/usr/share/avogadro/builder/amino/d-val.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 11 12 13 14 15 16 | N 0.000000 0.000000 0.000000 0 0 0 -0.245026 N
C 1.482917 0.000000 0.000000 1 0 0 0.089955 CA
C 1.526578 105.880998 0.000000 2 1 0 0.217973 C
O 1.205383 129.232375 242.836109 3 2 1 -0.287198 O
H 1.126351 108.107859 245.468510 2 1 3 0.055950 CB
H 1.018711 110.943956 289.827928 1 2 3 0.141370 CG2
C 1.557080 115.533191 122.195735 2 1 3 -0.022712 CG1
H 1.120368 108.054900 301.105019 7 2 1 0.031517 HA
C 1.530035 110.273465 182.599274 7 2 1 -0.060794 H
H 1.096352 112.235005 300.139265 9 7 2 0.023293 HB
H 1.097074 111.103343 180.248418 9 7 2 0.023293 HG21
H 1.096883 112.083396 61.007768 9 7 2 0.023293 HG22
C 1.530292 110.197606 59.956600 7 2 1 -0.060794 HG23
H 1.096269 111.998079 55.775763 13 7 2 0.023293 HG11
H 1.095195 112.255211 294.191637 13 7 2 0.023293 HG12
H 1.097399 110.870031 174.943719 13 7 2 0.023293 HG13
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