Army officer in charge is a pain (5)
I believe the answer is:
colic
'pain' is the definition.
(colic is a kind of pain)
'army officer in charge' is the wordplay.
'army officer' becomes 'col' (I've seen this in other clues).
'in charge' becomes 'ic'.
'col'+'ic'='COLIC'
'is a' is the link.
(Other definitions for colic that I've seen before include "Severe abdominal pain" , "Intestinal infection" , "unpleasant gut feeling" , "Abdominal spasm" , "Early pain" .)