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THU-ATOM
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PDBbind_test

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Add batch 23

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  1. 6p8y/6p8y_ligand.mol2 +150 -0
  2. 6p8y/6p8y_ligand.sdf +140 -0
  3. 6p8y/6p8y_protein_alphafold_aligned_tr_fix.pdb +0 -0
  4. 6p8y/6p8y_protein_esmfold_aligned_tr_fix.pdb +0 -0
  5. 6p8y/6p8y_protein_processed_fix.pdb +0 -0
  6. 6p8y/6p8y_rdkit_ligand.pdb +98 -0
  7. 6p8z/6p8z_ligand.mol2 +171 -0
  8. 6p8z/6p8z_ligand.sdf +161 -0
  9. 6p8z/6p8z_protein_alphafold_aligned_tr_fix.pdb +0 -0
  10. 6p8z/6p8z_protein_esmfold_aligned_tr_fix.pdb +0 -0
  11. 6p8z/6p8z_protein_processed_fix.pdb +0 -0
  12. 6p8z/6p8z_rdkit_ligand.pdb +112 -0
  13. 6pgo/6pgo_ligand.mol2 +138 -0
  14. 6pgo/6pgo_ligand.sdf +128 -0
  15. 6pgo/6pgo_protein_alphafold_aligned_tr_fix.pdb +0 -0
  16. 6pgo/6pgo_protein_esmfold_aligned_tr_fix.pdb +0 -0
  17. 6pgo/6pgo_protein_processed_fix.pdb +0 -0
  18. 6pgo/6pgo_rdkit_ligand.pdb +92 -0
  19. 6pgp/6pgp_ligand.mol2 +158 -0
  20. 6pgp/6pgp_ligand.sdf +148 -0
  21. 6pgp/6pgp_protein_alphafold_aligned_tr_fix.pdb +0 -0
  22. 6pgp/6pgp_protein_esmfold_aligned_tr_fix.pdb +0 -0
  23. 6pgp/6pgp_protein_processed_fix.pdb +0 -0
  24. 6pgp/6pgp_rdkit_ligand.pdb +106 -0
  25. 6pka/6pka_ligand.mol2 +232 -0
  26. 6pka/6pka_ligand.sdf +222 -0
  27. 6pka/6pka_protein_alphafold_aligned_tr_fix.pdb +0 -0
  28. 6pka/6pka_protein_esmfold_aligned_tr_fix.pdb +0 -0
  29. 6pka/6pka_protein_processed_fix.pdb +0 -0
  30. 6pka/6pka_rdkit_ligand.pdb +156 -0
  31. 6pnm/6pnm_ligand.mol2 +87 -0
  32. 6pnm/6pnm_ligand.sdf +77 -0
  33. 6pnm/6pnm_protein_alphafold_aligned_tr_fix.pdb +0 -0
  34. 6pnm/6pnm_protein_esmfold_aligned_tr_fix.pdb +0 -0
  35. 6pnm/6pnm_protein_processed_fix.pdb +0 -0
  36. 6pnm/6pnm_rdkit_ligand.pdb +54 -0
  37. 6pnn/6pnn_ligand.mol2 +90 -0
  38. 6pnn/6pnn_ligand.sdf +80 -0
  39. 6pnn/6pnn_protein_alphafold_aligned_tr_fix.pdb +0 -0
  40. 6pnn/6pnn_protein_esmfold_aligned_tr_fix.pdb +0 -0
  41. 6pnn/6pnn_protein_processed_fix.pdb +0 -0
  42. 6pnn/6pnn_rdkit_ligand.pdb +56 -0
  43. 6pno/6pno_ligand.mol2 +82 -0
  44. 6pno/6pno_ligand.sdf +72 -0
  45. 6pno/6pno_protein_alphafold_aligned_tr_fix.pdb +0 -0
  46. 6pno/6pno_protein_esmfold_aligned_tr_fix.pdb +0 -0
  47. 6pno/6pno_protein_processed_fix.pdb +0 -0
  48. 6pno/6pno_rdkit_ligand.pdb +50 -0
  49. 6py0/6py0_ligand.mol2 +122 -0
  50. 6py0/6py0_ligand.sdf +112 -0
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6p8y/6p8y_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6p8y/6p8y_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6p8y/6p8y_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6p8y/6p8y_rdkit_ligand.pdb ADDED
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+ CONECT 13 14 36
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+ CONECT 14 15 15 50
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+ CONECT 15 16 30
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+ CONECT 19 20 51 52
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+ CONECT 20 21 53 54
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+ CONECT 21 22 22 28
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+ CONECT 22 23 25
86
+ CONECT 23 24
87
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+ CONECT 26 27 59
90
+ CONECT 27 28 28 60
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+ CONECT 28 29
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+ CONECT 30 31 36 36
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+ CONECT 31 32 32 63
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+ CONECT 32 33 34
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+ CONECT 34 35 35 64
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+ CONECT 35 36 65
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+ END
6p8z/6p8z_ligand.mol2 ADDED
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+ ###
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+ M END
161
+ $$$$
6p8z/6p8z_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6p8z/6p8z_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6p8z/6p8z_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6p8z/6p8z_rdkit_ligand.pdb ADDED
@@ -0,0 +1,112 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ COMPND 6p8z_ligand
2
+ HETATM 1 C1 UNL 1 10.174 0.785 1.629 1.00 0.00 C
3
+ HETATM 2 C2 UNL 1 8.859 0.138 1.341 1.00 0.00 C
4
+ HETATM 3 C3 UNL 1 7.751 1.148 1.219 1.00 0.00 C
5
+ HETATM 4 O1 UNL 1 8.068 2.353 1.385 1.00 0.00 O
6
+ HETATM 5 N1 UNL 1 6.434 0.739 0.933 1.00 0.00 N
7
+ HETATM 6 C4 UNL 1 5.613 -0.424 0.675 1.00 0.00 C
8
+ HETATM 7 C5 UNL 1 4.835 0.489 -0.271 1.00 0.00 C
9
+ HETATM 8 C6 UNL 1 5.186 1.507 0.754 1.00 0.00 C
10
+ HETATM 9 N2 UNL 1 3.496 0.155 -0.554 1.00 0.00 N
11
+ HETATM 10 C7 UNL 1 2.957 0.045 -1.868 1.00 0.00 C
12
+ HETATM 11 O2 UNL 1 3.816 0.284 -2.753 1.00 0.00 O
13
+ HETATM 12 C8 UNL 1 1.592 -0.299 -2.216 1.00 0.00 C
14
+ HETATM 13 N3 UNL 1 0.662 -0.566 -1.185 1.00 0.00 N
15
+ HETATM 14 C9 UNL 1 -0.121 0.357 -0.577 1.00 0.00 C
16
+ HETATM 15 C10 UNL 1 -0.211 1.780 -0.781 1.00 0.00 C
17
+ HETATM 16 C11 UNL 1 -0.728 2.448 -1.983 1.00 0.00 C
18
+ HETATM 17 C12 UNL 1 0.701 2.718 -1.426 1.00 0.00 C
19
+ HETATM 18 C13 UNL 1 -0.931 -0.325 0.362 1.00 0.00 C
20
+ HETATM 19 C14 UNL 1 -1.929 0.281 1.251 1.00 0.00 C
21
+ HETATM 20 O3 UNL 1 -1.589 0.806 2.339 1.00 0.00 O
22
+ HETATM 21 N4 UNL 1 -3.307 0.314 0.948 1.00 0.00 N
23
+ HETATM 22 C15 UNL 1 -4.261 0.919 1.844 1.00 0.00 C
24
+ HETATM 23 C16 UNL 1 -5.264 1.716 1.033 1.00 0.00 C
25
+ HETATM 24 C17 UNL 1 -5.937 0.742 0.146 1.00 0.00 C
26
+ HETATM 25 C18 UNL 1 -7.301 0.804 -0.039 1.00 0.00 C
27
+ HETATM 26 O4 UNL 1 -8.053 1.759 0.584 1.00 0.00 O
28
+ HETATM 27 C19 UNL 1 -9.446 1.817 0.386 1.00 0.00 C
29
+ HETATM 28 C20 UNL 1 -7.950 -0.113 -0.872 1.00 0.00 C
30
+ HETATM 29 C21 UNL 1 -7.195 -1.075 -1.500 1.00 0.00 C
31
+ HETATM 30 C22 UNL 1 -5.837 -1.131 -1.310 1.00 0.00 C
32
+ HETATM 31 C23 UNL 1 -5.219 -0.234 -0.499 1.00 0.00 C
33
+ HETATM 32 C24 UNL 1 -3.761 -0.274 -0.285 1.00 0.00 C
34
+ HETATM 33 C25 UNL 1 -0.616 -1.642 0.300 1.00 0.00 C
35
+ HETATM 34 C26 UNL 1 -1.121 -2.711 1.011 1.00 0.00 C
36
+ HETATM 35 C27 UNL 1 -0.659 -3.988 0.798 1.00 0.00 C
37
+ HETATM 36 CL1 UNL 1 -1.295 -5.356 1.698 1.00 0.00 CL
38
+ HETATM 37 C28 UNL 1 0.307 -4.155 -0.135 1.00 0.00 C
39
+ HETATM 38 C29 UNL 1 0.820 -3.061 -0.859 1.00 0.00 C
40
+ HETATM 39 C30 UNL 1 1.877 -3.302 -1.861 1.00 0.00 C
41
+ HETATM 40 C31 UNL 1 0.371 -1.771 -0.662 1.00 0.00 C
42
+ HETATM 41 H1 UNL 1 10.112 1.737 2.167 1.00 0.00 H
43
+ HETATM 42 H2 UNL 1 10.807 0.896 0.703 1.00 0.00 H
44
+ HETATM 43 H3 UNL 1 10.756 0.076 2.276 1.00 0.00 H
45
+ HETATM 44 H4 UNL 1 8.587 -0.546 2.152 1.00 0.00 H
46
+ HETATM 45 H5 UNL 1 8.908 -0.395 0.357 1.00 0.00 H
