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I am a bit confused. What has this anything to do with your original question? vim-pathogen is for Vim editor itself, not for PyCharm. I don't know much about MacOS, so not sure how to help. Did you try the installation steps at https://github.com/tpope/vim-pathogen ?
But there are alternative plugin systems. My favorite is https://github.com/junegunn/vim-plug . I guess you should be able to install it with the instructions for "Unix, Linux", as MacOS would fall into that category. Make sure you install the right one Vim or Neo Vim, depending on which one you use.