/usr/share/avogadro/builder/amino/d-ser.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 | N 0.000000 0.000000 0.000000 0 0 0 -0.242989 N
C 1.484374 0.000000 0.000000 1 0 0 0.110570 CA
C 1.535451 108.531258 0.000000 2 1 0 0.220016 CB
O 1.205718 124.730095 155.137540 3 2 1 -0.287123 OG
H 1.126613 108.309211 244.636596 2 1 3 0.057995 HA
H 1.020871 110.603658 279.024394 1 2 3 0.141446 C
C 1.544573 114.135193 123.143441 2 1 3 0.068103 H 1
O 1.428181 108.859336 61.377421 7 2 1 -0.392982 H 2
H 1.107758 112.476804 307.336097 7 2 1 0.057743 O
H 1.106074 111.690650 184.686753 7 2 1 0.057743 H
H 0.979674 110.836134 77.881044 8 7 2 0.209479 H
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