By "Due Diligence Fee" are you talking about the earnest money that you typically include with your initial offer?
When I was house shopping I always provided 1% of the purchase price, rounded off to a whole number. For example if I was offering $295k I would put $3,000 earnest money.
According to my agent 1% is fairly standard, although she wasn't a very good agent, I ended up firing her after several of my offers were rejected, so maybe I should have been putting up more.
Ask your agent what is considered common in your area. Remember the money goes toward the purchase if the deal goes through and you get the money back if the seller doesn't accept your offer, so don't be afraid to go a little higher if you aren't sure.