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/usr/share/avogadro/builder/amino/d-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.

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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