At Antietam/Sharpsburg, the 5th South Carolina was attached to Jenkin’s Brigade, Jones’s Division.
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Jones' Division
BG David R. Jones

Jenkins' Brigade
Col Joseph Walker

1st South Carolina (Volunteers): Ltc Daniel Livingston (w)
2nd South Carolina Rifles: Col Robert A. Thompson
5th South Carolina: Cpt Thomas C. Beckham
6th South Carolina: Cpt Edward B. Cantey (w)
4th South Carolina Battalion: Lt W. T. Field
Palmetto (South Carolina) Sharpshooters: Cpt Alfred H. Foster (w), Cpt Franklin W. Kirkpatrick

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Here are two reports from the OR which note the 5th’s participation, see:

http://ehistory.osu.edu/books/official-records/027/0905
OR V19, Pt. 1, Ser. 27 pp. 905-8

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Inasmuch as Colonel Walker’s Jenkin's Brigade after action report did not call out the 5th South Carolina, Company F, or any other company, as it had for the 1st South Carolina, I would believe Company F was present.

I have checked the records for the officers of Company F, and find only Lt. Allison is recorded as having been wounded and captured at the battle.

However, Lt. Black who was commanding the company at the time, was shortly thereafter, court-martialed and cashiered from the service, November 23, 1862. There is nothing in the record revealing the charges against him nor of participation in the battle.

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Hugh J. Allison, 1st Sergeant, (2nd) Company F, 5th Regiment South Carolina Infantry, appointed 3rd Lieutenant, September 9, 1862, wounded in the battle of Sharpsburg, Md., September 17, 1862, believe captured and admitted to a Federal hospital near Sharpsburg, not dated, paroled in Maryland and exchanged November 8, 1862, at Aikens, Va.

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I checked the records of a few men of Company F and found nothing about Sharpsburg. What is the name of your ancestor in the company?