When corverting a SDF file to XYZ and to SDF again. The final SDF gives a
different molecule than the initial SDF, the charge has been removed and a
radical had be put. How can I overcome that?
Initial smiles:
RDKit 3D
21 20 0 0 0 0 0 0 0 0999 V2000
-3.3512 -0.2818 0.4171 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1548 -0.2898 -0.4241 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9046 0.0525 0.3971 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3516 0.0449 -0.4820 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6006 0.3870 0.3390 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8536 0.3790 -0.5403 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0407 0.7076 0.2566 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9773 0.9667 0.8851 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.2605 -0.9941 1.1777 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.1836 -0.5180 -0.1700 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.4902 0.6669 0.8351 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2772 0.4532 -1.2435 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0352 -1.2968 -0.8826 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0302 1.0593 0.8528 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7878 -0.6930 1.2142 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4755 -0.9624 -0.9377 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2330 0.7905 -1.2992 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4764 1.3948 0.7947 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7190 -0.3589 1.1564 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7526 1.1284 -1.3542 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9952 -0.6259 -0.9923 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 3 0
1 9 1 0
1 10 1 0
1 11 1 0
2 12 1 0
2 13 1 0
3 14 1 0
3 15 1 0
4 16 1 0
4 17 1 0
5 18 1 0
5 19 1 0
6 20 1 0
6 21 1 0
M CHG 1 1 1
M END
$$$$
Intermediate XYZ
21
N -3.35120 -0.28180 0.41710
C -2.15480 -0.28980 -0.42410
C -0.90460 0.05250 0.39710
C 0.35160 0.04490 -0.48200
C 1.60060 0.38700 0.33900
C 2.85360 0.37900 -0.54030
C 4.04070 0.70760 0.25660
N 4.97730 0.96670 0.88510
H -3.26050 -0.99410 1.17770
H -4.18360 -0.51800 -0.17000
H -3.49020 0.66690 0.83510
H -2.27720 0.45320 -1.24350
H -2.03520 -1.29680 -0.88260
H -1.03020 1.05930 0.85280
H -0.78780 -0.69300 1.21420
H 0.47550 -0.96240 -0.93770
H 0.23300 0.79050 -1.29920
H 1.47640 1.39480 0.79470
H 1.71900 -0.35890 1.15640
H 2.75260 1.12840 -1.35420
H 2.99520 -0.62590 -0.99230
Final SDF
OpenBabel07041715563D
21 20 0 0 0 0 0 0 0 0999 V2000
-3.3512 -0.2818 0.4171 N 0 0 0 0 0 0 0 0 0 0 0 0
-2.1548 -0.2898 -0.4241 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9046 0.0525 0.3971 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3516 0.0449 -0.4820 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6006 0.3870 0.3390 C 0 0 0 0 0 0 0 0 0 0 0 0
2.8536 0.3790 -0.5403 C 0 0 0 0 0 0 0 0 0 0 0 0
4.0407 0.7076 0.2566 C 0 0 0 0 0 0 0 0 0 0 0 0
4.9773 0.9667 0.8851 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.2605 -0.9941 1.1777 H 0 0 0 0 0 0 0 0 0 0 0 0
-4.1836 -0.5180 -0.1700 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.4902 0.6669 0.8351 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2772 0.4532 -1.2435 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.0352 -1.2968 -0.8826 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.0302 1.0593 0.8528 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7878 -0.6930 1.2142 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4755 -0.9624 -0.9377 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2330 0.7905 -1.2992 H 0 0 0 0 0 0 0 0 0 0 0 0
1.4764 1.3948 0.7947 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7190 -0.3589 1.1564 H 0 0 0 0 0 0 0 0 0 0 0 0
2.7526 1.1284 -1.3542 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9952 -0.6259 -0.9923 H 0 0 0 0 0 0 0 0 0 0 0 0
1 11 1 0 0 0 0
1 9 1 0 0 0 0
2 3 1 0 0 0 0
2 1 1 0 0 0 0
3 14 1 0 0 0 0
3 15 1 0 0 0 0
4 5 1 0 0 0 0
4 3 1 0 0 0 0
5 18 1 0 0 0 0
5 19 1 0 0 0 0
6 7 1 0 0 0 0
6 5 1 0 0 0 0
7 8 3 0 0 0 0
10 1 1 0 0 0 0
12 2 1 0 0 0 0
13 2 1 0 0 0 0
16 4 1 0 0 0 0
17 4 1 0 0 0 0
20 6 1 0 0 0 0
21 6 1 0 0 0 0
M RAD 1 8 3
M END
$$$$
Thanks for help.
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