Depending on which 'D' exactly must be replaced:

$_ =<<SQ;
ATOM   3316  N   TYR D  24      97.479  18.805   2.990  1.00 36.32    
+  D    N
ATOM   3322  CD1 TYR D  24      96.225  15.974   2.812  1.00 17.96    
+  D    C
SQ

s/(.+ CD1 .+) | (\b D \b)/$1 or X/gex;

__END__

STDOUT:
ATOM   3316  N   TYR X  24      97.479  18.805   2.990  1.00 36.32    
+  X    N
ATOM   3322  CD1 TYR D  24      96.225  15.974   2.812  1.00 17.96    
+  D    C
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Or in the other case:

$_ =<<SQ;
ATOM   3316  N   TYR D  24      97.479  18.805   2.990  1.00 36.32    
+  D    N
ATOM   3322  CD1 TYR D  24      96.225  15.974   2.812  1.00 17.96    
+  D    C
SQ

s/(?<!CD1 \s TYR \s)(\b D \b)/X/gx;

__END__

STDOUT:
ATOM   3316  N   TYR X  24      97.479  18.805   2.990  1.00 36.32    
+  X    N
ATOM   3322  CD1 TYR D  24      96.225  15.974   2.812  1.00 17.96    
+  X    C
[download]