/usr/share/avogadro/builder/amino/l-lys.zmat is in avogadro-data 1.2.0-3.
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 1.459393 0.000000 0.000000 1 0 0 0.087661 CA
C 1.537672 106.336501 0.000000 2 1 0 0.217713 C
O 1.229837 123.227953 331.496556 3 2 1 -0.287208 O
C 1.535060 110.372261 238.164665 2 1 3 -0.028924 CB
C 1.531314 113.836266 185.561189 5 2 1 -0.050050 CG
C 1.531595 111.227291 172.438450 6 5 2 -0.040588 CD
C 1.528038 111.240051 176.230006 7 6 5 -0.006904 CE
N 1.457086 110.332149 178.516026 8 7 6 -0.329979 NZ
H 1.096504 108.181007 117.239114 2 1 3 0.055690 HA
H 1.098059 109.714858 63.032582 5 2 1 0.028494 HB1
H 1.097766 108.930102 307.109066 5 2 1 0.028494 HB2
H 1.096488 109.865841 51.099389 6 5 2 0.026628 HG1
H 1.095478 109.820539 293.059055 6 5 2 0.026628 HG2
H 1.097377 109.512162 54.771009 7 6 5 0.027743 HD1
H 1.097445 109.318754 297.704958 7 6 5 0.027743 HD2
H 1.095155 110.197444 58.012815 8 7 6 0.042179 HE1
H 1.095641 110.131205 299.292074 8 7 6 0.042179 HE2
H 1.019091 109.537734 175.981666 9 8 7 0.118213 HZ1
H 1.019298 109.886289 59.525834 9 8 7 0.118213 HZ2
H 1.016043 117.249529 26.480655 1 2 3 0.141360 H
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