No, you may not.
The relevant sections of the tax code are in Pub561 and Pub526. Basically: the IRS would consider your custom website to have a FMV of $0, because it couldn't be sold to anyone else.
If you made a genuine software tool that was applicable to more than just the charity (and you successfully sold copies of that software), then the FMV would be the purchase price of the software in the open market.
There was a law passed in 2004 (can't remember which, sorry) that cracked down on the charitable donations of intangible property.
[1] http://www.irs.gov/publications/p561/index.html
[2] http://www.irs.gov/publications/p526/index.html