47
+ HETATM 46 H6 UNL 1 5.048 -0.723 1.588 1.00 0.00 H
48
+ HETATM 47 H7 UNL 1 6.113 -1.264 0.183 1.00 0.00 H
49
+ HETATM 48 H8 UNL 1 5.444 0.652 -1.186 1.00 0.00 H
50
+ HETATM 49 H9 UNL 1 4.657 1.493 1.708 1.00 0.00 H
51
+ HETATM 50 H10 UNL 1 5.370 2.490 0.294 1.00 0.00 H
52
+ HETATM 51 H11 UNL 1 2.852 -0.023 0.283 1.00 0.00 H
53
+ HETATM 52 H12 UNL 1 1.688 -1.138 -2.984 1.00 0.00 H
54
+ HETATM 53 H13 UNL 1 1.201 0.490 -2.952 1.00 0.00 H
55
+ HETATM 54 H14 UNL 1 -0.648 2.318 0.155 1.00 0.00 H
56
+ HETATM 55 H15 UNL 1 -1.460 3.275 -1.948 1.00 0.00 H
57
+ HETATM 56 H16 UNL 1 -0.649 2.025 -3.006 1.00 0.00 H
58
+ HETATM 57 H17 UNL 1 0.769 3.804 -1.060 1.00 0.00 H
59
+ HETATM 58 H18 UNL 1 1.570 2.521 -2.029 1.00 0.00 H
60
+ HETATM 59 H19 UNL 1 -3.777 1.536 2.627 1.00 0.00 H
61
+ HETATM 60 H20 UNL 1 -4.823 0.092 2.326 1.00 0.00 H
62
+ HETATM 61 H21 UNL 1 -4.680 2.438 0.430 1.00 0.00 H
63
+ HETATM 62 H22 UNL 1 -5.982 2.215 1.725 1.00 0.00 H
64
+ HETATM 63 H23 UNL 1 -9.678 1.863 -0.703 1.00 0.00 H
65
+ HETATM 64 H24 UNL 1 -9.885 0.932 0.860 1.00 0.00 H
66
+ HETATM 65 H25 UNL 1 -9.858 2.730 0.890 1.00 0.00 H
67
+ HETATM 66 H26 UNL 1 -9.023 -0.085 -1.034 1.00 0.00 H
68
+ HETATM 67 H27 UNL 1 -7.676 -1.816 -2.165 1.00 0.00 H
69
+ HETATM 68 H28 UNL 1 -5.220 -1.881 -1.794 1.00 0.00 H
70
+ HETATM 69 H29 UNL 1 -3.352 -1.308 -0.334 1.00 0.00 H
71
+ HETATM 70 H30 UNL 1 -3.314 0.252 -1.180 1.00 0.00 H
72
+ HETATM 71 H31 UNL 1 -1.899 -2.620 1.772 1.00 0.00 H
73
+ HETATM 72 H32 UNL 1 0.695 -5.154 -0.328 1.00 0.00 H
74
+ HETATM 73 H33 UNL 1 2.240 -4.376 -1.652 1.00 0.00 H
75
+ HETATM 74 H34 UNL 1 1.514 -3.425 -2.897 1.00 0.00 H
76
+ HETATM 75 H35 UNL 1 2.809 -2.757 -1.715 1.00 0.00 H
77
+ CONECT 1 2 41 42 43
78
+ CONECT 2 3 44 45
79
+ CONECT 3 4 4 5
80
+ CONECT 5 6 8
81
+ CONECT 6 7 46 47
82
+ CONECT 7 8 9 48
83
+ CONECT 8 49 50
84
+ CONECT 9 10 51
85
+ CONECT 10 11 11 12
86
+ CONECT 12 13 52 53
87
+ CONECT 13 14 40
88
+ CONECT 14 15 18 18
89
+ CONECT 15 16 17 54
90
+ CONECT 16 17 55 56
91
+ CONECT 17 57 58
92
+ CONECT 18 19 33
93
+ CONECT 19 20 20 21
94
+ CONECT 21 22 32
95
+ CONECT 22 23 59 60
96
+ CONECT 23 24 61 62
97
+ CONECT 24 25 25 31
98
+ CONECT 25 26 28
99
+ CONECT 26 27
100
+ CONECT 27 63 64 65
101
+ CONECT 28 29 29 66
102
+ CONECT 29 30 67
103
+ CONECT 30 31 31 68
104
+ CONECT 31 32
105
+ CONECT 32 69 70
106
+ CONECT 33 34 34 40
107
+ CONECT 34 35 71
108
+ CONECT 35 36 37 37
109
+ CONECT 37 38 72
110
+ CONECT 38 39 40 40
111
+ CONECT 39 73 74 75
112
+ END
6pgo/6pgo_ligand.mol2 ADDED
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1
+ ###
2
+ ### Created by X-TOOL on Mon Aug 2 16:11:39 2021
3
+ ###
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+
5
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+
6pgo/6pgo_ligand.sdf ADDED
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1
+ 6pgo_ligand
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+ 9.4209 -1.2618 42.4077 H 0 0 0 0 0
48
+ 11.1862 -1.3758 42.5056 H 0 0 0 0 0
49
+ 8.0345 -2.3423 43.8405 H 0 0 0 0 0
50
+ 8.5961 -3.6214 44.9327 H 0 0 0 0 0
51
+ 9.2611 -5.0063 43.0934 H 0 0 0 0 0
52
+ 7.5541 -4.4156 42.7852 H 0 0 0 0 0
53
+ 11.4018 -0.3931 49.4542 H 0 0 0 0 0
54
+ 12.1445 1.2291 51.1842 H 0 0 0 0 0
55
+ 13.1482 3.3916 50.5063 H 0 0 0 0 0
56
+ 13.4520 3.9267 48.1065 H 0 0 0 0 0
57
+ 12.7043 2.3141 46.3750 H 0 0 0 0 0
58
+ 14.3636 -0.0452 47.0667 H 0 0 0 0 0
59
+ 12.5831 -3.1300 43.6143 H 0 0 0 0 0
60
+ 16.5522 -2.8420 48.6415 H 0 0 0 0 0
61
+ 18.6154 -2.1574 48.0935 H 0 0 0 0 0
62
+ 20.0326 -0.9782 46.4379 H 0 0 0 0 0
63
+ 19.0175 -0.0726 44.3628 H 0 0 0 0 0
64
+ 1 2 1 0 0 0
65
+ 2 3 1 0 0 0
66
+ 3 4 2 0 0 0
67
+ 3 5 1 0 0 0
68
+ 5 6 1 0 0 0
69
+ 5 10 1 0 0 0
70
+ 6 7 1 0 0 0
71
+ 7 8 1 0 0 0
72
+ 8 9 1 0 0 0
73
+ 8 11 1 0 0 0
74
+ 9 10 1 0 0 0
75
+ 11 12 4 0 0 0
76
+ 11 27 4 0 0 0
77
+ 12 13 4 0 0 0
78
+ 13 14 4 0 0 0
79
+ 14 15 1 0 0 0
80
+ 14 21 4 0 0 0
81
+ 15 16 4 0 0 0
82
+ 15 20 4 0 0 0
83
+ 16 17 4 0 0 0
84
+ 17 18 4 0 0 0
85
+ 18 19 4 0 0 0
86
+ 19 20 4 0 0 0
87
+ 21 22 4 0 0 0
88
+ 21 27 4 0 0 0
89
+ 22 23 4 0 0 0
90
+ 23 24 4 0 0 0
91
+ 23 28 1 0 0 0
92
+ 24 25 1 0 0 0
93
+ 24 26 4 0 0 0
94
+ 26 27 4 0 0 0
95
+ 28 29 4 0 0 0
96
+ 28 34 4 0 0 0
97
+ 29 30 1 0 0 0
98
+ 29 31 4 0 0 0
99
+ 31 32 4 0 0 0
100
+ 32 33 4 0 0 0
101
+ 33 34 4 0 0 0
102
+ 34 35 1 0 0 0
103
+ 1 36 1 0 0 0
104
+ 1 37 1 0 0 0
105
+ 1 38 1 0 0 0
106
+ 2 39 1 0 0 0
107
+ 2 40 1 0 0 0
108
+ 6 41 1 0 0 0
109
+ 6 42 1 0 0 0
110
+ 7 43 1 0 0 0
111
+ 7 44 1 0 0 0
112
+ 9 45 1 0 0 0
113
+ 9 46 1 0 0 0
114
+ 10 47 1 0 0 0
115
+ 10 48 1 0 0 0
116
+ 16 49 1 0 0 0
117
+ 17 50 1 0 0 0
118
+ 18 51 1 0 0 0
119
+ 19 52 1 0 0 0
120
+ 20 53 1 0 0 0
121
+ 22 54 1 0 0 0
122
+ 26 55 1 0 0 0
123
+ 30 56 1 0 0 0
124
+ 31 57 1 0 0 0
125
+ 32 58 1 0 0 0
126
+ 33 59 1 0 0 0
127
+ M END
128
+ $$$$
6pgo/6pgo_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pgo/6pgo_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pgo/6pgo_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pgo/6pgo_rdkit_ligand.pdb ADDED
@@ -0,0 +1,92 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ COMPND 6pgo_ligand
2
+ HETATM 1 C1 UNL 1 8.134 1.501 -0.705 1.00 0.00 C
3
+ HETATM 2 C2 UNL 1 6.643 1.449 -0.580 1.00 0.00 C
4
+ HETATM 3 C3 UNL 1 6.205 0.457 0.432 1.00 0.00 C
5
+ HETATM 4 O1 UNL 1 7.093 -0.191 1.036 1.00 0.00 O
6
+ HETATM 5 N1 UNL 1 4.831 0.258 0.697 1.00 0.00 N
7
+ HETATM 6 C4 UNL 1 3.840 1.029 -0.025 1.00 0.00 C
8
+ HETATM 7 C5 UNL 1 2.896 0.025 -0.661 1.00 0.00 C
9
+ HETATM 8 N2 UNL 1 2.273 -0.708 0.410 1.00 0.00 N
10
+ HETATM 9 C6 UNL 1 2.936 -0.943 1.681 1.00 0.00 C
11
+ HETATM 10 C7 UNL 1 4.403 -0.694 1.669 1.00 0.00 C
12
+ HETATM 11 C8 UNL 1 0.965 -1.240 0.275 1.00 0.00 C
13
+ HETATM 12 N3 UNL 1 0.747 -2.565 0.141 1.00 0.00 N
14
+ HETATM 13 N4 UNL 1 -0.452 -3.097 -0.014 1.00 0.00 N
15
+ HETATM 14 C9 UNL 1 -1.571 -2.353 -0.052 1.00 0.00 C
16
+ HETATM 15 C10 UNL 1 -2.853 -3.023 -0.234 1.00 0.00 C
17
+ HETATM 16 C11 UNL 1 -3.928 -2.842 0.597 1.00 0.00 C
18
+ HETATM 17 C12 UNL 1 -5.100 -3.505 0.321 1.00 0.00 C
19
+ HETATM 18 C13 UNL 1 -5.277 -4.359 -0.752 1.00 0.00 C
20
+ HETATM 19 C14 UNL 1 -4.189 -4.530 -1.574 1.00 0.00 C
21
+ HETATM 20 C15 UNL 1 -3.008 -3.877 -1.318 1.00 0.00 C
22
+ HETATM 21 C16 UNL 1 -1.410 -0.991 0.079 1.00 0.00 C
23
+ HETATM 22 C17 UNL 1 -2.503 -0.154 0.041 1.00 0.00 C
24
+ HETATM 23 C18 UNL 1 -2.423 1.219 0.160 1.00 0.00 C
25
+ HETATM 24 C19 UNL 1 -1.162 1.749 0.324 1.00 0.00 C
26
+ HETATM 25 CL1 UNL 1 -0.975 3.493 0.485 1.00 0.00 CL
27
+ HETATM 26 C20 UNL 1 -0.039 0.952 0.367 1.00 0.00 C
28
+ HETATM 27 C21 UNL 1 -0.148 -0.415 0.244 1.00 0.00 C
29
+ HETATM 28 C22 UNL 1 -3.629 2.033 0.109 1.00 0.00 C
30
+ HETATM 29 C23 UNL 1 -4.087 2.516 -1.099 1.00 0.00 C
31
+ HETATM 30 O2 UNL 1 -3.355 2.191 -2.234 1.00 0.00 O
32
+ HETATM 31 C24 UNL 1 -5.237 3.297 -1.176 1.00 0.00 C
33
