Threonine
    Glutamine
    Alanine
    Asparatate
    Glutamine
    Alanine
    Threonine

[ Alanine ]
    89.1    13.7    -3.12   -10.09
    [ Asparatate ]
    133.1   30  -2.43   -10.35
    [ Glutamine ]
    146.1   42.7    -3.46   -10.23
    [ Threonine ]
    119.1   28.5    -2.43   -9.99

[ Threonine ]
    119.1   28.5    -2.43   -9.99
    [ Glutamine ]
    146.1   42.7    -3.46   -10.23
    [ Alanine ]
    89.1    13.7    -3.12   -10.09
    [ Asparatate ]
    133.1   30  -2.43   -10.35
    [ Glutamine ]
    146.1   42.7    -3.46   -10.23
    [ Alanine ]
    89.1    13.7    -3.12   -10.09
    [ Threonine ]
    119.1   28.5    -2.43   -9.99

awk 'FNR==NR { a[ "\[ " $1 " \]" ]; next } /^[/ { f=0 } { for (i in a) if ($0 ~ i) f=1 } f' file1.txt file2.txt > output.txt