/usr/share/avogadro/builder/amino/l-cys.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 | N 0.000000 0.000000 0.000000 0 0 0 -0.244472 N
C 1.465578 0.000000 0.000000 1 0 0 0.096333 CA
C 1.540418 105.891536 0.000000 2 1 0 0.218528 C
O 1.230946 122.856752 349.177701 3 2 1 -0.287179 O
H 1.097477 107.137842 116.232112 2 1 3 0.056504 HA
C 1.534386 111.391877 238.241360 2 1 3 0.014675 CB
H 1.094231 110.767291 314.226133 6 2 1 0.039379 HB1
S 1.827297 113.514658 194.319804 6 2 1 -0.176229 SG
H 1.096542 110.667145 72.771773 6 2 1 0.039379 HB2
H 1.342296 96.303940 171.147318 8 6 2 0.101693 HG
H 1.017627 116.966593 8.434510 1 2 3 0.141390 H
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