Greetings,
Is anybody aware of a good sdf to mol2 file converter that is not based on
OpenBabel? I want to avoid problems like the following, which I currently
solve with Maestro. Basically, the problem is with O40 which -according to
antechamber from AmberTools- should be sp3 within a non-aromatic pentameric
ring, as opposed to OpenBabel which wants it to be sp2 within an aromatic
pentameric ring.
OpenBabel (AmberTools complain about the valence of O40):
@<TRIPOS>MOLECULE
BACE7
98 102 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 C 4.4906 1.0444 -22.8214 C.3 1 LIG1 -0.0624
2 C 4.8922 0.9339 -21.3406 C.3 1 LIG1 -0.0421
3 C 4.7328 -0.5268 -20.8573 C.3 1 LIG1 -0.0504
4 C 5.8712 -1.4883 -21.3104 C.3 1 LIG1 -0.0528
5 C 5.8678 -2.8681 -20.5852 C.3 1 LIG1 -0.0516
6 C 5.7796 -2.6627 -19.0768 C.3 1 LIG1 -0.0371
7 C 6.0082 -3.8328 -18.1147 C.3 1 LIG1 0.0156
8 N 5.0491 -3.7436 -16.9811 N.am 1 LIG1 -0.2907
9 C 5.3910 -3.1904 -15.7259 C.2 1 LIG1 0.2471
10 O 4.9860 -3.7155 -14.6679 O.2 1 LIG1 -0.2700
11 C 6.1926 -1.9707 -15.7016 C.ar 1 LIG1 0.0384
12 C 7.2723 -1.8151 -14.8219 C.ar 1 LIG1 -0.0373
13 C 8.0748 -0.6639 -14.8950 C.ar 1 LIG1 0.0383
14 C 7.7594 0.3295 -15.8386 C.ar 1 LIG1 -0.0373
15 C 6.6529 0.1798 -16.6946 C.ar 1 LIG1 0.0381
16 C 5.9088 -0.9874 -16.6449 C.ar 1 LIG1 -0.0375
17 C 6.3758 1.1928 -17.7374 C.2 1 LIG1 0.2444
18 O 7.3575 1.7202 -18.3089 O.2 1 LIG1 -0.2702
19 N 5.0541 1.4981 -18.2116 N.am 1 LIG1 -0.3060
20 C 4.8315 2.5154 -19.2554 C.3 1 LIG1 0.0508
21 C 4.0479 1.9160 -20.4590 C.3 1 LIG1 -0.0295
22 C 4.1278 3.7525 -18.6377 C.3 1 LIG1 0.0859
23 C 4.9660 4.3781 -17.5041 C.3 1 LIG1 0.0240
24 N 4.2842 5.5876 -17.0101 N.3 1 LIG1 -0.3095
25 C 5.1777 6.6776 -16.6101 C.3 1 LIG1 0.0213
26 C 6.0118 7.1928 -17.7645 C.ar 1 LIG1 -0.0333
27 C 7.4134 7.0911 -17.6697 C.ar 1 LIG1 -0.0573
28 C 8.2301 7.5127 -18.7170 C.ar 1 LIG1 -0.0612
29 C 7.6590 8.0307 -19.8750 C.ar 1 LIG1 -0.0583
30 C 6.2656 8.1500 -19.9835 C.ar 1 LIG1 -0.0445
31 C 5.4430 7.7541 -18.9156 C.ar 1 LIG1 -0.0539
32 C 5.6601 8.6452 -21.2852 C.3 1 LIG1 -0.0215
33 C 4.7533 9.8610 -21.0668 C.3 1 LIG1 -0.0586
34 C 4.9002 7.5146 -21.9875 C.3 1 LIG1 -0.0586
35 O 3.9440 4.7344 -19.6282 O.3 1 LIG1 -0.3887
36 C 9.2604 -0.5139 -14.0265 C.ar 1 LIG1 0.2271
37 N 9.6773 -1.4569 -13.1548 N.ar 1 LIG1 -0.2175
38 C 10.7852 -0.9156 -12.6169 C.ar 1 LIG1 0.0663
39 C 11.0006 0.3233 -13.1739 C.ar 1 LIG1 0.1125
40 O 10.0422 0.5438 -14.0357 O.2 1 LIG1 -0.4436
41 C 3.7184 -4.3654 -17.1815 C.3 1 LIG1 0.0487
