/usr/share/avogadro/builder/amino/d-ala.zmat is in avogadro-data 1.0.3-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 | N 0.000000 0.000000 0.000000 0 0 0 -0.245562 N
C 1.476870 0.000000 0.000000 1 0 0 0.084861 CA
C 1.538499 111.699687 0.000000 2 1 0 0.217436 C
O 1.207703 129.348104 21.172179 3 2 1 -0.287218 O
H 1.127469 108.301021 241.128641 2 1 3 0.055413 H
H 1.017794 111.654185 294.669100 1 2 3 0.141350 HA
C 1.528100 110.672677 121.026523 2 1 3 -0.041085 CB
H 1.097874 111.357391 175.165484 7 2 1 0.024935 HB1
H 1.101438 110.112786 55.964180 7 2 1 0.024935 HB2
H 1.096834 112.687507 296.676601 7 2 1 0.024935 HB3
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