/usr/share/avogadro/builder/amino/d-arg.zmat is in avogadro-data 1.0.3-1ubuntu4.
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 11 12 13 14 15 16 17 18 19 20 21 22 23 | N 0.000000 0.000000 0.000000 0 0 0 -0.245284 N
C 1.481667 0.000000 0.000000 1 0 0 0.087761 CA
C 1.529928 105.545788 0.000000 2 1 0 0.217715 C
O 1.205646 130.286658 57.614229 3 2 1 -0.287208 O
C 1.542707 115.874819 120.040615 2 1 3 -0.026113 C
C 1.531084 111.478210 73.171062 5 2 1 -0.020371 H
C 1.537074 110.603980 179.765799 6 5 2 0.064706 H
N 1.498889 108.685588 179.194061 7 6 5 -0.276142 C
C 1.450128 114.105014 181.146931 8 7 6 0.376231 H
N 1.431841 113.882234 63.954343 9 8 7 -0.289263 H
N 1.298166 119.074381 244.360156 9 8 7 -0.129780 C
H 1.015136 111.023959 173.889632 1 2 3 0.141360 H
H 1.127731 108.119180 243.933087 2 1 3 0.055691 H
H 1.109154 110.119211 310.040602 5 2 1 0.028593 N
H 1.110256 109.607752 194.730396 5 2 1 0.028593 H
H 1.109448 109.990568 57.845188 6 5 2 0.029620 C
H 1.108283 110.834159 301.404336 6 5 2 0.029620 N
H 1.112879 110.268363 59.950746 7 6 5 0.065470 H
H 1.112989 110.538405 302.387050 7 6 5 0.065470 N
H 1.035320 110.553001 56.439623 8 7 6 0.257858 H
H 1.011937 115.589032 154.143651 10 9 8 0.254646 H
H 1.013845 116.289587 20.925783 10 9 8 0.254646 H
H 1.012953 120.630702 187.027441 11 9 8 0.306182 HA
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