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标题: 使用openbabel转换分子格式（mol2转mol2）发现苯环变成了六碳环，有人遇到过吗？ [打印本页]

作者
Author: yy_ds_yyds 时间: 2022-11-2 20:10
标题: 使用openbabel转换分子格式（mol2转mol2）发现苯环变成了六碳环，有人遇到过吗？
使用openbabel转换分子格式（mol2转mol2）发现苯环变成了六碳环，有人遇到过吗？
转换前分子mol2
@<TRIPOS>MOLECULE
46215462
72 78 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
   1 N          8.1315 1.1278 -0.0736 N3    1  LIG1    -0.2994
   2 N          1.3373 -2.5750 0.0701 Npl    1  LIG1    -0.2824
   3 N       -2.0759 -2.1067 0.0353 Nar    1  LIG1    -0.1787
   4 N       -0.8665 -1.5289 -0.0238 Nar    1  LIG1    -0.1257
   5 N       -0.7040 -3.8002 0.1935 Nar    1  LIG1    -0.1798
   6 N       -5.5681 -1.2256 -0.0501 Nar    1  LIG1    -0.1469
   7 N       -4.4239 -1.9630 0.0193 Nar    1  LIG1    -0.1290
   8 N       -3.0743 -4.2354 0.2430 Npl    1  LIG1    -0.3273
   9 C          7.1926 0.9239 1.0196 C3    1  LIG1       0.0110
   10 C          9.3053 0.2614 0.0296 C3    1  LIG1    -0.0008
   11 C          8.6658 2.4891 -0.1042 C3    1  LIG1    -0.0008
   12 C          6.7998 -0.5575 1.1277 C3    1  LIG1    -0.0333
   13 C          5.9978 1.8815 0.8938 C3    1  LIG1    -0.0333
   14 C       10.2852 0.8987 -0.9444 C3    1  LIG1    -0.0390
   15 C          9.8672 2.3634 -1.0296 C3    1  LIG1    -0.0390
   16 C          6.0609 -1.1378 -0.0818 C3    1  LIG1    -0.0260
   17 C          5.1283 1.6973 -0.3532 C3    1  LIG1    -0.0260
   18 C          4.5949 -0.7819 -0.1053 Car    1  LIG1    -0.0424
   19 C          4.1571 0.5490 -0.2325 Car    1  LIG1    -0.0440
   20 C          3.6418 -1.8108 -0.0081 Car    1  LIG1    -0.0370
   21 C          2.7773 0.8171 -0.2587 Car    1  LIG1    -0.0566
   22 C          2.2768 -1.5285 -0.0329 Car    1  LIG1       0.0339
   23 C          1.8443 -0.2139 -0.1582 Car    1  LIG1    -0.0402
   24 C       -4.7234 3.0882 0.7761 C3    1  LIG1    -0.0450
   25 C       -4.2090 2.2852 -0.4228 C3    1  LIG1    -0.0252
   26 C       -5.9633 2.5323 1.4839 C3    1  LIG1    -0.0268
   27 C       -0.0711 -2.5958 0.0763 Car    1  LIG1       0.2407
   28 C       -4.2783 0.7927 -0.2407 Car    1  LIG1    -0.0161
   29 C       -7.0262 1.9986 0.5518 Car    1  LIG1    -0.0381
   30 C       -6.7998 0.8247 -0.2082 Car    1  LIG1       0.0056
   31 C       -5.5043 0.1231 -0.1720 Car    1  LIG1       0.0969
   32 C       -3.1157 0.0321 -0.1672 Car    1  LIG1    -0.0103
   33 C       -3.2343 -1.3356 -0.0362 Car    1  LIG1       0.1797
   34 C       -8.2634 2.6573 0.4707 Car    1  LIG1    -0.0579
   35 C       -7.8438 0.3417 -1.0182 Car    1  LIG1    -0.0522
   36 C       -1.9706 -3.4566 0.1643 Car    1  LIG1       0.2187
   37 C       -9.2781 2.1630 -0.3461 Car    1  LIG1    -0.0615
   38 C       -9.0700 1.0051 -1.0871 Car    1  LIG1    -0.0611
   39 H          7.6893 1.1747 1.9689 1    1  LIG1       0.0463
   40 H          9.1102 -0.7726 -0.2711 1    1  LIG1       0.0427
   41 H          9.7350 0.2665 1.0397 1    1  LIG1       0.0427