+ HETATM 32 C25 UNL 1 -5.960 3.617 -0.049 1.00 0.00 C
34
+ HETATM 33 C26 UNL 1 -5.510 3.139 1.161 1.00 0.00 C
35
+ HETATM 34 C27 UNL 1 -4.370 2.367 1.222 1.00 0.00 C
36
+ HETATM 35 F1 UNL 1 -3.908 1.883 2.423 1.00 0.00 F
37
+ HETATM 36 H1 UNL 1 8.540 2.415 -0.244 1.00 0.00 H
38
+ HETATM 37 H2 UNL 1 8.423 1.429 -1.784 1.00 0.00 H
39
+ HETATM 38 H3 UNL 1 8.620 0.635 -0.199 1.00 0.00 H
40
+ HETATM 39 H4 UNL 1 6.195 1.140 -1.553 1.00 0.00 H
41
+ HETATM 40 H5 UNL 1 6.245 2.450 -0.345 1.00 0.00 H
42
+ HETATM 41 H6 UNL 1 3.311 1.662 0.702 1.00 0.00 H
43
+ HETATM 42 H7 UNL 1 4.325 1.626 -0.824 1.00 0.00 H
44
+ HETATM 43 H8 UNL 1 3.526 -0.656 -1.308 1.00 0.00 H
45
+ HETATM 44 H9 UNL 1 2.200 0.588 -1.306 1.00 0.00 H
46
+ HETATM 45 H10 UNL 1 2.382 -0.357 2.442 1.00 0.00 H
47
+ HETATM 46 H11 UNL 1 2.777 -2.017 1.964 1.00 0.00 H
48
+ HETATM 47 H12 UNL 1 4.669 -0.265 2.679 1.00 0.00 H
49
+ HETATM 48 H13 UNL 1 5.005 -1.642 1.620 1.00 0.00 H
50
+ HETATM 49 H14 UNL 1 -3.852 -2.190 1.480 1.00 0.00 H
51
+ HETATM 50 H15 UNL 1 -5.952 -3.363 0.976 1.00 0.00 H
52
+ HETATM 51 H16 UNL 1 -6.207 -4.874 -0.956 1.00 0.00 H
53
+ HETATM 52 H17 UNL 1 -4.230 -5.185 -2.449 1.00 0.00 H
54
+ HETATM 53 H18 UNL 1 -2.148 -4.032 -1.995 1.00 0.00 H
55
+ HETATM 54 H19 UNL 1 -3.492 -0.564 -0.108 1.00 0.00 H
56
+ HETATM 55 H20 UNL 1 0.957 1.368 0.507 1.00 0.00 H
57
+ HETATM 56 H21 UNL 1 -2.758 2.934 -2.610 1.00 0.00 H
58
+ HETATM 57 H22 UNL 1 -5.537 3.642 -2.163 1.00 0.00 H
59
+ HETATM 58 H23 UNL 1 -6.855 4.224 -0.098 1.00 0.00 H
60
+ HETATM 59 H24 UNL 1 -6.015 3.341 2.097 1.00 0.00 H
61
+ CONECT 1 2 36 37 38
62
+ CONECT 2 3 39 40
63
+ CONECT 3 4 4 5
64
+ CONECT 5 6 10
65
+ CONECT 6 7 41 42
66
+ CONECT 7 8 43 44
67
+ CONECT 8 9 11
68
+ CONECT 9 10 45 46
69
+ CONECT 10 47 48
70
+ CONECT 11 12 12 27
71
+ CONECT 12 13
72
+ CONECT 13 14 14
73
+ CONECT 14 15 21
74
+ CONECT 15 16 16 20
75
+ CONECT 16 17 49
76
+ CONECT 17 18 18 50
77
+ CONECT 18 19 51
78
+ CONECT 19 20 20 52
79
+ CONECT 20 53
80
+ CONECT 21 22 27 27
81
+ CONECT 22 23 23 54
82
+ CONECT 23 24 28
83
+ CONECT 24 25 26 26
84
+ CONECT 26 27 55
85
+ CONECT 28 29 29 34
86
+ CONECT 29 30 31
87
+ CONECT 30 56
88
+ CONECT 31 32 32 57
89
+ CONECT 32 33 58
90
+ CONECT 33 34 34 59
91
+ CONECT 34 35
92
+ END
6pgp/6pgp_ligand.mol2 ADDED
@@ -0,0 +1,158 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ###
2
+ ### Created by X-TOOL on Mon Aug 2 16:11:39 2021
3
+ ###
4
+
5
+ @<TRIPOS>MOLECULE
6
+ 6pgp_ligand
7
+ 69 73 1 0 0
8
+ SMALL
9
+ GAST_HUCK
10
+
11
+
12
+ @<TRIPOS>ATOM
13
+ 1 C29 5.9070 0.2710 -12.9140 C.3 1 OHY -0.0544
14
+ 2 C28 4.4840 -0.1810 -13.2180 C.3 1 OHY -0.0149
15
+ 3 C30 4.4360 -1.0110 -14.5160 C.3 1 OHY -0.0544
16
+ 4 C11 3.5980 1.0760 -13.3310 C.ar 1 OHY -0.0099
17
+ 5 C12 3.8440 2.0600 -14.2990 C.ar 1 OHY -0.0695
18
+ 6 C13 3.0300 3.1850 -14.3650 C.ar 1 OHY -0.0809
19
+ 7 C14 1.9780 3.3590 -13.4730 C.ar 1 OHY -0.0788
20
+ 8 C15 1.7390 2.3850 -12.5070 C.ar 1 OHY -0.0388
21
+ 9 C10 2.5470 1.2520 -12.4410 C.ar 1 OHY 0.1019
22
+ 10 N2 2.2560 0.3080 -11.4330 N.am 1 OHY -0.1619
23
+ 11 C2 2.7130 0.4800 -10.1130 C.ar 1 OHY 0.1178
24
+ 12 C3 3.5010 1.5830 -9.7760 C.ar 1 OHY -0.0205
25
+ 13 C9 1.4610 -0.7890 -11.7460 C.2 1 OHY 0.2726
26
+ 14 O1 1.0600 -0.9280 -12.9050 O.2 1 OHY -0.3885
27
+ 15 N1 1.1470 -1.6900 -10.8040 N.2 1 OHY -0.2504
28
+ 16 C8 1.5640 -1.5690 -9.5280 C.2 1 OHY 0.1269
29
+ 17 N3 1.1810 -2.5930 -8.6520 N.pl3 1 OHY -0.2751
30
+ 18 C24 2.0940 -3.0130 -7.5790 C.3 1 OHY 0.0566
31
+ 19 C23 2.0610 -4.5140 -7.3550 C.3 1 OHY 0.0551
32
+ 20 C21 -0.0370 -3.3850 -8.9530 C.3 1 OHY 0.0566
33
+ 21 C22 -0.4790 -4.2560 -7.7880 C.3 1 OHY 0.0551
34
+ 22 N4 0.6590 -4.9850 -7.1690 N.am 1 OHY -0.2692
35
+ 23 C25 0.4370 -6.0740 -6.4330 C.2 1 OHY 0.1783
36
+ 24 O3 1.3800 -6.6800 -5.9240 O.2 1 OHY -0.3969
37
+ 25 C26 -0.9890 -6.5900 -6.2410 C.3 1 OHY 0.0346
38
+ 26 C27 -1.1630 -7.9090 -6.9920 C.3 1 OHY -0.0482
39
+ 27 C1 2.3630 -0.4690 -9.1520 C.ar 1 OHY 0.0698
40
+ 28 C6 2.8290 -0.2810 -7.8550 C.ar 1 OHY -0.0363
41
+ 29 C5 3.6110 0.8290 -7.5210 C.ar 1 OHY 0.0395
42
+ 30 CL1 4.1360 0.9940 -5.8890 Cl 1 OHY -0.0812
43
+ 31 C4 3.9660 1.7810 -8.4820 C.ar 1 OHY -0.0112
44
+ 32 C7 4.7690 2.9100 -8.2210 C.ar 1 OHY 0.0487
45
+ 33 C20 6.1290 2.7630 -7.8960 C.ar 1 OHY 0.1360
46
+ 34 F1 6.6920 1.5450 -7.7870 F 1 OHY -0.1832
47
+ 35 C19 6.9270 3.8830 -7.6500 C.ar 1 OHY -0.0364
48
+ 36 C18 6.3940 5.1600 -7.7510 C.ar 1 OHY -0.0705
49
+ 37 C17 5.0520 5.3220 -8.0860 C.ar 1 OHY -0.0339
50
+ 38 C16 4.2520 4.2040 -8.3290 C.ar 1 OHY 0.0989
51
+ 39 O2 2.9510 4.3900 -8.6600 O.3 1 OHY -0.3303
52
+ 40 H1 6.5609 -0.6094 -12.8283 H 1 OHY 0.0252
53
+ 41 H2 5.9196 0.8307 -11.9671 H 1 OHY 0.0252
54
+ 42 H3 6.2679 0.9179 -13.7272 H 1 OHY 0.0252
55
+ 43 H4 4.1190 -0.8057 -12.3895 H 1 OHY 0.0434
56
+ 44 H5 3.4001 -1.3244 -14.7127 H 1 OHY 0.0252
57
+ 45 H6 5.0736 -1.9006 -14.4062 H 1 OHY 0.0252
58
+ 46 H7 4.7999 -0.4003 -15.3554 H 1 OHY 0.0252
59
+ 47 H8 4.6673 1.9438 -14.9945 H 1 OHY 0.0521
60
+ 48 H9 3.2182 3.9371 -15.1226 H 1 OHY 0.0495
61
+ 49 H10 1.3516 4.2419 -13.5288 H 1 OHY 0.0528
62
+ 50 H11 0.9225 2.5086 -11.8048 H 1 OHY 0.0514
63
+ 51 H12 3.7564 2.3035 -10.5445 H 1 OHY 0.0526
64
+ 52 H13 1.8008 -2.5089 -6.6464 H 1 OHY 0.0553
65
+ 53 H14 3.1185 -2.7173 -7.8492 H 1 OHY 0.0553
66
+ 54 H15 2.6469 -4.7586 -6.4567 H 1 OHY 0.0543
67
+ 55 H16 2.4996 -5.0197 -8.2278 H 1 OHY 0.0543
68
+ 56 H17 0.1705 -4.0334 -9.8170 H 1 OHY 0.0553
69
+ 57 H18 -0.8537 -2.6917 -9.2025 H 1 OHY 0.0553
70
+ 58 H19 -1.2133 -4.9894 -8.1525 H 1 OHY 0.0543
71
+ 59 H20 -0.9471 -3.6166 -7.0251 H 1 OHY 0.0543
72
+ 60 H21 -1.7020 -5.8494 -6.6323 H 1 OHY 0.0500
73
+ 61 H22 -1.1787 -6.7512 -5.1696 H 1 OHY 0.0500
74
+ 62 H23 -2.1898 -8.2779 -6.8521 H 1 OHY 0.0254
75
+ 63 H24 -0.4506 -8.6504 -6.6010 H 1 OHY 0.0254
76
+ 64 H25 -0.9739 -7.7485 -8.0637 H 1 OHY 0.0254
77
+ 65 H26 2.5816 -1.0078 -7.0897 H 1 OHY 0.0665
78
+ 66 H27 7.9685 3.7536 -7.3787 H 1 OHY 0.0517
79
+ 67 H28 7.0189 6.0271 -7.5701 H 1 OHY 0.0594
80
+ 68 H29 4.6282 6.3171 -8.1581 H 1 OHY 0.0513
81
+ 69 H30 2.5097 4.8528 -7.9575 H 1 OHY 0.2502
82
+ @<TRIPOS>BOND
83
+ 1 1 2 1
84
+ 2 2 3 1
85
+ 3 2 4 1
86
+ 4 4 5 ar
87
+ 5 4 9 ar
88
+ 6 5 6 ar
89
+ 7 6 7 ar
90
+ 8 7 8 ar
91
+ 9 8 9 ar
92
+ 10 9 10 1
93
+ 11 10 11 1
94
+ 12 10 13 am
95
+ 13 11 12 ar
96
+ 14 11 27 ar
97
+ 15 12 31 ar
98
+ 16 13 14 2
99
+ 17 13 15 1
100
+ 18 15 16 2
101
+ 19 16 17 1
102
+ 20 16 27 1
103
+ 21 17 18 1
104
+ 22 17 20 1
105
+ 23 18 19 1
106
+ 24 19 22 1
107
+ 25 20 21 1
108
+ 26 21 22 1
109
+ 27 22 23 am
110
+ 28 23 24 2
111
+ 29 23 25 1
112
+ 30 25 26 1
113
+ 31 27 28 ar
114
+ 32 28 29 ar
115
+ 33 29 30 1
116
+ 34 29 31 ar
117
+ 35 31 32 1
118
+ 36 32 33 ar
119
+ 37 32 38 ar
120
+ 38 33 34 1
121
+ 39 33 35 ar
122
+ 40 35 36 ar
123
+ 41 36 37 ar
124
+ 42 37 38 ar
125
+ 43 38 39 1
126
+ 44 1 40 1
127
+ 45 1 41 1
128
+ 46 1 42 1
129
+ 47 2 43 1
130
+ 48 3 44 1
131
+ 49 3 45 1
