Actually, the concept of stop words no longer exists with semantic search. These words are now found as important factors in determining search intent. Yes, for the most part, a, as, it, they, and so forth are words with less importance overall, however, they are no longer ignored. As well, their proximity to keywords becomes very important in determining semantic search intent.
This was a lesson learned in 2008 with all the research work found in Scholar. You will notice that Scholar has disappeared. This is because Scholar has been rolled into the Google search algorithms over the years and is no longer needed. During this process, it was discovered that stop words have value and began to be indexed to support citations and semantic intent.
Now to answer your question: Since stop words are no longer a factor, Google, Bing, and Yahoo! can fairly easily determine the intent of it as you wrote it. There are still some growing pains in other languages, but for English content, this whole process works extremely well.
If you listen to Google carefully over the past couple of years with Panda, Penguin, and so forth, there is a subtle message to stop thinking in terms of keywords per se' and focus on conversational title tags, header tags, links, and using keywords less as keywords to manage but rather as natural elements of the content where each HTML element supports the content overall.
Recently, Google has been discounting lists of keywords favoring natural uses. I found that even with semi-conversational uses of lists, performance can drop. I had to adjust sentences like Research domain example.com whois, dns, IP address. and drop the listed words whois, dns, IP address leaving only Research domain example.com.. Google is rewarding not using keywords in this manner and successfully finds the search intent by finding these keywords in the content thus increasing keyword importance within content. I did not lose the value of whois, dns, and IP address as a result. It actually increased because these terms are found in the content rather than in HTML elements such as title, headers, etc. In content, use of keywords has increased importance.
Why did I tell you this? Simple. Google is seriously focusing on conversational uses within tags and content more these days and is able to more accurately determine content topic and value. Google is trying to erase traditional SEO keyword manipulations thinking that discounting keyword focus is a major step toward stopping spamdexing. Google has been stressing using conversational HTML elements and not to focus on older SEO ideologies. Google is rewarding the use of conversational title tags and header tags. They no longer want you to think in terms of keywords and focus on natural content.
Final Thought: Do not worry about keywords as we have been trained to do. (Old habits die hard.) Yes, pay attention to the keywords you use, but make them a natural part of developing content and not as something to manage. Do not worry about how you use keywords as clues to search engines but rather if you are reflecting your topic accurately with the words (not keywords) you chose.