There is a similar web page, U.S. Merchant Ships Sunk or Damaged in World War II (http://usmm.org/shipsunkdamaged.html) that lists Captain Moore's book as one of its numerous sources.
Neither of these web pages include a ship named SANTA CLARA as one of the ships sunk during World War II, either at Normandy or any other location.
This web page, List of ships of the United States Army (http://en.wikipedia.org/wiki/List_of_ships_of_the_United_States_Army) lists a number of US Army Transport ships including ships named USAT SANTA BARBARA, USAT SANTA MARIA and USAT SANTA ROSA but no USAT SANTA CLARA.
According to this web page, http://www.transchool.eustis.army.mil/MUSEUM/Mulberry.htm, the four US Army transport ships that carried troops to Normandy during June 1944 were:
USAT BORINQUEN (your ship)
USAT GEORGE S. SIMONDS
Further research for a ship named SANTA CLARA, however, yields some interesting information. There was a ship named the SUSAN B. ANTHONY (AP-72) that sank at Normandy after hitting a mine; that ship had originally been named SANTA CLARA. See, for example, this page from the U.S. Navy's Dictionary of American Naval Fighting Ships, http://www.history.navy.mil/danfs/s20/susan_b_anthony.htm. The description of the loss of this ship is very similar to your recollection, except that there was no loss of life in the sinking.
A similar although shorter description is found at http://history.navy.mil/photos/sh-usn/usnsh-s/ap72.htm in which the ship is referred to as the USS SUSAN B. ANTHONY. USS, of course, designates a ship of the U.S. Navy so presumably it would be improper to refer to this ship as USAT, which designated ships belonging to the U.S. Army Transportation Service. This fact may also explain the absence of this ship from the first two web pages mentioned at the beginning of this message. The two pages speak of merchant ships lost during World War II, whereas the USS SUSAN B. ANTHONY would be a naval vessel, not a merchant vessel.
So your general recollection is correct but the ship was known by a different name at the time.
Ron Carlson, Webmaster
Armed Guard website www.armed-guard.com