Sorry, I fell asleep and could not upload during the weekend.
So, the answer is University of Tokyo.
It seems their Hongo campus also has this same restaurant.
I went to their Komaba campus, which is third station from Shibuya by local train on Keio-Inokashira line.
The lunch is.... salad, main ( you can choose one from meat, fish or pasta) and bread for 800 yen.
I think coffee was 200 yen, if you order lunch. Dessert is not included, but it sounded so tempting and we both ordered dessert. In the campus, it is located in Faculty House.
I ordered fish for main. It was good deal. Also, it is nice to walk around in the campus. They have trees and some historical buildings. I found museum also. Since I did not have time, this time I couldn't stop by, but next time, I will check out the museum !