   42 H          8.9972 2.8254 0.8866 1    1  LIG1       0.0427
   43 H          7.9602 3.2205 -0.5099 1    1  LIG1       0.0427
   44 H          6.1708 -0.6797 2.0211 1    1  LIG1       0.0283
   45 H          7.6816 -1.1758 1.3340 1    1  LIG1       0.0283
   46 H          6.3412 2.9223 0.9307 1    1  LIG1       0.0283
   47 H          5.3698 1.7683 1.7889 1    1  LIG1       0.0283
   48 H       10.2093 0.4342 -1.9347 1    1  LIG1       0.0278
   49 H       11.3194 0.7916 -0.6017 1    1  LIG1       0.0278
   50 H       10.6780 3.0342 -0.7278 1    1  LIG1       0.0278
   51 H          9.5929 2.6105 -2.0620 1    1  LIG1       0.0278
   52 H          6.5246 -0.8401 -1.0293 1    1  LIG1       0.0314
   53 H          6.1633 -2.2300 -0.0391 1    1  LIG1       0.0314
   54 H          4.5646 2.6273 -0.5043 1    1  LIG1       0.0314
   55 H          5.7318 1.5735 -1.2598 1    1  LIG1       0.0314
   56 H          3.9741 -2.8428 0.0894 1    1  LIG1       0.0639
   57 H          2.4183 1.8391 -0.3576 1    1  LIG1       0.0621
   58 H          0.8040 0.0794 -0.1855 1    1  LIG1       0.0636
   59 H          1.7879 -3.4842 0.1558 1    1  LIG1       0.1551
   60 H       -3.9225 3.1752 1.5218 1    1  LIG1       0.0272
   61 H       -4.9293 4.1106 0.4339 1    1  LIG1       0.0272
   62 H       -4.7811 2.5515 -1.3218 1    1  LIG1       0.0314
   63 H       -3.1799 2.5990 -0.6395 1    1  LIG1       0.0314
   64 H       -6.3792 3.3183 2.1273 1    1  LIG1       0.0313
   65 H       -5.6720 1.7290 2.1741 1    1  LIG1       0.0313
   66 H       -2.1562 0.5375 -0.2198 1    1  LIG1       0.0659
   67 H       -8.4465 3.5585 1.0507 1    1  LIG1       0.0620
   68 H       -7.7066 -0.5551 -1.6194 1    1  LIG1       0.0624
   69 H       -10.2319 2.6795 -0.4004 1    1  LIG1       0.0618
   70 H       -9.8605 0.6177 -1.7234 1    1  LIG1       0.0618
   71 H       -4.0214 -3.8739 0.2118 1    1  LIG1       0.1452
   72 H       -2.9980 -5.2431 0.3397 1    1  LIG1       0.1452
@<TRIPOS>BOND
   1    1    9 1
   2    1 10 1
   3    1 11 1
   4    2 22 1
   5    2 27 1
   6    2 59 1
   7    3    4 ar
   8    3 33 1
   9    3 36 ar
10    4 27 ar
11    5 27 ar
12    5 36 ar
13    6    7 ar
14    6 31 ar
15    7 33 ar
16    8 36 1
17    8 71 1
18    8 72 1
19    9 12 1
20    9 13 1
21    9 39 1
22 10 14 1
23 10 40 1
24 10 41 1
25 11 15 1
26 11 42 1
27 11 43 1
28 12 16 1
29 12 44 1
30 12 45 1
31 13 17 1
32 13 46 1
33 13 47 1
34 14 15 1
35 14 48 1
36 14 49 1
37 15 50 1
38 15 51 1
39 16 18 1
40 16 52 1
41 16 53 1
42 17 19 1
43 17 54 1
44 17 55 1
45 18 19 ar
46 18 20 ar
47 19 21 ar
48 20 22 ar
49 20 56 1
50 21 23 ar
51 21 57 1
52 22 23 ar
53 23 58 1
54 24 25 1
55 24 26 1
56 24 60 1
57 24 61 1
58 25 28 1
59 25 62 1
60 25 63 1
61 26 29 1
62 26 64 1
63 26 65 1
64 28 31 ar
65 28 32 ar
66 29 30 ar
67 29 34 ar
68 30 31 1
69 30 35 ar
70 32 33 ar
71 32 66 1
72 34 37 ar
73 34 67 1
74 35 38 ar
75 35 68 1
76 37 38 ar
77 37 69 1
78 38 70 1

