I installed pycharm normally via bin/pycharm.sh, but the mistake I made was doing bash pycharm.sh while the pycharm directory has inside the D
First start pyCharm from it's bin folder via command line
$ ./pycharm.sh
Then, goto
Tools -> Create Desktop Entry.
It will create a correct Desktop file in the correct place. Afterward you can initiate it from the menu and pin the icon or drag and drop it to the bar. This way, you don't have to deal with .desktop files and mumbo jumbo..