/usr/share/avogadro/builder/amino/d-met.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 | N 0.000000 0.000000 0.000000 0 0 0 -0.245259 N
C 1.476314 0.000000 0.000000 1 0 0 0.088400 CA
C 1.536321 111.959055 0.000000 2 1 0 0.217740 C
O 1.207290 129.335522 22.566012 3 2 1 -0.287208 O
C 1.545410 111.051018 120.858787 2 1 3 -0.019936 CB
H 1.112875 109.081161 188.744066 5 2 1 0.029282 CG
H 1.109523 110.074064 304.526581 5 2 1 0.029282 SD
C 1.520821 110.746909 67.140763 5 2 1 -0.004715 CE
H 1.108268 111.339421 301.579960 8 5 2 0.037679 HA
H 1.109169 111.604395 59.933337 8 5 2 0.037679 HB1
S 1.815430 110.087744 177.702427 8 5 2 -0.164064 HB2
C 1.805813 103.348291 79.652286 11 8 5 -0.018102 HG1
H 1.094426 111.887024 293.595783 12 11 8 0.034049 HG2
H 1.095178 112.021430 56.237455 12 11 8 0.034049 HE1
H 1.098832 107.705692 174.813609 12 11 8 0.034049 HE2
H 1.127018 108.281722 240.973376 2 1 3 0.055716 HE3
H 1.017339 111.724155 297.931003 1 2 3 0.141360 H
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