转换后分子mol2
@<TRIPOS>MOLECULE
46215462
72 78 0 0 0
SMALL
GASTEIGER

@<TRIPOS>ATOM
   1 N          8.1315 1.1278 -0.0736 N3    1  LIG11    -0.2994
   2 N          1.3373 -2.5750 0.0701 Npl    1  LIG11    -0.2824
   3 N       -2.0759 -2.1067 0.0353 Nar    1  LIG11    -0.1787
   4 N       -0.8665 -1.5289 -0.0238 Nar    1  LIG11    -0.1257
   5 N       -0.7040 -3.8002 0.1935 Nar    1  LIG11    -0.1798
   6 N       -5.5681 -1.2256 -0.0501 Nar    1  LIG11    -0.1469
   7 N       -4.4239 -1.9630 0.0193 Nar    1  LIG11    -0.1290
   8 N       -3.0743 -4.2354 0.2430 Npl    1  LIG11    -0.3273
   9 C          7.1926 0.9239 1.0196 C3    1  LIG11    0.0110
   10 C          9.3053 0.2614 0.0296 C3    1  LIG11    -0.0008
   11 C          8.6658 2.4891 -0.1042 C3    1  LIG11    -0.0008
   12 C          6.7998 -0.5575 1.1277 C3    1  LIG11    -0.0333
   13 C          5.9978 1.8815 0.8938 C3    1  LIG11    -0.0333
   14 C       10.2852 0.8987 -0.9444 C3    1  LIG11    -0.0390
   15 C          9.8672 2.3634 -1.0296 C3    1  LIG11    -0.0390
   16 C          6.0609 -1.1378 -0.0818 C3    1  LIG11    -0.0260
   17 C          5.1283 1.6973 -0.3532 C3    1  LIG11    -0.0260
   18 C          4.5949 -0.7819 -0.1053 Car    1  LIG11    -0.0424
   19 C          4.1571 0.5490 -0.2325 Car    1  LIG11    -0.0440
   20 C          3.6418 -1.8108 -0.0081 Car    1  LIG11    -0.0370
   21 C          2.7773 0.8171 -0.2587 Car    1  LIG11    -0.0566
   22 C          2.2768 -1.5285 -0.0329 Car    1  LIG11    0.0339
   23 C          1.8443 -0.2139 -0.1582 Car    1  LIG11    -0.0402
   24 C       -4.7234 3.0882 0.7761 C3    1  LIG11    -0.0450
   25 C       -4.2090 2.2852 -0.4228 C3    1  LIG11    -0.0252
   26 C       -5.9633 2.5323 1.4839 C3    1  LIG11    -0.0268
   27 C       -0.0711 -2.5958 0.0763 Car    1  LIG11    0.2407
   28 C       -4.2783 0.7927 -0.2407 Car    1  LIG11    -0.0161
   29 C       -7.0262 1.9986 0.5518 Car    1  LIG11    -0.0381
   30 C       -6.7998 0.8247 -0.2082 Car    1  LIG11    0.0056
   31 C       -5.5043 0.1231 -0.1720 Car    1  LIG11    0.0969
   32 C       -3.1157 0.0321 -0.1672 Car    1  LIG11    -0.0103
   33 C       -3.2343 -1.3356 -0.0362 Car    1  LIG11    0.1797
   34 C       -8.2634 2.6573 0.4707 Car    1  LIG11    -0.0579
   35 C       -7.8438 0.3417 -1.0182 Car    1  LIG11    -0.0522
   36 C       -1.9706 -3.4566 0.1643 Car    1  LIG11    0.2187
   37 C       -9.2781 2.1630 -0.3461 Car    1  LIG11    -0.0615
   38 C       -9.0700 1.0051 -1.0871 Car    1  LIG11    -0.0611
   39 H          7.6893 1.1747 1.9689 1    1  LIG11    0.0463
   40 H          9.1102 -0.7726 -0.2711 1    1  LIG11    0.0427
   41 H          9.7350 0.2665 1.0397 1    1  LIG11    0.0427
   42 H          8.9972 2.8254 0.8866 1    1  LIG11    0.0427
   43 H          7.9602 3.2205 -0.5099 1    1  LIG11    0.0427
   44 H          6.1708 -0.6797 2.0211 1    1  LIG11    0.0283
   45 H          7.6816 -1.1758 1.3340 1    1  LIG11    0.0283
