/usr/share/avogadro/builder/amino/d-phe.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 | N 0.000000 0.000000 0.000000 0 0 0 -0.244958 N
C 1.490544 0.000000 0.000000 1 0 0 0.091600 CA
C 1.538140 105.737751 0.000000 2 1 0 0.218041 C
O 1.203591 124.440628 304.179213 3 2 1 -0.287197 O
C 1.541243 108.829879 123.066529 2 1 3 -0.003643 CB
H 1.112012 110.259339 204.221762 5 2 1 0.033301 CG
H 1.115255 109.288896 319.897068 5 2 1 0.033301 CD2
C 1.504651 111.034777 81.927805 5 2 1 -0.045419 CE2
C 1.402313 119.984775 259.040589 8 5 2 -0.058511 CZ
H 1.089738 120.080524 359.123153 9 8 5 0.062030 CE1
C 1.397547 120.002448 179.371774 9 8 5 -0.061501 CD1
H 1.089402 119.800757 179.803200 11 9 8 0.061766 H
C 1.398093 120.194558 359.874011 11 9 8 -0.061742 HA
H 1.088577 120.081639 180.180112 13 11 9 0.061758 HB1
C 1.398790 119.850802 0.315368 13 11 9 -0.061501 HB2
H 1.089349 119.850861 179.782858 15 13 11 0.061766 HD2
C 1.396989 120.216447 359.814054 15 13 11 -0.058511 HE2
H 1.088449 119.791914 179.672250 17 15 13 0.062030 HZ
H 1.127655 113.347091 244.578617 2 1 3 0.056017 HE1
H 1.020506 110.724546 57.496302 1 2 3 0.141371 HD1
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