are derived from their real-world counterparts. For example, Cafe Leblanc is the home of the protagonist, Joker, and while the name is different, there is a cafe that you can visit in the real world that looks the same as the one in the game. The cafe is called Rain on the Roof and is found in the Setagaya ward of Tokyo. While the neighborhood of Yongen-Jaya is fictional, it is based on the actual Sangen-Jaya neighborhood in Setagaya.