In the Settings/Preferences dialog (Ctrl+Alt+S), select the page Vagrant, and enter the Vagrant executable and Vagrant instance folder.
Pay attention to the Vagrant menu commands under the Tools menu. These commands correspond to the standard Vagrant actions. Once a Vagrant box is created, you have to initialize it in project root. To do that, on the main menu, point to Tools | Vagrant, and then choose Init in Project Root.
Choose the folder, if required. Note that you have this choice if there are several projects opened in the same window. Choose the Vagrant box you are going to initialize.
Now open the Settings/Preferences dialog again and select the page Project Interpreter. Here you can select an interpreter from the drop-down list, but what if none of the suggested interpreters meets your needs? Then click the icon to define your own one. Select Add on the drop-down menu.