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
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
|