132
+ 50 3 46 1
133
+ 51 5 47 1
134
+ 52 6 48 1
135
+ 53 7 49 1
136
+ 54 8 50 1
137
+ 55 12 51 1
138
+ 56 18 52 1
139
+ 57 18 53 1
140
+ 58 19 54 1
141
+ 59 19 55 1
142
+ 60 20 56 1
143
+ 61 20 57 1
144
+ 62 21 58 1
145
+ 63 21 59 1
146
+ 64 25 60 1
147
+ 65 25 61 1
148
+ 66 26 62 1
149
+ 67 26 63 1
150
+ 68 26 64 1
151
+ 69 28 65 1
152
+ 70 35 66 1
153
+ 71 36 67 1
154
+ 72 37 68 1
155
+ 73 39 69 1
156
+ @<TRIPOS>SUBSTRUCTURE
157
+ 1 OHY 1
158
+
6pgp/6pgp_ligand.sdf ADDED
@@ -0,0 +1,148 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 6pgp_ligand
2
+ -I-interpret-
3
+
4
+ 69 73 0 0 0 0 0 0 0 0999 V2000
5
+ 5.9070 0.2710 -12.9140 C 0 0 0 0 0
6
+ 4.4840 -0.1810 -13.2180 C 0 0 0 0 0
7
+ 4.4360 -1.0110 -14.5160 C 0 0 0 0 0
8
+ 3.5980 1.0760 -13.3310 C 0 0 0 0 0
9
+ 3.8440 2.0600 -14.2990 C 0 0 0 0 0
10
+ 3.0300 3.1850 -14.3650 C 0 0 0 0 0
11
+ 1.9780 3.3590 -13.4730 C 0 0 0 0 0
12
+ 1.7390 2.3850 -12.5070 C 0 0 0 0 0
13
+ 2.5470 1.2520 -12.4410 C 0 0 0 0 0
14
+ 2.2560 0.3080 -11.4330 N 0 0 0 0 0
15
+ 2.7130 0.4800 -10.1130 C 0 0 0 0 0
16
+ 3.5010 1.5830 -9.7760 C 0 0 0 0 0
17
+ 1.4610 -0.7890 -11.7460 C 0 0 0 0 0
18
+ 1.0600 -0.9280 -12.9050 O 0 0 0 0 0
19
+ 1.1470 -1.6900 -10.8040 N 0 0 0 0 0
20
+ 1.5640 -1.5690 -9.5280 C 0 0 0 0 0
21
+ 1.1810 -2.5930 -8.6520 N 0 0 0 0 0
22
+ 2.0940 -3.0130 -7.5790 C 0 0 0 0 0
23
+ 2.0610 -4.5140 -7.3550 C 0 0 0 0 0
24
+ -0.0370 -3.3850 -8.9530 C 0 0 0 0 0
25
+ -0.4790 -4.2560 -7.7880 C 0 0 0 0 0
26
+ 0.6590 -4.9850 -7.1690 N 0 0 0 0 0
27
+ 0.4370 -6.0740 -6.4330 C 0 0 0 0 0
28
+ 1.3800 -6.6800 -5.9240 O 0 0 0 0 0
29
+ -0.9890 -6.5900 -6.2410 C 0 0 0 0 0
30
+ -1.1630 -7.9090 -6.9920 C 0 0 0 0 0
31
+ 2.3630 -0.4690 -9.1520 C 0 0 0 0 0
32
+ 2.8290 -0.2810 -7.8550 C 0 0 0 0 0
33
+ 3.6110 0.8290 -7.5210 C 0 0 0 0 0
34
+ 4.1360 0.9940 -5.8890 Cl 0 0 0 0 0
35
+ 3.9660 1.7810 -8.4820 C 0 0 0 0 0
36
+ 4.7690 2.9100 -8.2210 C 0 0 0 0 0
37
+ 6.1290 2.7630 -7.8960 C 0 0 0 0 0
38
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39
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40
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41
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42
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43
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+ 39 69 1 0 0 0
147
+ M END
148
+ $$$$
6pgp/6pgp_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pgp/6pgp_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pgp/6pgp_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pgp/6pgp_rdkit_ligand.pdb ADDED
@@ -0,0 +1,106 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ COMPND 6pgp_ligand
2
+ HETATM 1 C1 UNL 1 -2.370 3.994 -1.289 1.00 0.00 C
3
+ HETATM 2 C2 UNL 1 -2.735 2.528 -1.173 1.00 0.00 C
4
+ HETATM 3 C3 UNL 1 -3.792 2.288 -2.230 1.00 0.00 C
5
+ HETATM 4 C4 UNL 1 -3.283 2.292 0.181 1.00 0.00 C
6
+ HETATM 5 C5 UNL 1 -4.615 2.603 0.347 1.00 0.00 C
7
+ HETATM 6 C6 UNL 1 -5.271 2.451 1.559 1.00 0.00 C
8
+ HETATM 7 C7 UNL 1 -4.540 1.970 2.622 1.00 0.00 C
9
+ HETATM 8 C8 UNL 1 -3.207 1.657 2.467 1.00 0.00 C
10
+ HETATM 9 C9 UNL 1 -2.590 1.817 1.257 1.00 0.00 C
11
+ HETATM 10 N1 UNL 1 -1.227 1.477 1.057 1.00 0.00 N
12
+ HETATM 11 C10 UNL 1 -1.016 0.185 0.732 1.00 0.00 C
13
+ HETATM 12 C11 UNL 1 -2.038 -0.736 0.593 1.00 0.00 C
14
+ HETATM 13 C12 UNL 1 -0.245 2.374 1.181 1.00 0.00 C
15
+ HETATM 14 O1 UNL 1 -0.500 3.596 1.493 1.00 0.00 O
16
+ HETATM 15 N2 UNL 1 1.022 1.974 0.972 1.00 0.00 N
17
+ HETATM 16 C13 UNL 1 1.345 0.683 0.638 1.00 0.00 C
18
+ HETATM 17 N3 UNL 1 2.689 0.288 0.474 1.00 0.00 N
19
+ HETATM 18 C14 UNL 1 3.372 -0.354 1.554 1.00 0.00 C
20
+ HETATM 19 C15 UNL 1 4.863 -0.176 1.505 1.00 0.00 C
21
+ HETATM 20 C16 UNL 1 3.336 0.553 -0.809 1.00 0.00 C
22
+ HETATM 21 C17 UNL 1 4.508 -0.439 -0.924 1.00 0.00 C
23
+ HETATM 22 N4 UNL 1 5.407 -0.147 0.157 1.00 0.00 N
24
+ HETATM 23 C18 UNL 1 6.783 0.163 0.036 1.00 0.00 C
25
+ HETATM 24 O2 UNL 1 7.488 0.397 1.092 1.00 0.00 O
26
+ HETATM 25 C19 UNL 1 7.514 0.246 -1.226 1.00 0.00 C
27
+ HETATM 26 C20 UNL 1 8.484 -0.913 -1.350 1.00 0.00 C
28
+ HETATM 27 C21 UNL 1 0.308 -0.200 0.521 1.00 0.00 C
29
+ HETATM 28 C22 UNL 1 0.547 -1.515 0.173 1.00 0.00 C
30
+ HETATM 29 C23 UNL 1 -0.511 -2.425 0.040 1.00 0.00 C
31
+ HETATM 30 CL1 UNL 1 -0.177 -4.101 -0.402 1.00 0.00 CL
32
+ HETATM 31 C24 UNL 1 -1.799 -2.062 0.243 1.00 0.00 C
33
+ HETATM 32 C25 UNL 1 -2.956 -2.914 0.132 1.00 0.00 C
34
+ HETATM 33 C26 UNL 1 -3.466 -3.636 1.192 1.00 0.00 C
35
+ HETATM 34 F1 UNL 1 -2.809 -3.511 2.391 1.00 0.00 F
36
+ HETATM 35 C27 UNL 1 -4.575 -4.438 1.059 1.00 0.00 C
37
+ HETATM 36 C28 UNL 1 -5.207 -4.539 -0.149 1.00 0.00 C
38
+ HETATM 37 C29 UNL 1 -4.727 -3.834 -1.234 1.00 0.00 C
39
+ HETATM 38 C30 UNL 1 -3.601 -3.026 -1.075 1.00 0.00 C
40
+ HETATM 39 O3 UNL 1 -3.137 -2.329 -2.169 1.00 0.00 O
41
+ HETATM 40 H1 UNL 1 -3.157 4.543 -1.864 1.00 0.00 H
42
+ HETATM 41 H2 UNL 1 -1.372 4.164 -1.746 1.00 0.00 H
43
+ HETATM 42 H3 UNL 1 -2.423 4.445 -0.268 1.00 0.00 H
44
+ HETATM 43 H4 UNL 1 -1.796 1.998 -1.380 1.00 0.00 H
45
+ HETATM 44 H5 UNL 1 -4.432 3.173 -2.393 1.00 0.00 H
46
+ HETATM 45 H6 UNL 1 -4.488 1.481 -1.853 1.00 0.00 H
47
+ HETATM 46 H7 UNL 1 -3.354 1.916 -3.179 1.00 0.00 H
48
+ HETATM 47 H8 UNL 1 -5.204 2.988 -0.503 1.00 0.00 H
49
+ HETATM 48 H9 UNL 1 -6.307 2.684 1.718 1.00 0.00 H
50
+ HETATM 49 H10 UNL 1 -4.970 1.821 3.606 1.00 0.00 H
51
+ HETATM 50 H11 UNL 1 -2.649 1.270 3.354 1.00 0.00 H
52
+ HETATM 51 H12 UNL 1 -3.047 -0.383 0.769 1.00 0.00 H
53
+ HETATM 52 H13 UNL 1 3.093 -1.411 1.605 1.00 0.00 H
54
+ HETATM 53 H14 UNL 1 3.041 0.086 2.540 1.00 0.00 H
55
+ HETATM 54 H15 UNL 1 5.326 -1.044 2.018 1.00 0.00 H
56
+ HETATM 55 H16 UNL 1 5.166 0.722 2.080 1.00 0.00 H
57
+ HETATM 56 H17 UNL 1 2.669 0.419 -1.670 1.00 0.00 H
58
+ HETATM 57 H18 UNL 1 3.801 1.560 -0.812 1.00 0.00 H
59
+ HETATM 58 H19 UNL 1 4.125 -1.478 -0.786 1.00 0.00 H
60
+ HETATM 59 H20 UNL 1 4.998 -0.294 -1.889 1.00 0.00 H
61
+ HETATM 60 H21 UNL 1 8.111 1.197 -1.234 1.00 0.00 H
62
+ HETATM 61 H22 UNL 1 6.864 0.254 -2.094 1.00 0.00 H
63
+ HETATM 62 H23 UNL 1 9.523 -0.581 -1.107 1.00 0.00 H
64
+ HETATM 63 H24 UNL 1 8.244 -1.735 -0.630 1.00 0.00 H
65
+ HETATM 64 H25 UNL 1 8.517 -1.292 -2.394 1.00 0.00 H
66
+ HETATM 65 H26 UNL 1 1.547 -1.828 -0.011 1.00 0.00 H
67
+ HETATM 66 H27 UNL 1 -4.937 -4.977 1.901 1.00 0.00 H
68
+ HETATM 67 H28 UNL 1 -6.082 -5.172 -0.254 1.00 0.00 H
69
+ HETATM 68 H29 UNL 1 -5.233 -3.919 -2.186 1.00 0.00 H
70
+ HETATM 69 H30 UNL 1 -2.845 -2.849 -2.981 1.00 0.00 H
71
+ CONECT 1 2 40 41 42
72
+ CONECT 2 3 4 43
73
+ CONECT 3 44 45 46
74
+ CONECT 4 5 5 9
75
+ CONECT 5 6 47
76
+ CONECT 6 7 7 48
77
+ CONECT 7 8 49
78
+ CONECT 8 9 9 50
79
+ CONECT 9 10
80
+ CONECT 10 11 13
81
+ CONECT 11 12 12 27
82
+ CONECT 12 31 51
83
+ CONECT 13 14 14 15
84
+ CONECT 15 16 16
85
+ CONECT 16 17 27
86
+ CONECT 17 18 20
87
+ CONECT 18 19 52 53
88
+ CONECT 19 22 54 55
