Kamisama Nanka Shinjinai Bokura No Eden summary:

One day, science-loving wallflower Shikito Takai smells an overwhelmingly alluring scent coming from his classmate Kaito Nishio, whom he's always admired. Then, when Nishio becomes flushed and weak during gym class, Shikito tries to take him to the Nurse's office, but the two somehow end up in the disused equipment storeroom...This is the story of the human race's first Alpha and Omega, the inception of the omegaverse.+