42 C 3.6849 -5.7921 -16.6077 C.3 1 LIG1 -0.0422
43 C 2.5948 -3.4594 -16.6885 C.ar 1 LIG1 -0.0273
44 C 2.1036 -2.4496 -17.5372 C.ar 1 LIG1 -0.0568
45 C 1.0992 -1.5797 -17.1055 C.ar 1 LIG1 -0.0614
46 C 0.5629 -1.7113 -15.8244 C.ar 1 LIG1 -0.0617
47 C 1.0304 -2.7139 -14.9731 C.ar 1 LIG1 -0.0614
48 C 2.0402 -3.5825 -15.3976 C.ar 1 LIG1 -0.0568
49 H 5.9644 1.2247 -21.2739 H 1 LIG1 0.0299
50 H 5.7964 2.8799 -19.6624 H 1 LIG1 0.0524
51 H 3.1462 3.4322 -18.2096 H 1 LIG1 0.0624
52 H 3.5467 -4.5027 -18.2736 H 1 LIG1 0.0548
53 H 3.4150 0.7979 -22.9558 H 1 LIG1 0.0232
54 H 5.1004 0.3599 -23.4465 H 1 LIG1 0.0232
55 H 4.6652 2.0788 -23.1866 H 1 LIG1 0.0232
56 H 4.7166 -0.4534 -19.7587 H 1 LIG1 0.0268
57 H 3.7500 -0.9452 -21.1700 H 1 LIG1 0.0268
58 H 5.7965 -1.6618 -22.4043 H 1 LIG1 0.0265
59 H 6.8502 -1.0012 -21.1167 H 1 LIG1 0.0265
60 H 5.0053 -3.4737 -20.9333 H 1 LIG1 0.0266
61 H 6.8042 -3.4123 -20.8288 H 1 LIG1 0.0266
62 H 6.5254 -1.8809 -18.8351 H 1 LIG1 0.0280
63 H 4.7440 -2.3354 -18.8997 H 1 LIG1 0.0280
64 H 7.0562 -3.8126 -17.7420 H 1 LIG1 0.0465
65 H 5.8794 -4.7982 -18.6486 H 1 LIG1 0.0465
66 H 7.5041 -2.6037 -14.1147 H 1 LIG1 0.0633
67 H 8.3749 1.2174 -15.9128 H 1 LIG1 0.0633
68 H 4.9935 -1.0449 -17.2115 H 1 LIG1 0.0633
69 H 4.2242 1.0811 -17.7380 H 1 LIG1 0.1494
70 H 3.1207 1.4242 -20.0987 H 1 LIG1 0.0286
71 H 3.7154 2.7566 -21.1017 H 1 LIG1 0.0286
72 H 5.9766 4.6051 -17.9036 H 1 LIG1 0.0450
73 H 5.0959 3.6528 -16.6730 H 1 LIG1 0.0450
74 H 3.6902 5.3236 -16.1884 H 1 LIG1 0.1223
75 H 4.5586 7.5177 -16.2301 H 1 LIG1 0.0473
76 H 5.8155 6.3352 -15.7648 H 1 LIG1 0.0473
77 H 7.8777 6.6663 -16.7890 H 1 LIG1 0.0621
78 H 9.3069 7.4243 -18.6376 H 1 LIG1 0.0618
79 H 8.3068 8.3297 -20.6899 H 1 LIG1 0.0620
80 H 4.3652 7.8246 -18.9948 H 1 LIG1 0.0623
81 H 6.4721 8.9668 -21.9757 H 1 LIG1 0.0343
82 H 3.8505 9.5898 -20.4774 H 1 LIG1 0.0235
83 H 4.4204 10.2688 -22.0459 H 1 LIG1 0.0235
84 H 5.3112 10.6606 -20.5315 H 1 LIG1 0.0235
85 H 4.0349 7.1733 -21.3729 H 1 LIG1 0.0235
86 H 5.5826 6.6513 -22.1567 H 1 LIG1 0.0235
87 H 4.5216 7.8616 -22.9744 H 1 LIG1 0.0235
88 H 2.9876 4.7176 -19.8960 H 1 LIG1 0.2099
89 H 11.4027 -1.3995 -11.8736 H 1 LIG1 0.0862
90 H 11.8106 1.0050 -12.9533 H 1 LIG1 0.1046
91 H 4.4232 -6.4241 -17.1449 H 1 LIG1 0.0251
92 H 3.9428 -5.8167 -15.5315 H 1 LIG1 0.0251
93 H 2.6779 -6.2381 -16.7493 H 1 LIG1 0.0251
94 H 2.4938 -2.3324 -18.5377 H 1 LIG1 0.0621
95 H 0.7330 -0.8047 -17.7661 H 1 LIG1 0.0618
96 H -0.2211 -1.0413 -15.4952 H 1 LIG1 0.0618
97 H 0.6133 -2.8141 -13.9796 H 1 LIG1 0.0618
