Most open access journals require authors to pay the article processing fees only after their paper has been accepted for publication. This is because an average manuscript goes through multiple journals and rounds of peer review before it is accepted, and authors cannot be expected to pay for each submission. Only journals of questionable reputation would ask for the processing fee to be paid at the time of submission.
Unfortunately, there are several such questionable journals that are offering authors rapid and guaranteed publication while charging exorbitant fees, and unwitting authors fall prey to these unethical practices. Being indexed in PubMed is not a definite indicator that the journal is from a legitimate and trustworthy publisher. There are several other criteria that should be considered while selecting a journal, to ensure that it is not a "predatory" or questionable journal. Our interview with Jeffrey Beall will give you more information about predatory journals and how to identify them.
You should evaulate the journal you have submitted to against these criteria. If the journal seems questionable, I'm sad to say you might have to forego the money you have transferred. On the bright side, since the paper has not been officially submitted, you can resubmit to another journal without fear of it being considered duplicate submission.
Make sure you study the next journal you submit to well before submitting. The best way is to consult a senior colleague or submit to a journal that's well read by other researchers in your field. Hope this helps!