on run.py module:

1. line 46:
   self.db.users.update_one( {'chat.id': message.chat.id}, {'$set': message.json}, upsert=True )
   should be:
   db.users.update_one( {'chat.id': message.chat.id}, {'$set': message.json}, upsert=True )
   since you relocated the db to separate folder again from the Bot class so we should remove self from the beginning of it

2. I'm not sure about this one but I guess we should also remove last line of code in run.py (nashenas_bot.run()), since we don't have run attribute for our class anymore, so I guess you forgot to remove it as well.