Skip to content

Commit 23e4550

Browse files
atravitzatravitz
authored
Merge pull request #284 from OpenFreeEnergy/cofactors_cookbook
add cofactor example as a cookbook
2 parents 714542b + 9f8d99f commit 23e4550

File tree

4 files changed

+13703
-0
lines changed

4 files changed

+13703
-0
lines changed

‎cookbook/assets/cofactors/eg5_cofactor_charged.sdf‎

Lines changed: 98 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,98 @@
1+
3L9H
2+
RDKit 3D
3+
4+
39 41 0 0 0 0 0 0 0 0999 V2000
5+
17.7103 1.3810 16.7258 P 0 0 0 0 0 5 0 0 0 0 0 0
6+
16.2918 1.9380 16.9415 O 0 0 0 0 0 0 0 0 0 0 0 0
7+
17.7048 -0.1381 16.4765 O 0 0 0 0 0 0 0 0 0 0 0 0
8+
18.4945 2.1622 15.6604 O 0 0 0 0 0 0 0 0 0 0 0 0
9+
20.1704 1.9553 18.6598 P 0 0 1 0 0 5 0 0 0 0 0 0
10+
21.0614 1.4768 17.5414 O 0 0 0 0 0 0 0 0 0 0 0 0
11+
20.2345 3.3559 19.2252 O 0 0 0 0 0 0 0 0 0 0 0 0
12+
18.5522 1.6400 18.2257 O 0 0 0 0 0 0 0 0 0 0 0 0
13+
20.3327 0.8377 19.9634 O 0 0 0 0 0 0 0 0 0 0 0 0
14+
19.5869 1.0879 21.1452 C 0 0 0 0 0 0 0 0 0 0 0 0
15+
20.4613 1.1653 22.4074 C 0 0 1 0 0 0 0 0 0 0 0 0
16+
21.0911 -0.0950 22.5958 O 0 0 0 0 0 0 0 0 0 0 0 0
17+
21.6078 2.1760 22.3912 C 0 0 1 0 0 0 0 0 0 0 0 0
18+
21.7761 2.7834 23.6633 O 0 0 0 0 0 0 0 0 0 0 0 0
19+
22.8150 1.3580 21.9342 C 0 0 1 0 0 0 0 0 0 0 0 0
20+
24.0771 1.7580 22.4399 O 0 0 0 0 0 0 0 0 0 0 0 0
21+
22.4830 -0.0283 22.4899 C 0 0 2 0 0 0 0 0 0 0 0 0
22+
22.9954 -1.1724 21.6426 N 0 0 0 0 0 0 0 0 0 0 0 0
23+
22.4947 -1.6440 20.4842 C 0 0 0 0 0 0 0 0 0 0 0 0
24+
23.2096 -2.5994 19.9459 N 0 0 0 0 0 0 0 0 0 0 0 0
25+
24.2457 -2.7439 20.7874 C 0 0 0 0 0 0 0 0 0 0 0 0
26+
25.3696 -3.6002 20.7533 C 0 0 0 0 0 0 0 0 0 0 0 0
27+
25.5873 -4.5319 19.7432 N 0 0 0 0 0 0 0 0 0 0 0 0
28+
26.2748 -3.5190 21.7663 N 0 0 0 0 0 0 0 0 0 0 0 0
29+
26.0465 -2.6305 22.7424 C 0 0 0 0 0 0 0 0 0 0 0 0
30+
25.0272 -1.7702 22.8844 N 0 0 0 0 0 0 0 0 0 0 0 0
31+
24.1457 -1.8743 21.8585 C 0 0 0 0 0 0 0 0 0 0 0 0
32+
18.9006 0.2596 21.2825 H 0 0 0 0 0 0 0 0 0 0 0 0
33+
18.9668 1.9826 21.0671 H 0 0 0 0 0 0 0 0 0 0 0 0
34+
19.7967 1.3439 23.2547 H 0 0 0 0 0 0 0 0 0 0 0 0
35+
21.4113 2.9719 21.6708 H 0 0 0 0 0 0 0 0 0 0 0 0
36+
22.6054 3.2689 23.6516 H 0 0 0 0 0 0 0 0 0 0 0 0
37+
22.8340 1.3030 20.8442 H 0 0 0 0 0 0 0 0 0 0 0 0
38+
24.3615 2.5656 21.9940 H 0 0 0 0 0 0 0 0 0 0 0 0
39+
22.8770 -0.1608 23.5002 H 0 0 0 0 0 0 0 0 0 0 0 0
40+
21.5746 -1.2447 20.0891 H 0 0 0 0 0 0 0 0 0 0 0 0
41+
26.3917 -5.1389 19.8129 H 0 0 0 0 0 0 0 0 0 0 0 0
42+
24.9075 -4.6313 19.0027 H 0 0 0 0 0 0 0 0 0 0 0 0
43+
26.7890 -2.6030 23.5264 H 0 0 0 0 0 0 0 0 0 0 0 0
44+
1 2 2 0
45+
1 3 1 0
46+
1 4 1 0
47+
1 8 1 0
48+
5 6 2 0
49+
5 7 1 1
50+
5 8 1 0
51+
5 9 1 0
52+
9 10 1 0
53+
10 11 1 0
54+
10 28 1 0
55+
10 29 1 0
56+
11 12 1 0
57+
11 13 1 0
58+
11 30 1 1
59+
12 17 1 0
60+
13 14 1 0
61+
13 15 1 0
62+
13 31 1 6
63+
14 32 1 0
64+
15 16 1 0
65+
15 17 1 0
66+
15 33 1 6
67+
16 34 1 0
68+
17 18 1 0
69+
17 35 1 1
70+
18 19 1 0
71+
18 27 1 0
72+
19 20 2 0
73+
19 36 1 0
74+
20 21 1 0
75+
21 22 1 0
76+
21 27 2 0
77+
22 23 1 0
78+
22 24 2 0
79+
23 37 1 0
80+
23 38 1 0
81+
24 25 1 0
82+
25 26 2 0
83+
25 39 1 0
84+
26 27 1 0
85+
M CHG 3 3 -1 4 -1 7 -1
86+
M END
87+
88+
> <ofe-name>
89+
3L9H
90+
91+
> <atom.dprop.PartialCharge>
92+
1.3988487435897436 -0.91321825641025633 -0.91321825641025633 -0.91321825641025633 1.5677487435897437 -0.67705125641025643 -0.67705125641025643 -0.77085125641025642 -0.59125125641025633
93+
0.1833487435897436 0.088048743589743572 -0.42865125641025642 0.064048743589743579 -0.59785125641025638 0.080048743589743579 -0.6198512564102564 0.27474874358974355 -0.28105125641025647
94+
0.35164874358974357 -0.76515125641025639 -0.11125125641025642 0.54814874358974364 -0.89255125641025634 -0.77805125641025641 0.56384874358974357 -0.71505125641025635 0.38374874358974354
95+
0.06664874358974357 0.06664874358974357 0.034648743589743576 0.16864874358974358 0.38094874358974357 0.11064874358974358 0.40294874358974359 0.042648743589743576 0.15174874358974358
96+
0.35724874358974357 0.35724874358974357 0.0010487435897435762
97+
98+
$$$$

0 commit comments

Comments
 (0)