98 H 2.3830 -4.3416 -14.7100 H 1 LIG1 0.0621
@<TRIPOS>BOND
1 1 2 1
2 1 53 1
3 1 54 1
4 1 55 1
5 2 49 1
6 2 21 1
7 2 3 1
8 3 4 1
9 3 56 1
10 3 57 1
11 4 5 1
12 4 58 1
13 4 59 1
14 5 6 1
15 5 60 1
16 5 61 1
17 6 7 1
18 6 62 1
19 6 63 1
20 7 8 1
21 7 64 1
22 7 65 1
23 8 9 am
24 8 41 1
25 9 10 2
26 9 11 1
27 11 16 ar
28 11 12 ar
29 12 13 ar
30 12 66 1
31 13 14 ar
32 13 36 1
33 14 15 ar
34 14 67 1
35 15 16 ar
36 15 17 1
37 16 68 1
38 17 18 2
39 17 19 am
40 19 20 1
41 19 69 1
42 20 50 1
43 20 21 1
44 20 22 1
45 21 70 1
46 21 71 1
47 22 51 1
48 22 23 1
49 22 35 1
50 23 24 1
51 23 72 1
52 23 73 1
53 24 25 1
54 24 74 1
55 25 26 1
56 25 75 1
57 25 76 1
58 26 31 ar
59 26 27 ar
60 27 28 ar
61 27 77 1
62 28 29 ar
63 28 78 1
64 29 30 ar
65 29 79 1
66 30 31 ar
67 30 32 1
68 31 80 1
69 32 33 1
70 32 34 1
71 32 81 1
72 33 82 1
73 33 83 1
74 33 84 1
75 34 85 1
76 34 86 1
77 34 87 1
78 35 88 1
79 36 40 ar
80 36 37 ar
81 37 38 ar
82 38 39 ar
83 38 89 1
84 39 40 ar
85 39 90 1
86 41 52 1
87 41 42 1
88 41 43 1
89 42 91 1
90 42 92 1
91 42 93 1
92 43 48 ar
93 43 44 ar
94 44 45 ar
95 44 94 1
96 45 46 ar
97 45 95 1
98 46 47 ar
99 46 96 1
100 47 48 ar
101 47 97 1
102 48 98 1
Meastro (AmberTools consider this correct):
@<TRIPOS>MOLECULE
BACE7
98 102 1
SMALL
USER_CHARGES
@<TRIPOS>ATOM
1 C1 4.4906 1.0444 -22.8214 C.3 1 UNK
0.0000
2 C2 4.8922 0.9339 -21.3406 C.3 1 UNK
0.0000
3 C3 4.7328 -0.5268 -20.8573 C.3 1 UNK
0.0000
4 C4 5.8712 -1.4883 -21.3104 C.3 1 UNK
0.0000
5 C5 5.8678 -2.8681 -20.5852 C.3 1 UNK
0.0000
6 C6 5.7796 -2.6627 -19.0768 C.3 1 UNK
0.0000
7 C7 6.0082 -3.8328 -18.1147 C.3 1 UNK
0.0000
8 N8 5.0491 -3.7436 -16.9811 N.am 1 UNK
0.0000
9 C9 5.3910 -3.1904 -15.7259 C.2 1 UNK
0.0000
10 O10 4.9860 -3.7155 -14.6679 O.2 1 UNK
0.0000
11 C11 6.1926 -1.9707 -15.7016 C.ar 1 UNK
0.0000
12 C12 7.2723 -1.8151 -14.8219 C.ar 1 UNK
0.0000
13 C13 8.0748 -0.6639 -14.8950 C.ar 1 UNK
0.0000
14 C14 7.7594 0.3295 -15.8386 C.ar 1 UNK
0.0000
15 C15 6.6529 0.1798 -16.6946 C.ar 1 UNK
0.0000
16 C16 5.9088 -0.9874 -16.6449 C.ar 1 UNK
0.0000
17 C17 6.3758 1.1928 -17.7374 C.2 1 UNK
0.0000
18 O18 7.3575 1.7202 -18.3089 O.2 1 UNK
0.0000
19 N19 5.0541 1.4981 -18.2116 N.am 1 UNK
0.0000
20 C20 4.8315 2.5154 -19.2554 C.3 1 UNK
0.0000
21 C21 4.0479 1.9160 -20.4590 C.3 1 UNK
0.0000
22 C22 4.1278 3.7525 -18.6377 C.3 1 UNK
0.0000
23 C23 4.9660 4.3781 -17.5041 C.3 1 UNK
0.0000
24 N24 4.2842 5.5876 -17.0101 N.3 1 UNK
0.0000
25 C25 5.1777 6.6776 -16.6101 C.3 1 UNK
0.0000
26 C26 6.0118 7.1928 -17.7645 C.ar 1 UNK
