unable to see my anything in database pycharm
you do not need to go to Create New -> Data Source -> SQlite(Xerial). 
if your setting.py database config is as is ('ENGINE': 'django.db.backends.sqlite3')  the database is autogenerated when you run makemigrations  then migrate.
to recreate the database (you said you deleted):

remove previous migrations (delete all files in your app's migration folder except the init.py)
Ctrl+Alt+R (or tools -> run manage.py)
then in the manage.py terminal run makemigrations andmigrate`

a new database will be created and migrations applied......... you dont have to worry about seeing the entries in the database directly.
If you're able to create superuser and login to the admin site and manipulate model data, then you're up and running
I really am at a loss here. I am using Pycharm 5.0.4 and running a virtual env with Python3 and Django 2.0.1. 
I am trying to get my database up and running for my project, but no matter what I do I cannot seem to get anything to show up in the database tool window drop down in Pycharm. I have 'ENGINE': 'django.db.backends.sqlite3' set in my settings.py, and in Pycharm i am going to:
 Create New -> Data Source -> SQlite(Xerial). 
I then makemigrations and migrate but nothing shows up in the database. I can even go to the project website and succesfully add/create models in the admin site. But I cannot figure out where they are or see them...   
It was working at one point but I deleted my database because I was getting some errors and now I am trying to recreate it.