awk '
NF == 3 {
        if(!($1 in rh)) {
                # Add a new row heading.
                row[++nr] = $1  
                rh[$1]
                if(length($1) > rw) rw = length($1)
        }
        if(!($2 in ch)) {
                # Add a new column heading.
                col[++nc] = $2
                ch[$2]
                cw[nc] = length($2)
        }
        # Add a datapoint.
        d[$1, $2] = $3
}
END {   printf("%*s", rw, "") 
        for(i = 1; i <= nc; i++) {
                if(cw[i] < 11) cw[i] = 12
                printf(" %*.*s", cw[i], cw[i], col[i])
        }
        printf("\n")
        for(i = 1; i <= nr; i++) {
                printf("%*.*s", -rw, rw, row[i])
                for(j = 1; j <= nc; j++)
                        if((row[i], col[j]) in d)
                                printf(" %*.6f", cw[i], d[row[i], col[j]])
                        else    printf(" %*s", cw[i], "")
                printf("\n")
        }
}' input

             CPLX9PC-4943     CpxID123     CpxID126 CPLX9PC-5763      CpxID13 CPLX9PC-6163 CPLX9PC-6164 CPLX9PC-6165
CPLX9PC-4943     1.000000     0.000000     0.000000     0.500000     0.000000     0.000000     0.040000     0.027027

             a            b            c
a     1.000000     2.000000     4.000000
b     2.000000     1.000000     7.000000
c     4.000000     7.000000     1.000000