I tried to use Navicat with MongoDB Atlas but I couldn't and after doing some search, I found a way to do it and I hope it'll help anyone. Here's the steps to connect MongoDB Atlas
with Navicat
From MongoDB Atlas's Dashboard
Choose Connect your application
Then pick the version 2.2.12 or later
On Navicat click connection, then MongoDB
Pick the SSL
tab and make sure to enable Weak certificate validation
Click on URI on the bottom and enter the URI you got from MongoDB