   46 H          6.3412 2.9223 0.9307 1    1  LIG11    0.0283
   47 H          5.3698 1.7683 1.7889 1    1  LIG11    0.0283
   48 H       10.2093 0.4342 -1.9347 1    1  LIG11    0.0278
   49 H       11.3194 0.7916 -0.6017 1    1  LIG11    0.0278
   50 H       10.6780 3.0342 -0.7278 1    1  LIG11    0.0278
   51 H          9.5929 2.6105 -2.0620 1    1  LIG11    0.0278
   52 H          6.5246 -0.8401 -1.0293 1    1  LIG11    0.0314
   53 H          6.1633 -2.2300 -0.0391 1    1  LIG11    0.0314
   54 H          4.5646 2.6273 -0.5043 1    1  LIG11    0.0314
   55 H          5.7318 1.5735 -1.2598 1    1  LIG11    0.0314
   56 H          3.9741 -2.8428 0.0894 1    1  LIG11    0.0639
   57 H          2.4183 1.8391 -0.3576 1    1  LIG11    0.0621
   58 H          0.8040 0.0794 -0.1855 1    1  LIG11    0.0636
   59 H          1.7879 -3.4842 0.1558 1    1  LIG11    0.1551
   60 H       -3.9225 3.1752 1.5218 1    1  LIG11    0.0272
   61 H       -4.9293 4.1106 0.4339 1    1  LIG11    0.0272
   62 H       -4.7811 2.5515 -1.3218 1    1  LIG11    0.0314
   63 H       -3.1799 2.5990 -0.6395 1    1  LIG11    0.0314
   64 H       -6.3792 3.3183 2.1273 1    1  LIG11    0.0313
   65 H       -5.6720 1.7290 2.1741 1    1  LIG11    0.0313
   66 H       -2.1562 0.5375 -0.2198 1    1  LIG11    0.0659
   67 H       -8.4465 3.5585 1.0507 1    1  LIG11    0.0620
   68 H       -7.7066 -0.5551 -1.6194 1    1  LIG11    0.0624
   69 H       -10.2319 2.6795 -0.4004 1    1  LIG11    0.0618
   70 H       -9.8605 0.6177 -1.7234 1    1  LIG11    0.0618
   71 H       -4.0214 -3.8739 0.2118 1    1  LIG11    0.1452
   72 H       -2.9980 -5.2431 0.3397 1    1  LIG11    0.1452
@<TRIPOS>BOND
   1    1    9 1
   2    1 10 1
   3    1 11 1
   4    2 22 1
   5    2 27 1
   6    2 59 1
   7    3    4 1
   8    3 33 1
   9    3 36 1
10    4 27 1
11    5 27 1
12    5 36 1
13    6    7 1
14    6 31 1
15    7 33 1
16    8 36 1
17    8 71 1
18    8 72 1
19    9 12 1
20    9 13 1
21    9 39 1
22 10 14 1
23 10 40 1
24 10 41 1
25 11 15 1
26 11 42 1
27 11 43 1
28 12 16 1
29 12 44 1
30 12 45 1
31 13 17 1
32 13 46 1
33 13 47 1
34 14 15 1
35 14 48 1
36 14 49 1
37 15 50 1
38 15 51 1
39 16 18 1
40 16 52 1
41 16 53 1
42 17 19 1
43 17 54 1
44 17 55 1
45 18 19 1
46 18 20 1
47 19 21 1
48 20 22 1
49 20 56 1
50 21 23 1
51 21 57 1
52 22 23 1
53 23 58 1
54 24 25 1
55 24 26 1
56 24 60 1
57 24 61 1
58 25 28 1
59 25 62 1
60 25 63 1
61 26 29 1
62 26 64 1
63 26 65 1
64 28 31 1
65 28 32 1
66 29 30 1
67 29 34 1
68 30 31 1
69 30 35 1
70 32 33 1
71 32 66 1
72 34 37 1
73 34 67 1
74 35 38 1
75 35 68 1
76 37 38 1
77 37 69 1
78 38 70 1

作者
Author: sobereva 时间: 2022-11-3 09:12
mol2转mol2我没试过，如果是保证芳香环的判断，可以先转成pdb，然后pdb再转成mol2，到时候会自动判断

作者
Author: yy_ds_yyds 时间: 2022-11-3 14:47

sobereva 发表于 2022-11-3 09:12
mol2转mol2我没试过，如果是保证芳香环的判断，可以先转成pdb，然后pdb再转成mol2，到时候会自动判断

谢谢老师。我发现使用openbabel 2.4.1转换可以正常但是使用2.3.2 却不行可能是版本问题吧。

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