Do not calculate the penalty. Mail form 5329 completing section ix but write your RMD amount on the dotted line on line 54 in parentheses preceded by RC so it looks like
RC (your RMD amount). Put zeros in boxed 54 and 55. Include a short statement that you have now withdrawn the RMD and why you missed it. This will probably result in the IRS waiving a penalty.
https://www.irs.gov/pub/irs-pdf/f5329.pdf