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compunction (n.)

mid-14c., "remorse, contrition (for wrongdoing, as a means of attaining forgiveness of one;s sins)," from Old French compunction (12c., Modern French componction), from Late Latin compunctionem (nominative compunctio) "remorse; a stinging or pricking" (of the conscience), noun of action from past-participle stem of Latin compungere "to severely prick, sting," from com-, here perhaps an intensive prefix (see com-), + pungere "to prick, pierce" (from suffixed form of PIE root *peuk- "to prick").

The Latin word was used in a figurative sense by early Church writers. Originally a much more intense feeling, similar to "remorse," or "contrition."

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Definitions of compunction from WordNet

compunction (n.)
a feeling of deep regret (usually for some misdeed);
Synonyms: remorse / self-reproach
From wordnet.princeton.edu