i recently had "the talk" with two of my boys (and I thought Daddy would have covered it, but unfortunately it came up when he was away) so I feel for you this is a very difficult situation.
I would suggest that first you, gently, sit down and fully explain what "sex" is, use correct medical terms and explain to her what you believe is appropriate for her to understand. I gave a full explanation of all male and female parts, and how a man and a woman have intercourse. by confronting her and asking her about what she knows, she has already become defensive so you need to take the lead and just tell her about it, by you discussing it in a very relaxed manner, it will leave room for her to talk about what she is confused about. and by you taking the lead you will also show her that it is okay to talk about it, and what terms are appropriate to use when sex is discussed. after you explain it to her ask her if she has any questions, and if she isn't being defensive, then you may ask how all that you have talked about relates to what you found in the note/letters. you may also want to discuss what about sex is appropriate for her at her age, for ex. I told my boys that sex was for a husband and wife ( a biblical definition based on our beliefs) and that it sex was something that God created for our pleasure. meaning that it is not a bad thing or a dirty thing, but a good thing and when it was appropriate for them to have sex. I also might encourage you to give your daughter the words to say if/when someone approaches her about sex, so that she feels safe and comfortable saying "no" It seems that she has had some communication about sex with someone some where, and she isn't comfortable telling you about it, so you need to lead her to fully understand what sex is about and what an appropriate response to it. She may come around and tell you more info after she has had time to digest it all.
hang n there! feel free to PM me if you need some discussion ideas, it caught me completely off guard when I had to have the "talk" but it really went a lot easier than I thought it was going to go when it happened. I also talked to both of my boys separately so that they would have each of their questions answered without distraction of what the other brother was thinking.