Jack's "left over" was an omen (9)
I believe the answer is:
portended
'jack's left' is the definition.
Although both the answer and definition are past participle verbs, I cannot see how one could define the other.
'over was an omen' is the wordplay.
'over' means one lot of letters go next to another (in a down clue, some letters go over others).
'was an' becomes 'ed' (I can't justify this - if you can you should give a lot more credence to this answer).
'omen' becomes 'portend' (synonyms).
'ed' after 'portend' is 'PORTENDED'.
Can you help me to learn more?
(Another definition for portended that I've seen is " forecast".)