PRO 1
GLN 5.55112e-17
ILE -6.245e-17
THR 5.55112e-17

awk '{if($2!=1){print $1,"0"}else{print $0}}' file
PRO 1
GLN 0
ILE 0
THR 0

awk '$2!=1 {print $1,"0"} {print $0}' file
PRO 1
GLN 0
GLN 5.55112e-17
ILE 0
ILE -6.245e-17
THR 0
THR 5.55112e-17

awk '$2!=1 {print $1,"0"} {print $0}' file

awk '$2!=1 {print $1,"0"} $2==1 {print $0}' file

$ awk '$2!=1 {print $1,"0";next} {print $0}' file
PRO 1
GLN 0
ILE 0
THR 0

$ awk '$2 != 1 {print $1,"0";next}1' file
PRO 1
GLN 0
ILE 0
THR 0