89
+ CONECT 20 21 56 57
90
+ CONECT 21 22 58 59
91
+ CONECT 22 23
92
+ CONECT 23 24 24 25
93
+ CONECT 25 26 60 61
94
+ CONECT 26 62 63 64
95
+ CONECT 27 28 28
96
+ CONECT 28 29 65
97
+ CONECT 29 30 31 31
98
+ CONECT 31 32
99
+ CONECT 32 33 33 38
100
+ CONECT 33 34 35
101
+ CONECT 35 36 36 66
102
+ CONECT 36 37 67
103
+ CONECT 37 38 38 68
104
+ CONECT 38 39
105
+ CONECT 39 69
106
+ END
6pka/6pka_ligand.mol2 ADDED
@@ -0,0 +1,232 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ###
2
+ ### Created by X-TOOL on Mon Aug 2 16:11:24 2021
3
+ ###
4
+
5
+ @<TRIPOS>MOLECULE
6
+ 6pka_ligand
7
+ 105 111 1 0 0
8
+ SMALL
9
+ GAST_HUCK
10
+
11
+
12
+ @<TRIPOS>ATOM
13
+ 1 C48 -18.5260 67.9380 -40.3930 C.2 1 OO1 0.2877
14
+ 2 O49 -19.4660 68.6290 -40.7440 O.2 1 OO1 -0.3910
15
+ 3 N50 -17.7160 67.2300 -41.3110 N.am 1 OO1 -0.2233
16
+ 4 C51 -17.8410 67.3160 -42.7480 C.ar 1 OO1 0.0599
17
+ 5 C52 -17.8630 66.1610 -43.5060 C.ar 1 OO1 -0.0477
18
+ 6 C53 -17.9090 66.2750 -44.8900 C.ar 1 OO1 -0.0737
19
+ 7 C54 -17.8990 67.5240 -45.4980 C.ar 1 OO1 -0.0608
20
+ 8 C55 -17.9500 67.6110 -47.0070 C.3 1 OO1 -0.0382
21
+ 9 C56 -17.8580 68.6790 -44.7410 C.ar 1 OO1 -0.0737
22
+ 10 C57 -17.8050 68.5790 -43.3400 C.ar 1 OO1 -0.0477
23
+ 11 C -18.2700 69.7220 -37.9100 C.2 1 OO1 0.2059
24
+ 12 N -18.1450 67.7140 -39.0320 N.am 1 OO1 -0.2451
25
+ 13 O -17.4170 70.0120 -37.1300 O.2 1 OO1 -0.3942
26
+ 14 F1 -22.4380 64.8470 -35.5370 F 1 OO1 -0.1863
27
+ 15 F2 -18.6650 62.7340 -37.3200 F 1 OO1 -0.1863
28
+ 16 CA -18.8260 68.2980 -37.9570 C.3 1 OO1 0.1412
29
+ 17 CB -18.5070 67.5540 -36.6820 C.3 1 OO1 0.0195
30
+ 18 CG -19.2590 66.2090 -36.5780 C.ar 1 OO1 -0.0423
31
+ 19 CZ -20.5880 63.7280 -36.4100 C.ar 1 OO1 -0.0019
32
+ 20 CD1 -20.5430 66.1290 -36.0750 C.ar 1 OO1 -0.0308
33
+ 21 CD2 -18.6460 65.0430 -36.9960 C.ar 1 OO1 -0.0308
34
+ 22 CE1 -21.2070 64.8930 -36.0150 C.ar 1 OO1 0.1242
35
+ 23 CE2 -19.3050 63.8210 -36.8960 C.ar 1 OO1 0.1242
36
+ 24 N -18.7720 70.7000 -38.8530 N.am 1 OO1 -0.2589
37
+ 25 CA -18.2870 72.0240 -38.8790 C.3 1 OO1 0.1884
38
+ 26 C -19.4000 73.0480 -38.5930 C.2 1 OO1 0.2370
39
+ 27 O -20.5140 72.8810 -39.0000 O.2 1 OO1 -0.3824
40
+ 28 CB -17.7510 72.3130 -40.2550 C.3 1 OO1 0.2107
41
+ 29 OG -16.5530 71.5740 -40.2830 O.3 1 OO1 -0.2905
42
+ 30 N -19.0580 74.2270 -37.8420 N.am 1 OO1 -0.2124
43
+ 31 CA -17.8550 74.4780 -37.3610 C.3 1 OO1 0.1551
44
+ 32 C -17.6010 73.5670 -36.1630 C.2 1 OO1 0.2135
45
+ 33 O -18.4900 73.1370 -35.4660 O.2 1 OO1 -0.3934
46
+ 34 CB -17.9120 75.9430 -36.7460 C.3 1 OO1 -0.0019
47
+ 35 CG -19.4010 76.1260 -36.4920 C.2 1 OO1 -0.0883
48
+ 36 CD -20.0410 75.4330 -37.4420 C.2 1 OO1 0.0154
49
+ 37 C -14.1930 72.3900 -36.8330 C.2 1 OO1 0.2041
50
+ 38 N -16.2600 73.1230 -35.7860 N.am 1 OO1 -0.2493
51
+ 39 O -12.9890 72.5030 -36.9100 O.2 1 OO1 -0.3944
52
+ 40 CA -15.0290 73.5610 -36.4410 C.3 1 OO1 0.1337
53
+ 41 CB -14.2530 74.4010 -35.4260 C.3 1 OO1 -0.0121
54
+ 42 CD -15.4650 73.1980 -33.5490 C.3 1 OO1 -0.0321
55
+ 43 CE -16.1470 72.3150 -34.5690 C.3 1 OO1 0.0368
56
+ 44 CG -14.1790 73.7790 -34.0540 C.3 1 OO1 -0.0470
57
+ 45 N -14.8100 71.1120 -37.1150 N.am 1 OO1 -0.2640
58
+ 46 CA -13.9720 69.9900 -37.3800 C.3 1 OO1 0.1282
59
+ 47 C -14.3800 69.1260 -38.5330 C.2 1 OO1 0.2043
60
+ 48 O -14.6410 67.9530 -38.3850 O.2 1 OO1 -0.3943
61
+ 49 CB -13.9810 69.2260 -36.0620 C.3 1 OO1 -0.0244
62
+ 50 C -15.2850 72.1800 -39.9740 C.3 1 OO1 0.3121
63
+ 51 N -14.3740 69.7110 -39.8100 N.am 1 OO1 -0.2602
64
+ 52 O -15.1460 73.3320 -39.6260 O.3 1 OO1 -0.3408
65
+ 53 CA -14.0410 71.2670 -40.1700 C.3 1 OO1 0.1267
66
+ 54 CB -13.6720 71.2460 -41.4590 C.3 1 OO1 -0.0176
67
+ 55 CD -14.7260 69.0500 -41.1570 C.3 1 OO1 0.0372
68
+ 56 CE -13.8790 69.5360 -43.3690 C.3 1 OO1 -0.0605
69
+ 57 CG -14.5700 70.0310 -42.1220 C.3 1 OO1 -0.0211
70
+ 58 OXT -16.3980 71.7430 -40.1690 O.3 1 OO1 -0.2905
71
+ 59 H1 -17.0082 66.6287 -40.9402 H 1 OO1 0.2232
72
+ 60 H2 -17.8448 65.1867 -43.0311 H 1 OO1 0.0485
73
+ 61 H3 -17.9531 65.3808 -45.5011 H 1 OO1 0.0520
74
+ 62 H4 -17.9342 68.6671 -47.3141 H 1 OO1 0.0362
75
+ 63 H5 -18.8737 67.1372 -47.3706 H 1 OO1 0.0362
76
+ 64 H6 -17.0791 67.0920 -47.4339 H 1 OO1 0.0362
77
+ 65 H7 -17.8666 69.6506 -45.2217 H 1 OO1 0.0520
78
+ 66 H8 -17.7371 69.4710 -42.7277 H 1 OO1 0.0485
79
+ 67 H9 -17.3642 67.1189 -38.8418 H 1 OO1 0.1885
80
+ 68 H10 -19.9129 68.3019 -38.1262 H 1 OO1 0.0821
81
+ 69 H11 -18.7905 68.1837 -35.8258 H 1 OO1 0.0472
82
+ 70 H12 -17.4253 67.3567 -36.6499 H 1 OO1 0.0472
83
+ 71 H13 -21.0940 62.7719 -36.3403 H 1 OO1 0.0532
84
+ 72 H14 -21.0411 67.0257 -35.7245 H 1 OO1 0.0508
85
+ 73 H15 -17.6430 65.0804 -37.4054 H 1 OO1 0.0508
86
+ 74 H16 -19.4818 70.4291 -39.5033 H 1 OO1 0.1885
87
+ 75 H17 -17.4879 72.1322 -38.1309 H 1 OO1 0.0857
88
+ 76 H18 -18.3137 72.9177 -40.9814 H 1 OO1 0.0965
89
+ 77 H19 -17.0780 74.3733 -38.1325 H 1 OO1 0.0883
90
+ 78 H20 -17.5342 76.6902 -37.4594 H 1 OO1 0.0385
91
+ 79 H21 -17.3370 76.0056 -35.8104 H 1 OO1 0.0385
92
+ 80 H22 -19.8575 76.7078 -35.6926 H 1 OO1 0.0218
93
+ 81 H23 -21.0252 75.6435 -37.8579 H 1 OO1 0.0803
94
+ 82 H24 -15.2690 74.1601 -37.3318 H 1 OO1 0.0802
95
+ 83 H25 -14.7455 75.3805 -35.3370 H 1 OO1 0.0312
96
+ 84 H26 -13.2279 74.5386 -35.8005 H 1 OO1 0.0312
97
+ 85 H27 -15.2519 72.5989 -32.6514 H 1 OO1 0.0285
98
+ 86 H28 -16.1445 74.0224 -33.2868 H 1 OO1 0.0285
99
+ 87 H29 -15.5436 71.4156 -34.7612 H 1 OO1 0.0524
100
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6pka/6pka_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pka/6pka_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pka/6pka_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pka/6pka_rdkit_ligand.pdb ADDED
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+ HETATM 52 O8 UNL 1 -1.044 1.233 1.255 1.00 0.00 O
54
+ HETATM 53 C36 UNL 1 -2.199 3.016 0.058 1.00 0.00 C
55
+ HETATM 54 C37 UNL 1 -2.860 3.387 1.365 1.00 0.00 C
56
+ HETATM 55 C38 UNL 1 -3.641 4.561 -0.617 1.00 0.00 C
57
+ HETATM 56 C39 UNL 1 -3.321 5.830 1.444 1.00 0.00 C
58
+ HETATM 57 C40 UNL 1 -3.804 4.506 0.902 1.00 0.00 C
59
+ HETATM 58 O9 UNL 1 -1.775 0.947 -0.966 1.00 0.00 O
60
+ HETATM 59 H1 UNL 1 5.385 1.936 -2.173 1.00 0.00 H
61
+ HETATM 60 H2 UNL 1 8.377 1.504 -1.283 1.00 0.00 H
62
+ HETATM 61 H3 UNL 1 10.281 0.347 -2.395 1.00 0.00 H
63
+ HETATM 62 H4 UNL 1 11.138 -1.584 -3.730 1.00 0.00 H
64
+ HETATM 63 H5 UNL 1 10.378 -1.141 -5.303 1.00 0.00 H
65
+ HETATM 64 H6 UNL 1 9.930 -2.667 -4.440 1.00 0.00 H
66
+ HETATM 65 H7 UNL 1 7.637 -1.955 -4.734 1.00 0.00 H
67
+ HETATM 66 H8 UNL 1 5.704 -0.790 -3.616 1.00 0.00 H
68
+ HETATM 67 H9 UNL 1 3.688 2.013 -0.354 1.00 0.00 H
69
+ HETATM 68 H10 UNL 1 4.118 -0.282 1.549 1.00 0.00 H
70
+ HETATM 69 H11 UNL 1 4.653 1.867 2.486 1.00 0.00 H
71
+ HETATM 70 H12 UNL 1 3.085 2.574 2.127 1.00 0.00 H
72
+ HETATM 71 H13 UNL 1 2.051 -0.368 7.039 1.00 0.00 H
73
+ HETATM 72 H14 UNL 1 1.095 1.748 3.411 1.00 0.00 H
74
