/usr/share/avogadro/builder/amino/d-lys.zmat is in avogadro-data 1.0.3-10.1.
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 17 18 19 20 21 | N 0.000000 0.000000 0.000000 0 0 0 -0.245286 N
C 1.476333 0.000000 0.000000 1 0 0 0.087661 CA
C 1.537882 111.664329 0.000000 2 1 0 0.217713 C
O 1.207509 129.435495 23.826217 3 2 1 -0.287208 O
C 1.542326 111.381360 120.992358 2 1 3 -0.028924 CB
C 1.534040 111.277439 68.605732 5 2 1 -0.050050 CG
H 1.127214 108.192925 241.344195 2 1 3 0.055690 CD
H 1.108258 110.288940 306.354782 5 2 1 0.028494 CE
H 1.109628 109.169603 189.971110 5 2 1 0.028494 NZ
H 1.110613 109.635201 302.843197 6 5 2 0.026628 HA
C 1.532508 111.156445 180.630589 6 5 2 -0.040588 HB1
H 1.017383 111.845728 295.339764 1 2 3 0.141360 HB2
H 1.107666 109.966839 58.451575 6 5 2 0.026628 HG1
H 1.106910 109.884332 59.180823 11 6 5 0.027743 HG2
H 1.106755 109.996155 302.942017 11 6 5 0.027743 HD1
C 1.540394 111.118725 180.990613 11 6 5 -0.006904 HD2
N 1.485356 114.270338 180.420862 16 11 6 -0.329979 HE1
H 1.112963 110.224094 58.749972 16 11 6 0.042179 HE2
H 1.113021 110.188498 302.105620 16 11 6 0.042179 HZ1
H 1.015440 110.906794 59.513388 17 16 11 0.118213 HZ2
H 1.015134 110.926511 300.762453 17 16 11 0.118213 H
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