While testing 2D to 3D conversion with random drawn structures, I've noticed that Jmol sometimes fails to calculate a hydrogen for a carbon that has 3 substituents. Today an example has shown this dramatically.
I am using "minimize addHydrogens" or just "calculate hydrogens" with same
result. Tested
now on 12.1.13 and 12.1.21, probably also other versions.
The data is loaded into Jmol unsigned applet as text in 2D MOL format using
loadinline, but
I've just verified that saving to a file and loading it into Jmol app does the
same.
Example (also attached):
------------------
Ketcher 11141015152D 1 1.00000 0.00000 0
14 15 0 0 0 999 V2000
-1.1250 0.2250 0.0000 C 0 0 0 0 0 0 0 0 0 0
-0.2340 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
-0.2340 -1.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
-1.1250 -1.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0
-1.9910 -1.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
-1.9910 -0.2750 0.0000 C 0 0 0 0 0 0 0 0 0 0
0.7171 0.0340 0.0000 C 0 0 0 0 0 0 0 0 0 0
1.3049 -0.7750 0.0000 C 0 0 0 0 0 0 0 0 0 0
0.7171 -1.5840 0.0000 C 0 0 0 0 0 0 0 0 0 0
-1.1311 1.2250 0.0000 C 0 0 0 0 0 0 0 0 0 0
-0.2682 1.7303 0.0000 C 0 0 0 0 0 0 0 0 0 0
-2.0002 1.7197 0.0000 C 0 0 0 0 0 0 0 0 0 0
1.0261 0.9851 0.0000 N 0 0 0 0 0 0 0 0 0 0
2.3049 -0.7750 0.0000 O 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0
2 3 1 0 0 0
3 4 1 0 0 0
4 5 1 0 0 0
5 6 1 0 0 0
6 1 1 0 0 0
2 7 1 0 0 0
7 8 1 0 0 0
8 9 1 0 0 0
9 3 1 0 0 0
1 10 1 0 0 0
10 11 1 0 0 0
10 12 1 0 0 0
7 13 1 1 0 0
8 14 1 1 0 0
M END
------------------
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Date: 14 Nov 2010, 15:16
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