It's a vary simple solution, it sorts based on the first number in (), I hope that there are no () signs before the third column.

Unfortunately, this does not work for the same index number repeated more then once. If I find some time, I'll try to find a better solution. Until then, maybe this will help. Feel free to ask any questions.

#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my %lines;

while (<DATA>) {
    /
        \(      # find the first ( sign
        (\d+)   # then, capture the number in the brackets
    /x;
    
    $lines{$1} = $_;
}

#print Dumper %lines;

for (sort {$a <=> $b} keys %lines) {
    print $lines{$_};
}

__DATA__
1opj-A    100.0    M309(67)*    F401(159)*    Y340(85)
2hyy-A    99.2    F382(147)*    M290(55)*    M309(67)
2pl0-A    48.3    Y318(88)*    F383(159)*
1xbb-A    42.0    L501(134)*    A400(38)*
1t46-A    39.4    K623(59)*    M309(67)*
2oiq-A    48.9    M314(59)*    Y340(85)*
[download]

The output:

2oiq-A    48.9    M314(59)*    Y340(85)*
1opj-A    100.0    M309(67)*    F401(159)*    Y340(85)
2pl0-A    48.3    Y318(88)*    F383(159)*
1xbb-A    42.0    L501(134)*    A400(38)*
2hyy-A    99.2    F382(147)*    M290(55)*    M309(67)
[download]