Hello
I am using version 2.4.1 and run in the following issue:
when I convert the following PDB file to mol2 the atoms in the rings are
aromatic
REMARK AtomGroup 3got_lig
HETATM 1 N1 A2F A 91 -12.060 -9.865 9.375 1.00
34.52 N
HETATM 2 C2 A2F A 91 -11.647 -11.140 9.446 1.00
36.07 C
HETATM 3 N3 A2F A 91 -11.218 -11.795 8.356 1.00
35.26 N
HETATM 4 C4 A2F A 91 -11.199 -11.188 7.163 1.00
34.93 C
HETATM 5 C5 A2F A 91 -11.626 -9.872 7.057 1.00
34.33 C
HETATM 6 C6 A2F A 91 -12.054 -9.212 8.203 1.00
34.11 C
HETATM 7 N6 A2F A 91 -12.392 -7.927 8.148 1.00
31.63 N
HETATM 8 N7 A2F A 91 -11.502 -9.521 5.780 1.00
34.42 N
HETATM 9 C8 A2F A 91 -11.013 -10.561 5.109 1.00
34.57 C
HETATM 10 N9 A2F A 91 -10.826 -11.579 5.948 1.00
34.76 N
HETATM 11 F A2F A 91 -11.661 -11.789 10.626 1.00
35.98 F
but if the atom order is changed
HETATM 1 F A2F A 91 -11.661 -11.789 10.626 1.00
35.98 F
HETATM 2 C2 A2F A 91 -11.647 -11.140 9.446 1.00
36.07 C
HETATM 3 N3 A2F A 91 -11.218 -11.795 8.356 1.00
35.26 N
HETATM 4 N1 A2F A 91 -12.060 -9.865 9.375 1.00
34.52 N
HETATM 5 C6 A2F A 91 -12.054 -9.212 8.203 1.00
34.11 C
HETATM 6 N6 A2F A 91 -12.392 -7.927 8.148 1.00
31.63 N
HETATM 7 C5 A2F A 91 -11.626 -9.872 7.057 1.00
34.33 C
HETATM 8 C4 A2F A 91 -11.199 -11.188 7.163 1.00
34.93 C
HETATM 9 N7 A2F A 91 -11.502 -9.521 5.780 1.00
34.42 N
HETATM 10 C8 A2F A 91 -11.013 -10.561 5.109 1.00
34.57 C
HETATM 11 N9 A2F A 91 -10.826 -11.579 5.948 1.00
34.76 N
none of the atoms or bonds is aromatic
-Michel
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