+ HETATM 73 H15 UNL 1 5.065 0.323 4.102 1.00 0.00 H
75
+ HETATM 74 H16 UNL 1 2.129 0.577 -1.077 1.00 0.00 H
76
+ HETATM 75 H17 UNL 1 -0.195 -0.757 0.255 1.00 0.00 H
77
+ HETATM 76 H18 UNL 1 -0.203 0.836 -2.378 1.00 0.00 H
78
+ HETATM 77 H19 UNL 1 -2.435 -1.662 -1.472 1.00 0.00 H
79
+ HETATM 78 H20 UNL 1 -3.393 -4.144 -1.709 1.00 0.00 H
80
+ HETATM 79 H21 UNL 1 -2.708 -3.238 -3.160 1.00 0.00 H
81
+ HETATM 80 H22 UNL 1 -1.461 -5.668 -2.505 1.00 0.00 H
82
+ HETATM 81 H23 UNL 1 0.717 -4.515 -1.918 1.00 0.00 H
83
+ HETATM 82 H24 UNL 1 -4.462 -1.773 -0.926 1.00 0.00 H
84
+ HETATM 83 H25 UNL 1 -5.958 -2.048 1.706 1.00 0.00 H
85
+ HETATM 84 H26 UNL 1 -6.594 -1.673 0.082 1.00 0.00 H
86
+ HETATM 85 H27 UNL 1 -5.538 -5.025 2.084 1.00 0.00 H
87
+ HETATM 86 H28 UNL 1 -4.492 -5.242 0.633 1.00 0.00 H
88
+ HETATM 87 H29 UNL 1 -3.173 -4.175 2.253 1.00 0.00 H
89
+ HETATM 88 H30 UNL 1 -4.366 -2.919 2.635 1.00 0.00 H
90
+ HETATM 89 H31 UNL 1 -5.843 -3.997 -0.671 1.00 0.00 H
91
+ HETATM 90 H32 UNL 1 -7.002 -3.982 0.677 1.00 0.00 H
92
+ HETATM 91 H33 UNL 1 -5.190 1.509 0.636 1.00 0.00 H
93
+ HETATM 92 H34 UNL 1 -4.163 0.005 -1.821 1.00 0.00 H
94
+ HETATM 93 H35 UNL 1 -6.088 0.621 -2.856 1.00 0.00 H
95
+ HETATM 94 H36 UNL 1 -6.710 0.384 -1.205 1.00 0.00 H
96
+ HETATM 95 H37 UNL 1 -6.322 2.030 -1.782 1.00 0.00 H
97
+ HETATM 96 H38 UNL 1 -1.396 1.784 1.996 1.00 0.00 H
98
+ HETATM 97 H39 UNL 1 -1.500 3.882 -0.166 1.00 0.00 H
99
+ HETATM 98 H40 UNL 1 -3.376 2.535 1.797 1.00 0.00 H
100
+ HETATM 99 H41 UNL 1 -2.051 3.805 2.025 1.00 0.00 H
101
+ HETATM 100 H42 UNL 1 -2.680 5.128 -0.797 1.00 0.00 H
102
+ HETATM 101 H43 UNL 1 -4.477 4.958 -1.151 1.00 0.00 H
103
+ HETATM 102 H44 UNL 1 -3.860 6.057 2.384 1.00 0.00 H
104
+ HETATM 103 H45 UNL 1 -3.455 6.623 0.683 1.00 0.00 H
105
+ HETATM 104 H46 UNL 1 -2.235 5.700 1.674 1.00 0.00 H
106
+ HETATM 105 H47 UNL 1 -4.833 4.259 1.166 1.00 0.00 H
107
+ CONECT 1 2 2 3 12
108
+ CONECT 3 4 59
109
+ CONECT 4 5 5 10
110
+ CONECT 5 6 60
111
+ CONECT 6 7 7 61
112
+ CONECT 7 8 9
113
+ CONECT 8 62 63 64
114
+ CONECT 9 10 10 65
115
+ CONECT 10 66
116
+ CONECT 11 13 13 16 24
117
+ CONECT 12 16 67
118
+ CONECT 14 22
119
+ CONECT 15 23
120
+ CONECT 16 17 68
121
+ CONECT 17 18 69 70
122
+ CONECT 18 20 20 21
123
+ CONECT 19 22 22 23 71
124
+ CONECT 20 22 72
125
+ CONECT 21 23 23 73
126
+ CONECT 24 25 74
127
+ CONECT 25 26 28 75
128
+ CONECT 26 27 27 30
129
+ CONECT 28 29 58 76
130
+ CONECT 29 50
131
+ CONECT 30 31 36
132
+ CONECT 31 32 34 77
133
+ CONECT 32 33 33 38
134
+ CONECT 34 35 78 79
135
+ CONECT 35 36 36 80
136
+ CONECT 36 81
137
+ CONECT 37 39 39 40 45
138
+ CONECT 38 40 43
139
+ CONECT 40 41 82
140
+ CONECT 41 44 83 84
141
+ CONECT 42 43 44 85 86
142
+ CONECT 43 87 88
143
+ CONECT 44 89 90
144
+ CONECT 45 46 91
145
+ CONECT 46 47 49 92
146
+ CONECT 47 48 48 51
147
+ CONECT 49 93 94 95
148
+ CONECT 50 52 53 58
149
+ CONECT 51 53 55
150
+ CONECT 52 96
151
+ CONECT 53 54 97
152
+ CONECT 54 57 98 99
153
+ CONECT 55 57 100 101
154
+ CONECT 56 57 102 103 104
155
+ CONECT 57 105
156
+ END
6pnm/6pnm_ligand.mol2 ADDED
@@ -0,0 +1,87 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ###
2
+ ### Created by X-TOOL on Mon Aug 2 16:11:39 2021
3
+ ###
4
+
5
+ @<TRIPOS>MOLECULE
6
+ 6pnm_ligand
7
+ 35 36 1 0 0
8
+ SMALL
9
+ GAST_HUCK
10
+
11
+
12
+ @<TRIPOS>ATOM
13
+ 1 C1 15.8460 12.3350 36.8630 C.3 1 XX0 0.0317
14
+ 2 C2 14.5130 12.4390 37.6520 C.2 1 XX0 0.2007
15
+ 3 O2 13.9820 13.5220 37.8530 O.2 1 XX0 -0.3851
16
+ 4 N3 14.0970 11.3150 38.2400 N.am 1 XX0 -0.2338
17
+ 5 C4 13.0180 11.4110 39.0730 C.ar 1 XX0 0.0686
18
+ 6 C51 12.7640 12.5940 39.7850 C.ar 1 XX0 -0.0140
19
+ 7 C52 12.2580 10.3070 39.3290 C.ar 1 XX0 -0.0404
20
+ 8 C62 11.2000 10.3960 40.2140 C.ar 1 XX0 -0.0597
21
+ 9 C7 10.9480 11.5400 40.9090 C.ar 1 XX0 0.0503
22
+ 10 CL7 9.7560 11.5200 41.8190 Cl 1 XX0 -0.0829
23
+ 11 C61 11.7120 12.6670 40.6820 C.ar 1 XX0 0.1089
24
+ 12 S7 11.3850 14.2520 41.5130 S.o2 1 XX0 0.0678
25
+ 13 O71 12.4020 15.2140 41.2090 O.2 1 XX0 -0.1503
26
+ 14 O72 11.1970 13.6800 42.8520 O.2 1 XX0 -0.1503
27
+ 15 N8 10.1670 14.8790 41.0490 N.am 1 XX0 -0.2299
28
+ 16 C91 9.7530 16.1790 41.6760 C.3 1 XX0 0.0531
29
+ 17 CA1 8.2190 16.3560 41.5620 C.3 1 XX0 0.0647
30
+ 18 OB 7.8380 16.1320 40.1850 O.3 1 XX0 -0.3766
31
+ 19 CA2 9.0110 16.1960 39.2860 C.3 1 XX0 0.0647
32
+ 20 C92 10.0320 15.0410 39.5960 C.3 1 XX0 0.0531
33
+ 21 H1 16.1504 11.2802 36.7950 H 1 XX0 0.0472
34
+ 22 H2 16.6264 12.9089 37.3842 H 1 XX0 0.0472
35
+ 23 H3 15.7057 12.7421 35.8508 H 1 XX0 0.0472
36
+ 24 H4 14.5550 10.4409 38.0779 H 1 XX0 0.2259
37
+ 25 H5 13.3983 13.4594 39.6308 H 1 XX0 0.0523
38
+ 26 H6 12.4827 9.3655 38.8411 H 1 XX0 0.0503
39
+ 27 H7 10.5562 9.5359 40.3582 H 1 XX0 0.0584
40
+ 28 H8 10.2551 17.0096 41.1583 H 1 XX0 0.0501
41
+ 29 H9 10.0421 16.1801 42.7373 H 1 XX0 0.0501
42
+ 30 H10 7.9386 17.3757 41.8645 H 1 XX0 0.0576
43
+ 31 H11 7.7111 15.6280 42.2117 H 1 XX0 0.0576
44
+ 32 H12 9.5140 17.1648 39.4216 H 1 XX0 0.0576
45
+ 33 H13 8.6698 16.1026 38.2445 H 1 XX0 0.0576
46
+ 34 H14 9.6667 14.1016 39.1554 H 1 XX0 0.0501
47
+ 35 H15 11.0115 15.2925 39.1632 H 1 XX0 0.0501
48
+ @<TRIPOS>BOND
49
+ 1 1 2 1
50
+ 2 2 3 2
51
+ 3 2 4 am
52
+ 4 4 5 1
53
+ 5 5 6 ar
54
+ 6 5 7 ar
55
+ 7 6 11 ar
56
+ 8 7 8 ar
57
+ 9 8 9 ar
58
+ 10 9 10 1
59
+ 11 9 11 ar
60
+ 12 11 12 1
61
+ 13 12 13 2
62
+ 14 12 14 2
63
+ 15 12 15 am
64
+ 16 15 16 1
65
+ 17 15 20 1
66
+ 18 16 17 1
67
+ 19 17 18 1
68
+ 20 18 19 1
69
+ 21 19 20 1
70
+ 22 1 21 1
71
+ 23 1 22 1
72
+ 24 1 23 1
73
+ 25 4 24 1
74
+ 26 6 25 1
75
+ 27 7 26 1
76
+ 28 8 27 1
77
+ 29 16 28 1
78
+ 30 16 29 1
79
+ 31 17 30 1
80
+ 32 17 31 1
81
+ 33 19 32 1
82
+ 34 19 33 1
83
+ 35 20 34 1
84
+ 36 20 35 1
85
+ @<TRIPOS>SUBSTRUCTURE
86
+ 1 XX0 1
87
+
6pnm/6pnm_ligand.sdf ADDED
@@ -0,0 +1,77 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 6pnm_ligand
2
+ -I-interpret-
3
+
4
+ 35 36 0 0 0 0 0 0 0 0999 V2000
5
+ 15.8460 12.3350 36.8630 C 0 0 0 0 0
6
+ 14.5130 12.4390 37.6520 C 0 0 0 0 0
7
+ 13.9820 13.5220 37.8530 O 0 0 0 0 0
8
+ 14.0970 11.3150 38.2400 N 0 0 0 0 0
9
+ 13.0180 11.4110 39.0730 C 0 0 0 0 0
10
+ 12.7640 12.5940 39.7850 C 0 0 0 0 0
11
+ 12.2580 10.3070 39.3290 C 0 0 0 0 0
12
+ 11.2000 10.3960 40.2140 C 0 0 0 0 0
13
+ 10.9480 11.5400 40.9090 C 0 0 0 0 0
14
+ 9.7560 11.5200 41.8190 Cl 0 0 0 0 0
15
+ 11.7120 12.6670 40.6820 C 0 0 0 0 0
16
+ 11.3850 14.2520 41.5130 S 0 0 0 0 0
17
+ 12.4020 15.2140 41.2090 O 0 0 0 0 0
18
+ 11.1970 13.6800 42.8520 O 0 0 0 0 0
19
+ 10.1670 14.8790 41.0490 N 0 0 0 0 0
20
+ 9.7530 16.1790 41.6760 C 0 0 0 0 0
21
+ 8.2190 16.3560 41.5620 C 0 0 0 0 0
22
+ 7.8380 16.1320 40.1850 O 0 0 0 0 0
23
+ 9.0110 16.1960 39.2860 C 0 0 0 0 0
24
+ 10.0320 15.0410 39.5960 C 0 0 0 0 0
25
+ 15.7057 12.7387 35.8603 H 0 0 0 0 0
26
+ 16.6183 12.9041 37.3804 H 0 0 0 0 0
27
+ 16.1466 11.2894 36.7963 H 0 0 0 0 0
28
+ 14.5642 10.4235 38.0747 H 0 0 0 0 0
