/usr/share/avogadro/builder/amino/d-thr.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 | N 0.000000 0.000000 0.000000 0 0 0 -0.242718 N
C 1.475189 0.000000 0.000000 1 0 0 0.113126 CA
C 1.527524 115.391522 0.000000 2 1 0 0.220298 C
O 1.206152 129.362142 165.993159 3 2 1 -0.287112 O
O 2.464145 77.827537 125.083660 2 1 3 -0.390029 CG2
C 1.421585 36.636855 182.563376 5 2 1 0.076258 CB
C 1.521791 110.943414 236.522592 6 5 2 -0.037002 OG1
H 0.986121 91.106714 56.687267 5 2 1 0.209848 HG21
H 1.118121 101.784228 117.865671 6 5 2 0.061081 HG22
H 1.095524 112.580962 65.925301 7 6 5 0.025505 HG23
H 1.099792 110.317304 306.659685 7 6 5 0.025505 HB
H 1.098326 111.591456 187.792403 7 6 5 0.025505 HA
H 1.130129 106.902531 242.730935 2 1 3 0.058278 HG1
H 1.020990 110.739340 287.621003 1 2 3 0.141456 H
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