0.0000
27 C27 7.4134 7.0911 -17.6697 C.ar 1 UNK
0.0000
28 C28 8.2301 7.5127 -18.7170 C.ar 1 UNK
0.0000
29 C29 7.6590 8.0307 -19.8750 C.ar 1 UNK
0.0000
30 C30 6.2656 8.1500 -19.9835 C.ar 1 UNK
0.0000
31 C31 5.4430 7.7541 -18.9156 C.ar 1 UNK
0.0000
32 C32 5.6601 8.6452 -21.2852 C.3 1 UNK
0.0000
33 C33 4.7533 9.8610 -21.0668 C.3 1 UNK
0.0000
34 C34 4.9002 7.5146 -21.9875 C.3 1 UNK
0.0000
35 O35 3.9440 4.7344 -19.6282 O.3 1 UNK
0.0000
36 C36 9.2604 -0.5139 -14.0265 C.2 1 UNK
0.0000
37 N37 9.6773 -1.4569 -13.1548 N.2 1 UNK
0.0000
38 C38 10.7852 -0.9156 -12.6169 C.2 1 UNK
0.0000
39 C39 11.0006 0.3233 -13.1739 C.2 1 UNK
0.0000
40 O40 10.0422 0.5438 -14.0357 O.3 1 UNK
0.0000
41 C41 3.7184 -4.3654 -17.1815 C.3 1 UNK
0.0000
42 C42 3.6849 -5.7921 -16.6077 C.3 1 UNK
0.0000
43 C43 2.5948 -3.4594 -16.6885 C.ar 1 UNK
0.0000
44 C44 2.1036 -2.4496 -17.5372 C.ar 1 UNK
0.0000
45 C45 1.0992 -1.5797 -17.1055 C.ar 1 UNK
0.0000
46 C46 0.5629 -1.7113 -15.8244 C.ar 1 UNK
0.0000
47 C47 1.0304 -2.7139 -14.9731 C.ar 1 UNK
0.0000
48 C48 2.0402 -3.5825 -15.3976 C.ar 1 UNK
0.0000
49 H49 5.9644 1.2247 -21.2739 H 1 UNK
0.0000
50 H50 5.7964 2.8799 -19.6624 H 1 UNK
0.0000
51 H51 3.1462 3.4322 -18.2096 H 1 UNK
0.0000
52 H52 3.5467 -4.5027 -18.2736 H 1 UNK
0.0000
53 H53 3.4150 0.7979 -22.9558 H 1 UNK
0.0000
54 H54 5.1004 0.3599 -23.4465 H 1 UNK
0.0000
55 H55 4.6652 2.0788 -23.1866 H 1 UNK
0.0000
56 H56 4.7166 -0.4534 -19.7587 H 1 UNK
0.0000
57 H57 3.7500 -0.9452 -21.1700 H 1 UNK
0.0000
58 H58 5.7965 -1.6618 -22.4043 H 1 UNK
0.0000
59 H59 6.8502 -1.0012 -21.1167 H 1 UNK
0.0000
60 H60 5.0053 -3.4737 -20.9333 H 1 UNK
0.0000
61 H61 6.8042 -3.4123 -20.8288 H 1 UNK
0.0000
62 H62 6.5254 -1.8809 -18.8351 H 1 UNK
0.0000
63 H63 4.7440 -2.3354 -18.8997 H 1 UNK
0.0000
64 H64 7.0562 -3.8126 -17.7420 H 1 UNK
0.0000
65 H65 5.8794 -4.7982 -18.6486 H 1 UNK
0.0000
66 H66 7.5041 -2.6037 -14.1147 H 1 UNK
0.0000
67 H67 8.3749 1.2174 -15.9128 H 1 UNK
0.0000
68 H68 4.9935 -1.0449 -17.2115 H 1 UNK
0.0000
69 H69 4.2242 1.0811 -17.7380 H 1 UNK
0.0000
70 H70 3.1207 1.4242 -20.0987 H 1 UNK
0.0000
71 H71 3.7154 2.7566 -21.1017 H 1 UNK
0.0000
72 H72 5.9766 4.6051 -17.9036 H 1 UNK
0.0000
73 H73 5.0959 3.6528 -16.6730 H 1 UNK
0.0000
74 H74 3.6902 5.3236 -16.1884 H 1 UNK
0.0000
75 H75 4.5586 7.5177 -16.2301 H 1 UNK
0.0000
76 H76 5.8155 6.3352 -15.7648 H 1 UNK
0.0000
77 H77 7.8777 6.6663 -16.7890 H 1 UNK
0.0000
78 H78 9.3069 7.4243 -18.6376 H 1 UNK
0.0000
79 H79 8.3068 8.3297 -20.6899 H 1 UNK
0.0000
