One person, 100,000yen is high end. Two people I'd understand, but for that you can get a decent 3 bedroom apartment 30mins from Tokyo/Shinjuku station, or a largish single bedroom 15minutes from anywhere in inner Tokyo (chuo-ku, minato-ku, etc). One person, 60-70,000 would be about right.
Food is spot on. Utilities is right for one person, but if you were using a 100,000yen apartment right utilities would be about 35,000ish. Remember, internet and phone are 'utilities' too.
(I pay 10,000 electric, 5,000 gas, 3,000 water and sewage, 7,000 internet, 7,000 mobile phone - 3 bedroom flat with 3 people)
Transportation would be right at a glance - a trainpass would cost on average 8,000yen for a 30minute commute. BUT, you would go to places outside the pass from time to time, on average 500yen per trip (assuming around 250yen there and again same back). So maybe realistically 10-11,000.