There’s literally thousands of anime that are good and that aren’t from shounen mags. It’s a vague criteria to recommend for, especially since anything can run in a shounen mag nowadays.
Since you like books, you may like some of the works that focus on or are heavily referential to literature. Bungaki Shoujo and Mawaru Penguindrum are respectively true to those two categories. Some of the tales within Kino no Tabi are very much of the same appeal as topics found in books, being that it was originally a book.The movies Harmonie and Eve no Jikan would probably be good to watch too.
Aside from that, here’s some generic recommendations:
Usagi Drop, Kawaisou, Plastic Memories, Kaiba, Kowarekake no Orgel, Hourou Musuko, Haibane Renmei.