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I wish to obtain a list of all known enzymes and then get rid of the ones that use cofactors, the ones that use ATP, and a few others. What is the easiest way to do this?

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You should be able to filter the UniProt database for this. For example, this search query:

ec:* NOT cofactor:(chebi:*) NOT annotation:(type:"catalytic activity" atp) AND reviewed:yes

...gives you all manually curated (reviewed:yes) enzymes (ec:*) that don't have a cofactor (NOT cofactor:(chebi:*)) and don't catalyze reactions with ATP (NOT annotation:(type:"catalytic activity" atp)).

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