29
+ 13.4018 13.4642 39.6299 H 0 0 0 0 0
30
+ 12.4840 9.3603 38.8384 H 0 0 0 0 0
31
+ 10.5527 9.5311 40.3590 H 0 0 0 0 0
32
+ 10.2485 17.0007 41.1590 H 0 0 0 0 0
33
+ 10.0368 16.1764 42.7284 H 0 0 0 0 0
34
+ 7.9345 17.3621 41.8701 H 0 0 0 0 0
35
+ 7.7108 15.6433 42.2115 H 0 0 0 0 0
36
+ 9.5122 17.1521 39.4371 H 0 0 0 0 0
37
+ 8.6663 16.0877 38.2576 H 0 0 0 0 0
38
+ 9.6689 14.1102 39.1602 H 0 0 0 0 0
39
+ 11.0027 15.2914 39.1680 H 0 0 0 0 0
40
+ 1 2 1 0 0 0
41
+ 2 3 2 0 0 0
42
+ 2 4 1 0 0 0
43
+ 4 5 1 0 0 0
44
+ 5 6 4 0 0 0
45
+ 5 7 4 0 0 0
46
+ 6 11 4 0 0 0
47
+ 7 8 4 0 0 0
48
+ 8 9 4 0 0 0
49
+ 9 10 1 0 0 0
50
+ 9 11 4 0 0 0
51
+ 11 12 1 0 0 0
52
+ 12 13 2 0 0 0
53
+ 12 14 2 0 0 0
54
+ 12 15 1 0 0 0
55
+ 15 16 1 0 0 0
56
+ 15 20 1 0 0 0
57
+ 16 17 1 0 0 0
58
+ 17 18 1 0 0 0
59
+ 18 19 1 0 0 0
60
+ 19 20 1 0 0 0
61
+ 1 21 1 0 0 0
62
+ 1 22 1 0 0 0
63
+ 1 23 1 0 0 0
64
+ 4 24 1 0 0 0
65
+ 6 25 1 0 0 0
66
+ 7 26 1 0 0 0
67
+ 8 27 1 0 0 0
68
+ 16 28 1 0 0 0
69
+ 16 29 1 0 0 0
70
+ 17 30 1 0 0 0
71
+ 17 31 1 0 0 0
72
+ 19 32 1 0 0 0
73
+ 19 33 1 0 0 0
74
+ 20 34 1 0 0 0
75
+ 20 35 1 0 0 0
76
+ M END
77
+ $$$$
6pnm/6pnm_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pnm/6pnm_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pnm/6pnm_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pnm/6pnm_rdkit_ligand.pdb ADDED
@@ -0,0 +1,54 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ COMPND 6pnm_ligand
2
+ HETATM 1 C1 UNL 1 4.439 0.305 2.699 1.00 0.00 C
3
+ HETATM 2 C2 UNL 1 3.588 0.619 1.542 1.00 0.00 C
4
+ HETATM 3 O1 UNL 1 3.094 1.781 1.483 1.00 0.00 O
5
+ HETATM 4 N1 UNL 1 3.277 -0.268 0.492 1.00 0.00 N
6
+ HETATM 5 C3 UNL 1 2.448 0.053 -0.626 1.00 0.00 C
7
+ HETATM 6 C4 UNL 1 1.078 -0.159 -0.595 1.00 0.00 C
8
+ HETATM 7 C5 UNL 1 2.974 0.586 -1.785 1.00 0.00 C
9
+ HETATM 8 C6 UNL 1 2.167 0.893 -2.858 1.00 0.00 C
10
+ HETATM 9 C7 UNL 1 0.820 0.670 -2.792 1.00 0.00 C
11
+ HETATM 10 CL1 UNL 1 -0.172 1.080 -4.195 1.00 0.00 CL
12
+ HETATM 11 C8 UNL 1 0.260 0.139 -1.651 1.00 0.00 C
13
+ HETATM 12 S1 UNL 1 -1.460 -0.115 -1.643 1.00 0.00 S
14
+ HETATM 13 O2 UNL 1 -1.765 -1.077 -2.782 1.00 0.00 O
15
+ HETATM 14 O3 UNL 1 -2.169 1.176 -2.001 1.00 0.00 O
16
+ HETATM 15 N2 UNL 1 -2.029 -0.774 -0.175 1.00 0.00 N
17
+ HETATM 16 C9 UNL 1 -1.753 0.124 0.892 1.00 0.00 C
18
+ HETATM 17 C10 UNL 1 -3.111 0.605 1.424 1.00 0.00 C
19
+ HETATM 18 O4 UNL 1 -3.670 -0.530 2.021 1.00 0.00 O
20
+ HETATM 19 C11 UNL 1 -4.100 -1.381 1.022 1.00 0.00 C
21
+ HETATM 20 C12 UNL 1 -3.352 -1.268 -0.259 1.00 0.00 C
22
+ HETATM 21 H1 UNL 1 5.267 1.063 2.707 1.00 0.00 H
23
+ HETATM 22 H2 UNL 1 3.916 0.409 3.667 1.00 0.00 H
24
+ HETATM 23 H3 UNL 1 4.919 -0.685 2.636 1.00 0.00 H
25
+ HETATM 24 H4 UNL 1 3.673 -1.230 0.520 1.00 0.00 H
26
+ HETATM 25 H5 UNL 1 0.655 -0.577 0.308 1.00 0.00 H
27
+ HETATM 26 H6 UNL 1 4.035 0.755 -1.821 1.00 0.00 H
28
+ HETATM 27 H7 UNL 1 2.583 1.319 -3.785 1.00 0.00 H
29
+ HETATM 28 H8 UNL 1 -1.242 -0.343 1.758 1.00 0.00 H
30
+ HETATM 29 H9 UNL 1 -1.160 0.975 0.521 1.00 0.00 H
31
+ HETATM 30 H10 UNL 1 -3.730 0.892 0.533 1.00 0.00 H
32
+ HETATM 31 H11 UNL 1 -3.019 1.456 2.094 1.00 0.00 H
33
+ HETATM 32 H12 UNL 1 -3.999 -2.419 1.402 1.00 0.00 H
34
+ HETATM 33 H13 UNL 1 -5.200 -1.207 0.892 1.00 0.00 H
35
+ HETATM 34 H14 UNL 1 -3.938 -0.602 -0.940 1.00 0.00 H
36
+ HETATM 35 H15 UNL 1 -3.325 -2.264 -0.789 1.00 0.00 H
37
+ CONECT 1 2 21 22 23
38
+ CONECT 2 3 3 4
39
+ CONECT 4 5 24
40
+ CONECT 5 6 6 7
41
+ CONECT 6 11 25
42
+ CONECT 7 8 8 26
43
+ CONECT 8 9 27
44
+ CONECT 9 10 11 11
45
+ CONECT 11 12
46
+ CONECT 12 13 13 14 14
47
+ CONECT 12 15
48
+ CONECT 15 16 20
49
+ CONECT 16 17 28 29
50
+ CONECT 17 18 30 31
51
+ CONECT 18 19
52
+ CONECT 19 20 32 33
53
+ CONECT 20 34 35
54
+ END
6pnn/6pnn_ligand.mol2 ADDED
@@ -0,0 +1,90 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ###
2
+ ### Created by X-TOOL on Mon Aug 2 16:11:39 2021
3
+ ###
4
+
5
+ @<TRIPOS>MOLECULE
6
+ 6pnn_ligand
7
+ 37 37 1 0 0
8
+ SMALL
9
+ GAST_HUCK
10
+
11
+
12
+ @<TRIPOS>ATOM
13
+ 1 CAA 18.2860 -7.6220 13.6290 C.3 1 OR7 0.0317
14
+ 2 CAC 17.8360 -6.4360 14.3700 C.2 1 OR7 0.2007
15
+ 3 OAD 18.5810 -5.4640 14.3610 O.2 1 OR7 -0.3851
16
+ 4 NAE 16.5470 -6.5100 14.8530 N.am 1 OR7 -0.2338
17
+ 5 CAF 16.0560 -5.5260 15.6420 C.ar 1 OR7 0.0686
18
+ 6 CAH 16.9330 -4.6830 16.3910 C.ar 1 OR7 -0.0140
19
+ 7 CAG 14.6740 -5.3780 15.7890 C.ar 1 OR7 -0.0404
20
+ 8 CAI 14.2050 -4.3790 16.6340 C.ar 1 OR7 -0.0597
21
+ 9 CAK 15.0980 -3.5390 17.3440 C.ar 1 OR7 0.0503
22
+ 10 CLA 14.4970 -2.3320 18.3230 Cl 1 OR7 -0.0829
23
+ 11 CAJ 16.4900 -3.6590 17.2340 C.ar 1 OR7 0.1089
24
+ 12 SAM 17.7840 -2.4650 18.2510 S.o2 1 OR7 0.0675
25
+ 13 OAN 17.3600 -2.5260 19.7180 O.2 1 OR7 -0.1503
26
+ 14 OAO 19.2980 -2.8250 18.0940 O.2 1 OR7 -0.1503
27
+ 15 NAP 17.8800 -0.7160 17.8170 N.am 1 OR7 -0.2351
28
+ 16 CAQ 16.5720 -0.0980 17.5230 C.3 1 OR7 0.0183
29
+ 17 CAR 18.9060 -0.5160 16.7600 C.3 1 OR7 0.0527
30
+ 18 CAS 18.5170 -1.2980 15.4570 C.3 1 OR7 0.0643
31
+ 19 OAT 19.2740 -2.5220 15.1850 O.3 1 OR7 -0.3814
32
+ 20 CAU 18.9760 -2.9460 13.8240 C.3 1 OR7 0.0365
33
+ 21 H1 17.5312 -8.4173 13.7167 H 1 OR7 0.0472
34
+ 22 H2 19.2406 -7.9748 14.0464 H 1 OR7 0.0472
35
+ 23 H3 18.4231 -7.3619 12.5690 H 1 OR7 0.0472
36
+ 24 H4 15.9721 -7.2942 14.6194 H 1 OR7 0.2259
37
+ 25 H5 18.0009 -4.8461 16.3009 H 1 OR7 0.0523
38
+ 26 H6 13.9858 -6.0255 15.2578 H 1 OR7 0.0503
39
+ 27 H7 13.1364 -4.2401 16.7519 H 1 OR7 0.0584
40
+ 28 H8 16.7164 0.9625 17.2689 H 1 OR7 0.0442
41
+ 29 H9 15.9217 -0.1780 18.4066 H 1 OR7 0.0442
42
+ 30 H10 16.1033 -0.6178 16.6744 H 1 OR7 0.0442
43
+ 31 H11 19.8769 -0.8822 17.1249 H 1 OR7 0.0501
44
+ 32 H12 18.9821 0.5567 16.5285 H 1 OR7 0.0501
45
+ 33 H13 18.6595 -0.6191 14.6034 H 1 OR7 0.0576
46
+ 34 H14 17.4544 -1.5714 15.5347 H 1 OR7 0.0576
47
+ 35 H15 19.5345 -3.8659 13.5960 H 1 OR7 0.0523
48
+ 36 H16 19.2712 -2.1539 13.1202 H 1 OR7 0.0523
49
+ 37 H17 17.8973 -3.1386 13.7278 H 1 OR7 0.0523
50
+ @<TRIPOS>BOND
51
+ 1 1 2 1
52
+ 2 2 3 2
53
+ 3 2 4 am
54
+ 4 4 5 1
55
+ 5 5 6 ar
56
+ 6 5 7 ar
57
+ 7 6 11 ar
58
+ 8 7 8 ar
59
+ 9 8 9 ar
60
+ 10 9 10 1
61
+ 11 9 11 ar
62
+ 12 11 12 1
63
+ 13 12 13 2
64
+ 14 12 14 2
65
+ 15 12 15 am
66
+ 16 15 16 1
67
+ 17 15 17 1
68
+ 18 17 18 1
69
+ 19 18 19 1
70
+ 20 19 20 1
71
+ 21 1 21 1
72
+ 22 1 22 1
73
+ 23 1 23 1
74
+ 24 4 24 1
75
+ 25 6 25 1
76
+ 26 7 26 1
77
+ 27 8 27 1
78
+ 28 16 28 1
79
+ 29 16 29 1
80
+ 30 16 30 1
81
+ 31 17 31 1
82
+ 32 17 32 1
83
+ 33 18 33 1
84
+ 34 18 34 1
85
+ 35 20 35 1
86
+ 36 20 36 1
87
+ 37 20 37 1
88
+ @<TRIPOS>SUBSTRUCTURE
89
+ 1 OR7 1
90
+
6pnn/6pnn_ligand.sdf ADDED
@@ -0,0 +1,80 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 6pnn_ligand
2
+ -I-interpret-
3
+
4
+ 37 37 0 0 0 0 0 0 0 0999 V2000
5
+ 18.2860 -7.6220 13.6290 C 0 0 0 0 0
6
+ 17.8360 -6.4360 14.3700 C 0 0 0 0 0
7
+ 18.5810 -5.4640 14.3610 O 0 0 0 0 0
8
