The correct option is D Q P S R
Q follows the subject "the clerk" because the words "left the money" refer to an action performed by the clerk.
P follows Q as "on the desk" indicates the place where "the money" was kept.
S follows P as the which-clause (which he should have...) forms the second part of the sentence. The sentence is formed by a clause that depicts a real situation, versus a clause that depicts a hypothetical one (should have).
R follows S as the words "in the safe" tell the place where "he should have locked up".
Hence the logical sequence is QPSR: The clerk left the money on the desk which he should have locked up in the safe.
Hence option D is correct.
Options A, B and C are incorrect because they do not form a logical sequence.