This file is indexed.

/usr/share/avogadro/builder/amino/l-lys.zmat is in avogadro-data 1.2.0-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

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N    0.000000    0.000000    0.000000     0   0   0   -0.245286  N 
C    1.459393    0.000000    0.000000     1   0   0    0.087661  CA
C    1.537672  106.336501    0.000000     2   1   0    0.217713  C 
O    1.229837  123.227953  331.496556     3   2   1   -0.287208  O 
C    1.535060  110.372261  238.164665     2   1   3   -0.028924  CB
C    1.531314  113.836266  185.561189     5   2   1   -0.050050  CG
C    1.531595  111.227291  172.438450     6   5   2   -0.040588  CD
C    1.528038  111.240051  176.230006     7   6   5   -0.006904  CE
N    1.457086  110.332149  178.516026     8   7   6   -0.329979  NZ
H    1.096504  108.181007  117.239114     2   1   3    0.055690  HA 
H    1.098059  109.714858   63.032582     5   2   1    0.028494  HB1
H    1.097766  108.930102  307.109066     5   2   1    0.028494  HB2
H    1.096488  109.865841   51.099389     6   5   2    0.026628  HG1
H    1.095478  109.820539  293.059055     6   5   2    0.026628  HG2
H    1.097377  109.512162   54.771009     7   6   5    0.027743  HD1
H    1.097445  109.318754  297.704958     7   6   5    0.027743  HD2
H    1.095155  110.197444   58.012815     8   7   6    0.042179  HE1
H    1.095641  110.131205  299.292074     8   7   6    0.042179  HE2
H    1.019091  109.537734  175.981666     9   8   7    0.118213  HZ1
H    1.019298  109.886289   59.525834     9   8   7    0.118213  HZ2
H    1.016043  117.249529   26.480655     1   2   3    0.141360  H