Don't put anything in box 2a.
If this is a QCD (Qualified Charitable Distribution - i.e., where the IRA trustee sent the money directly to a charity) AND if you are 70 1/2 or older, then in the screens after you enter the 1099-R, you will be asked a series of questions in which you will indicate that the money went to charity. Whether or not it was your RMD amount won't affect its taxability.
Once you answer these questions, the QCD amount will be removed from income (the amount will appear on line 4a but not 4b).