/usr/share/avogadro/builder/amino/d-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 1.478143 0.000000 0.000000 1 0 0 0.096333 CA
C 1.538028 111.567327 0.000000 2 1 0 0.218528 C
O 1.207082 128.901033 16.295499 3 2 1 -0.287179 O
C 1.528540 109.771016 121.124767 2 1 3 0.014675 HA
S 1.816614 108.899648 65.563556 5 2 1 -0.176229 CB
H 1.130324 108.998082 241.160784 2 1 3 0.056504 HB1
H 1.106801 112.244149 303.425876 5 2 1 0.039379 SG
H 1.110461 111.112665 183.695478 5 2 1 0.039379 HB2
H 1.354868 99.318624 312.988701 6 5 2 0.101693 HG
H 1.020348 111.577655 307.781947 1 2 3 0.141390 H
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