If you've held the stock for more at least one year, you are correct, and you will be able to deduct the Fair Market Value of the donation.
However, if you have held the stock for less than one year, it is short term capital gains property, and you can only claim your basis as a deduction. See page 11 of this link: https://www.irs.gov/pub/irs-pdf/p526.pdf.
As long as you've held the property for one year, the amount that you enter for the basis will not affect your deduction.
