# How can I add double bonds to Triazine-derivatives for OpenBabel generation of pdbqt files?

The double bonds are initially present at the sdf file but disappear or are misplaced after .pdbqt conversion. I tried all kinds of combinations using renumbering atoms, manually including connect bonds or connect bonds, changing A atoms to Cs, NA atoms to N, small case lettering, .sdf, .pdb or .mol inputs. Nothing worked!!!.

When any of those alternative solutions were converted by OpenBabel to their corresponding .pdbqt, none of them interpret the double bonds of triazine (c1ncncn1) correctly. Furthermore, sometimes they introduced double bonds in other parts of the molecules, misplaced them or broke them.

I enclose two of my Triazine derivatives in the .sdf format.

136627870N3+2.2
MOLSOFT 09022111472D

29 30  0  0  0  0  0  0  0  0999 V2000
0.0000   -0.0000   -0.0000 O   0  0  0
1.2534    0.7910   -0.0000 C   0  0  0
-1.3507    0.7910   -0.0000 C   0  0  0
2.5067    0.0608   -0.0000 N   0  0  0
-2.7014    0.0608   -0.0000 C   0  0  0
2.4581   -1.3994   -0.0000 C   0  0  0
3.7601    0.8518   -0.0000 C   0  0  0
3.7114   -2.1295   -0.0000 N   0  0  0
1.1073   -2.1295   -0.0000 N   0  0  0
3.7114    2.4094   -0.0000 C   0  0  0
3.6628   -3.5898   -0.0000 C   0  0  0
1.0587   -3.5898   -0.0000 C   0  0  0
2.4337    3.1639   -0.0000 C   0  0  0
2.3120   -4.3199   -0.0000 N   0  0  0
4.9161   -4.3199    0.0000 N   0  0  0
-0.2920   -4.3199   -0.0000 N   0  0  0
2.3851    4.7214   -0.0000 C   0  0  0
4.8675   -5.7801    0.0000 C   0  0  3
6.1695   -3.5289   -0.0000 C   0  0  0
-1.6428   -3.5289   -0.0000 C   0  0  0
-0.3407   -5.7801   -0.0000 C   0  0  0
3.5167   -6.5102    0.0000 O   0  0  0
6.1208   -6.5102    0.0000 C   0  0  0
7.4229   -4.2590   -0.0000 C   0  0  0
-1.6914   -1.9713   -0.0000 O   0  0  0
-1.6914   -6.5102   -0.0000 C   0  0  0
7.3742   -5.7314   -0.0000 C   0  0  0
-3.0422   -5.7314   -0.0000 C   0  0  0
-4.3929   -6.4616   -0.0000 C   0  0  0
1  2  1
1  3  1
2  4  1
3  5  1
4  6  1
4  7  1
6  8  2
6  9  1
7 10  1
8 11  1
9 12  2
10 13  1
11 14  2
11 15  1
12 16  1
12 14  1
13 17  1
15 19  1
16 20  1
16 21  1
18 15  1
18 22  1
18 23  1
19 24  1
20 25  1
21 26  1
23 27  1
24 27  1
26 28  1
28 29  1
M  END
> <molFormula>
C20H38N6O3

> <smiles>
CCCCN(CO)c1nc(nc(n1)N1CCCCC1O)N(CCCC)COCC


135839733N3+1.3
MOLSOFT 09022111472D

25 27  0  0  0  0  0  0  0  0999 V2000
0.0000   -0.0000    0.0000 O   0  0  0
0.0250    1.4637    0.0000 C   0  0  3
-1.2260    2.2018    0.0000 N   0  0  0
1.2260    2.1768    0.0000 C   0  0  0
-2.4771    1.4387   -0.0000 C   0  0  0
-1.2761    3.7281   -0.0000 C   0  0  0
1.2135    3.7782   -0.0000 C   0  0  0
-3.8032    2.2269   -0.0000 N   0  0  0
-2.4521   -0.0626   -0.0000 N   0  0  0
-0.0500    4.5163   -0.0000 C   0  0  0
-5.0542    1.4637   -0.0000 C   0  0  0
-3.7031   -0.8257   -0.0000 C   0  0  0
-5.0292   -0.0375   -0.0000 N   0  0  0
-6.3803    2.2519   -0.0000 N   0  0  0
-3.6781   -2.3269   -0.0000 N   0  0  0
-6.4304    3.7782   -0.0000 C   0  0  0
-7.7065    1.5388   -0.0000 C   0  0  0
-2.3770   -3.0901   -0.0000 C   0  0  0
-5.0042   -3.0400   -0.0000 C   0  0  0
-7.7565    4.5663   -0.0000 C   0  0  0
-9.0326    2.3269   -0.0000 C   0  0  0
-1.0759   -2.3520   -0.0000 O   0  0  0
-5.0542   -4.4787   -0.0000 C   0  0  0
-9.0826    3.8532   -0.0000 C   0  0  0
-3.7531   -5.2419   -0.0000 C   0  0  0
2  1  1
2  3  1
2  4  1
3  5  1
3  6  1
4  7  1
5  8  2
5  9  1
6 10  1
7 10  1
8 11  1
9 12  2
11 13  2
11 14  1
12 15  1
12 13  1
14 16  1
14 17  1
15 18  1
15 19  1
16 20  1
17 21  1
18 22  1
19 23  1
20 24  1
21 24  1
23 25  1
M  END
> <molFormula>
C17H30N6O2

> <smiles>
CCCN(CO)c1nc(nc(n1)N1CCCCC1O)N1CCCCC1

\$

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