Shell Programming and Scripting

...... 
ATOM     91 H2'' G   A   3      17.357   8.753 -30.401  1.00   0.00           A 
ATOM     92  O2' G   A   3      16.590   9.059 -28.495  1.00   0.00           A 
ATOM     93  H2' G   A   3      16.670   9.792 -27.880  1.00   0.00           A 
ATOM     94  O3' G   A   3      16.875  11.895 -29.146  1.00   0.00           A 
ATOM     95    P U   A   4      17.646  13.251 -28.975  1.00   0.00           A 
ATOM     96  O1P U   A   4      18.619  13.509 -30.118  1.00   0.00           A 
ATOM     97  O2P U   A   4      18.188  13.245 -27.547  1.00   0.00           A 
.......

...... 
H3'   T     1.32 
C2'   T     2.01 
H2''  T     1.34 
H2'   T     1.34 
O3'   T     1.77 
P     G     2.15 
O1P   G     1.70 
O2P   G     1.70 
O5'   G     1.77 
H2''  G     1.34 
......

awk 'NR==FNR{a[$1FS$2]=$3;next}{print $0,a[$3FS$4]}' file2 file1

#!/bin/sh

cat /dev/null > file3
while read line1; do
  c1=$(echo ${line1} | cut -d' ' -f3-4)
  while read line2; do
    c2=$(echo ${line2} | cut -d' ' -f1-2)
    if [ "${c1}" = "${c2}" ]; then 
      echo "${line1} $(echo ${line2} | cut -d' ' -f3)" >> file3
    fi
  done < file2
done < file1

exit 0

awk '
		NR==FNR{   				# process first file(file2 as reference file)
				a[$1FS$2]=$3		# store file2 field $3 information in array a indexed by key $1FS$2 where FS is the original field separator
				next			# process next line
			}
			{				# process second file (file2)
				print $0,a[$3FS$4]	# print each line and the array a element where the key is $3FS$4 from second file(3rd and 4th field divided by FS)
			}
	' file2 file1