/usr/share/avogadro/builder/amino/d-pro.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 | N 0.000000 0.000000 0.000000 0 0 0 -0.229034 N
C 1.494797 0.000000 0.000000 1 0 0 0.090941 CA
C 1.527809 105.550429 0.000000 2 1 0 0.217989 C
O 1.207319 127.831292 264.854954 3 2 1 -0.287199 O
H 1.119708 111.126227 244.754163 2 1 3 0.055965 HA
C 1.497645 106.511727 256.960226 1 2 3 0.014812 CD
H 1.113450 107.121032 93.975355 6 1 2 0.044093 HD1
H 1.104278 111.245361 211.055142 6 1 2 0.044093 HD2
C 1.543045 107.518454 335.187732 6 1 2 -0.036968 CG
H 1.102488 111.433649 260.424990 9 6 1 0.027862 HG1
H 1.102840 111.028639 141.942923 9 6 1 0.027862 HG2
C 1.540104 105.648687 21.155259 9 6 1 -0.027502 CB
H 1.101715 111.422528 229.882964 12 9 6 0.028543 HB1
H 1.106552 110.684738 111.424582 12 9 6 0.028543 HB2
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