80 H80 4.3652 7.8246 -18.9948 H 1 UNK
0.0000
81 H81 6.4721 8.9668 -21.9757 H 1 UNK
0.0000
82 H82 3.8505 9.5898 -20.4774 H 1 UNK
0.0000
83 H83 4.4204 10.2688 -22.0459 H 1 UNK
0.0000
84 H84 5.3112 10.6606 -20.5315 H 1 UNK
0.0000
85 H85 4.0349 7.1733 -21.3729 H 1 UNK
0.0000
86 H86 5.5826 6.6513 -22.1567 H 1 UNK
0.0000
87 H87 4.5216 7.8616 -22.9744 H 1 UNK
0.0000
88 H88 2.9876 4.7176 -19.8960 H 1 UNK
0.0000
89 H89 11.4027 -1.3995 -11.8736 H 1 UNK
0.0000
90 H90 11.8106 1.0050 -12.9533 H 1 UNK
0.0000
91 H91 4.4232 -6.4241 -17.1449 H 1 UNK
0.0000
92 H92 3.9428 -5.8167 -15.5315 H 1 UNK
0.0000
93 H93 2.6779 -6.2381 -16.7493 H 1 UNK
0.0000
94 H94 2.4938 -2.3324 -18.5377 H 1 UNK
0.0000
95 H95 0.7330 -0.8047 -17.7661 H 1 UNK
0.0000
96 H96 -0.2211 -1.0413 -15.4952 H 1 UNK
0.0000
97 H97 0.6133 -2.8141 -13.9796 H 1 UNK
0.0000
98 H98 2.3830 -4.3416 -14.7100 H 1 UNK
0.0000
@<TRIPOS>BOND
1 1 2 1
2 1 53 1
3 1 54 1
4 1 55 1
5 2 49 1
6 2 21 1
7 2 3 1
8 3 4 1
9 3 56 1
10 3 57 1
11 4 5 1
12 4 58 1
13 4 59 1
14 5 6 1
15 5 60 1
16 5 61 1
17 6 7 1
18 6 62 1
19 6 63 1
20 7 8 1
21 7 64 1
22 7 65 1
23 8 9 am BACKBONE|DICT|INTERRES
24 8 41 1
25 9 10 2
26 9 11 1
27 11 16 ar
28 11 12 ar
29 12 13 ar
30 12 66 1
31 13 14 ar
32 13 36 1
33 14 15 ar
34 14 67 1
35 15 16 ar
36 15 17 1
37 16 68 1
38 17 18 2
39 17 19 am BACKBONE|DICT|INTERRES
40 19 20 1
41 19 69 1
42 20 50 1
43 20 21 1
44 20 22 1
45 21 70 1
46 21 71 1
47 22 51 1
48 22 23 1
49 22 35 1
50 23 24 1
51 23 72 1
52 23 73 1
53 24 25 1
54 24 74 1
55 25 26 1
56 25 75 1
57 25 76 1
58 26 31 ar
59 26 27 ar
60 27 28 ar
61 27 77 1
62 28 29 ar
63 28 78 1
64 29 30 ar
65 29 79 1
66 30 31 ar
67 30 32 1
68 31 80 1
69 32 33 1
70 32 34 1
71 32 81 1
72 33 82 1
73 33 83 1
74 33 84 1
75 34 85 1
76 34 86 1
77 34 87 1
78 35 88 1
79 36 40 1
80 36 37 2
81 37 38 1
82 38 39 2
83 38 89 1
84 39 40 1
85 39 90 1
86 41 52 1
87 41 42 1
88 41 43 1
89 42 91 1
90 42 92 1
91 42 93 1
92 43 48 ar
93 43 44 ar
94 44 45 ar
95 44 94 1
96
97 45 95 1
98 46 47 ar
99 46 96 1
100 47 48 ar
101 47 97 1
102 48 98 1
@<TRIPOS>SUBSTRUCTURE
1 UNK 1 GROUP 0 **** 0 ROOT
--
======================================================================
Dr Thomas Evangelidis
Research Scientist
IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en>
Prague, Czech Republic
&
CEITEC - Central European Institute of Technology <https://www.ceitec.eu/>
Brno, Czech Republic
email: [email protected]
website: https://sites.google.com/site/thomasevangelidishomepage/
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