title_body: Converting pdf with table of content to Kindle format
upvoted_answer: A few quick thoughts. 
  
  First, if you are using a Kindle Fire tablet, there is no need to do a conversion. just download a PDF Reader app from the app store and read the file that way. 
  
  If you are using an eink Kindle, I would suggest sending the PDF to the Kindle Personal Document Service which will do the conversion for you. (It's free and a cool feature in your kindle account): 
  
  https://www.amazon.com/gp/help/customer/display.html/ref=hp_pdoc_main_short_us?nodeId=200767340
  
  I haven't really looked at PDF conversions from the PDS; I'm guessing it will look really ugly. But I suspect the Kindle conversions to PDF are better than calibre's (although calibre might let you fine tune it). Using Kindle eink to read PDFs is usually a disappointing experience unless the document is short and very simple. 
  
  I glanced at the document. (I have made similar kinds of documents using Docbook XML). This document was optimized for PDF; you will lose a lot of formatting by trying to convert it -- though ironically it's pretty easy to convert it from Docbook XML to epub files. 
  
  To answer your question, the .opf is a file that stores epub metadata; apparently calibre needs to convert the PDF first to epub, and then reconvert it to the kindle .mobi format. That's why the end result is so horrifying. 
  
  Also: If you have access to an android tablet, you could upload the file to Google Play Books website and then read the PDF perfectly in the Google Play Books app on your device.