+ 16.5470 -6.5100 14.8530 N 0 0 0 0 0
9
+ 16.0560 -5.5260 15.6420 C 0 0 0 0 0
10
+ 16.9330 -4.6830 16.3910 C 0 0 0 0 0
11
+ 14.6740 -5.3780 15.7890 C 0 0 0 0 0
12
+ 14.2050 -4.3790 16.6340 C 0 0 0 0 0
13
+ 15.0980 -3.5390 17.3440 C 0 0 0 0 0
14
+ 14.4970 -2.3320 18.3230 Cl 0 0 0 0 0
15
+ 16.4900 -3.6590 17.2340 C 0 0 0 0 0
16
+ 17.7840 -2.4650 18.2510 S 0 0 0 0 0
17
+ 17.3600 -2.5260 19.7180 O 0 0 0 0 0
18
+ 19.2980 -2.8250 18.0940 O 0 0 0 0 0
19
+ 17.8800 -0.7160 17.8170 N 0 0 0 0 0
20
+ 16.5720 -0.0980 17.5230 C 0 0 0 0 0
21
+ 18.9060 -0.5160 16.7600 C 0 0 0 0 0
22
+ 18.5170 -1.2980 15.4570 C 0 0 0 0 0
23
+ 19.2740 -2.5220 15.1850 O 0 0 0 0 0
24
+ 18.9760 -2.9460 13.8240 C 0 0 0 0 0
25
+ 18.4215 -7.3630 12.5789 H 0 0 0 0 0
26
+ 19.2319 -7.9706 14.0435 H 0 0 0 0 0
27
+ 17.5373 -8.4093 13.7167 H 0 0 0 0 0
28
+ 15.9606 -7.3099 14.6147 H 0 0 0 0 0
29
+ 18.0068 -4.8470 16.3004 H 0 0 0 0 0
30
+ 13.9820 -6.0291 15.2549 H 0 0 0 0 0
31
+ 13.1305 -4.2393 16.7526 H 0 0 0 0 0
32
+ 16.1086 -0.6140 16.6821 H 0 0 0 0 0
33
+ 15.9286 -0.1780 18.3992 H 0 0 0 0 0
34
+ 16.7164 0.9527 17.2714 H 0 0 0 0 0
35
+ 19.8638 -0.8889 17.1228 H 0 0 0 0 0
36
+ 18.9708 0.5470 16.5276 H 0 0 0 0 0
37
+ 18.7213 -0.6234 14.6255 H 0 0 0 0 0
38
+ 17.4791 -1.6050 15.5855 H 0 0 0 0 0
39
+ 17.9069 -3.1365 13.7300 H 0 0 0 0 0
40
+ 19.2689 -2.1603 13.1277 H 0 0 0 0 0
41
+ 19.5299 -3.8575 13.5993 H 0 0 0 0 0
42
+ 1 2 1 0 0 0
43
+ 2 3 2 0 0 0
44
+ 2 4 1 0 0 0
45
+ 4 5 1 0 0 0
46
+ 5 6 4 0 0 0
47
+ 5 7 4 0 0 0
48
+ 6 11 4 0 0 0
49
+ 7 8 4 0 0 0
50
+ 8 9 4 0 0 0
51
+ 9 10 1 0 0 0
52
+ 9 11 4 0 0 0
53
+ 11 12 1 0 0 0
54
+ 12 13 2 0 0 0
55
+ 12 14 2 0 0 0
56
+ 12 15 1 0 0 0
57
+ 15 16 1 0 0 0
58
+ 15 17 1 0 0 0
59
+ 17 18 1 0 0 0
60
+ 18 19 1 0 0 0
61
+ 19 20 1 0 0 0
62
+ 1 21 1 0 0 0
63
+ 1 22 1 0 0 0
64
+ 1 23 1 0 0 0
65
+ 4 24 1 0 0 0
66
+ 6 25 1 0 0 0
67
+ 7 26 1 0 0 0
68
+ 8 27 1 0 0 0
69
+ 16 28 1 0 0 0
70
+ 16 29 1 0 0 0
71
+ 16 30 1 0 0 0
72
+ 17 31 1 0 0 0
73
+ 17 32 1 0 0 0
74
+ 18 33 1 0 0 0
75
+ 18 34 1 0 0 0
76
+ 20 35 1 0 0 0
77
+ 20 36 1 0 0 0
78
+ 20 37 1 0 0 0
79
+ M END
80
+ $$$$
6pnn/6pnn_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pnn/6pnn_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pnn/6pnn_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pnn/6pnn_rdkit_ligand.pdb ADDED
@@ -0,0 +1,56 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ COMPND 6pnn_ligand
2
+ HETATM 1 C1 UNL 1 -6.359 1.066 -0.242 1.00 0.00 C
3
+ HETATM 2 C2 UNL 1 -5.299 0.063 0.156 1.00 0.00 C
4
+ HETATM 3 O1 UNL 1 -5.620 -0.883 0.892 1.00 0.00 O
5
+ HETATM 4 N1 UNL 1 -3.982 0.249 -0.330 1.00 0.00 N
6
+ HETATM 5 C3 UNL 1 -2.897 -0.590 -0.051 1.00 0.00 C
7
+ HETATM 6 C4 UNL 1 -1.661 -0.259 -0.615 1.00 0.00 C
8
+ HETATM 7 C5 UNL 1 -2.921 -1.706 0.720 1.00 0.00 C
9
+ HETATM 8 C6 UNL 1 -1.778 -2.482 0.940 1.00 0.00 C
10
+ HETATM 9 C7 UNL 1 -0.575 -2.140 0.378 1.00 0.00 C
11
+ HETATM 10 CL1 UNL 1 0.860 -3.100 0.645 1.00 0.00 CL
12
+ HETATM 11 C8 UNL 1 -0.526 -1.009 -0.410 1.00 0.00 C
13
+ HETATM 12 S1 UNL 1 0.976 -0.522 -1.152 1.00 0.00 S
14
+ HETATM 13 O2 UNL 1 1.451 -1.700 -1.986 1.00 0.00 O
15
+ HETATM 14 O3 UNL 1 0.731 0.605 -2.074 1.00 0.00 O
16
+ HETATM 15 N2 UNL 1 2.161 -0.219 0.041 1.00 0.00 N
17
+ HETATM 16 C9 UNL 1 1.838 0.825 0.939 1.00 0.00 C
18
+ HETATM 17 C10 UNL 1 3.493 -0.364 -0.385 1.00 0.00 C
19
+ HETATM 18 C11 UNL 1 4.192 0.830 -0.923 1.00 0.00 C
20
+ HETATM 19 O4 UNL 1 4.311 1.897 -0.042 1.00 0.00 O
21
+ HETATM 20 C12 UNL 1 5.037 1.598 1.081 1.00 0.00 C
22
+ HETATM 21 H1 UNL 1 -7.361 0.637 -0.032 1.00 0.00 H
23
+ HETATM 22 H2 UNL 1 -6.200 1.255 -1.324 1.00 0.00 H
24
+ HETATM 23 H3 UNL 1 -6.249 1.974 0.358 1.00 0.00 H
25
+ HETATM 24 H4 UNL 1 -3.839 1.105 -0.956 1.00 0.00 H
26
+ HETATM 25 H5 UNL 1 -1.610 0.630 -1.237 1.00 0.00 H
27
+ HETATM 26 H6 UNL 1 -3.831 -2.034 1.193 1.00 0.00 H
28
+ HETATM 27 H7 UNL 1 -1.827 -3.372 1.564 1.00 0.00 H
29
+ HETATM 28 H8 UNL 1 2.225 0.630 1.959 1.00 0.00 H
30
+ HETATM 29 H9 UNL 1 2.071 1.846 0.607 1.00 0.00 H
31
+ HETATM 30 H10 UNL 1 0.714 0.810 1.062 1.00 0.00 H
32
+ HETATM 31 H11 UNL 1 3.524 -1.161 -1.165 1.00 0.00 H
33
+ HETATM 32 H12 UNL 1 4.100 -0.750 0.483 1.00 0.00 H
34
+ HETATM 33 H13 UNL 1 3.817 1.156 -1.921 1.00 0.00 H
35
+ HETATM 34 H14 UNL 1 5.255 0.506 -1.132 1.00 0.00 H
36
+ HETATM 35 H15 UNL 1 6.078 1.294 0.775 1.00 0.00 H
37
+ HETATM 36 H16 UNL 1 5.103 2.520 1.697 1.00 0.00 H
38
+ HETATM 37 H17 UNL 1 4.603 0.798 1.709 1.00 0.00 H
39
+ CONECT 1 2 21 22 23
40
+ CONECT 2 3 3 4
41
+ CONECT 4 5 24
42
+ CONECT 5 6 6 7
43
+ CONECT 6 11 25
44
+ CONECT 7 8 8 26
45
+ CONECT 8 9 27
46
+ CONECT 9 10 11 11
47
+ CONECT 11 12
48
+ CONECT 12 13 13 14 14
49
+ CONECT 12 15
50
+ CONECT 15 16 17
51
+ CONECT 16 28 29 30
52
+ CONECT 17 18 31 32
53
+ CONECT 18 19 33 34
54
+ CONECT 19 20
55
+ CONECT 20 35 36 37
56
+ END
6pno/6pno_ligand.mol2 ADDED
@@ -0,0 +1,82 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ###
2
+ ### Created by X-TOOL on Mon Aug 2 16:11:40 2021
3
+ ###
4
+
5
+ @<TRIPOS>MOLECULE
6
+ 6pno_ligand
7
+ 33 33 1 0 0
8
+ SMALL
9
+ GAST_HUCK
10
+
11
+
12
+ @<TRIPOS>ATOM
13
+ 1 CAR 18.5370 -7.4600 13.5770 C.3 1 ORM 0.0317
14
+ 2 CAP 18.1290 -6.2490 14.3920 C.2 1 ORM 0.2007
15
+ 3 OAQ 18.8160 -5.1930 14.3480 O.2 1 ORM -0.3851
16
+ 4 NAH 16.9740 -6.4680 15.0230 N.am 1 ORM -0.2338
17
+ 5 CAC 16.4690 -5.5260 15.8380 C.ar 1 ORM 0.0686
18
+ 6 CAD 17.3040 -4.6650 16.5640 C.ar 1 ORM -0.0140
19
+ 7 CAB 15.1020 -5.5320 16.0100 C.ar 1 ORM -0.0404
20
+ 8 CAA 14.5260 -4.6100 16.8740 C.ar 1 ORM -0.0597
21
+ 9 CAF 15.3430 -3.7610 17.5980 C.ar 1 ORM 0.0503
22
+ 10 CLA 14.6250 -2.7090 18.5160 Cl 1 ORM -0.0829
23
+ 11 CAE 16.7320 -3.7720 17.4300 C.ar 1 ORM 0.1087
24
+ 12 SAI 17.7740 -2.7040 18.2950 S.o2 1 ORM 0.0656
25
+ 13 OAJ 19.1830 -2.8380 17.9050 O.2 1 ORM -0.1505
26
+ 14 OAK 17.5380 -3.1380 19.7900 O.2 1 ORM -0.1505
27
+ 15 NAL 17.2230 -1.1210 18.1880 N.am 1 ORM -0.2451
28
+ 16 CAM 17.0780 -0.4700 16.8500 C.3 1 ORM 0.0322
29
+ 17 CAO 15.6050 -0.0810 16.6350 C.3 1 ORM -0.0456
30
+ 18 CAN 17.5950 -1.2270 15.6180 C.3 1 ORM -0.0456
31
+ 19 H1 17.8185 -8.2754 13.7471 H 1 ORM 0.0472
32
+ 20 H2 19.5416 -7.7867 13.8835 H 1 ORM 0.0472
33
+ 21 H3 18.5469 -7.1969 12.5090 H 1 ORM 0.0472
34
+ 22 H4 16.4855 -7.3304 14.8900 H 1 ORM 0.2259
35
+ 23 H5 18.3804 -4.7055 16.4422 H 1 ORM 0.0523
36
+ 24 H6 14.4845 -6.2467 15.4781 H 1 ORM 0.0503
37
+ 25 H7 13.4485 -4.5564 16.9797 H 1 ORM 0.0584
38
+ 26 H8 16.9921 -0.6143 19.0186 H 1 ORM 0.1675
39
+ 27 H9 17.6647 0.4591 16.9005 H 1 ORM 0.0506
40
+ 28 H10 15.4923 0.3987 15.6515 H 1 ORM 0.0248
41
+ 29 H11 15.2921 0.6200 17.4229 H 1 ORM 0.0248
42
+ 30 H12 14.9775 -0.9835 16.6768 H 1 ORM 0.0248
43
+ 31 H13 17.4181 -0.6231 14.7157 H 1 ORM 0.0248
44
+ 32 H14 17.0638 -2.1860 15.5273 H 1 ORM 0.0248
45
+ 33 H15 18.6733 -1.4141 15.7284 H 1 ORM 0.0248
46
+ @<TRIPOS>BOND
47
+ 1 1 2 1
48
+ 2 2 3 2
49
+ 3 2 4 am
50
+ 4 4 5 1
51
+ 5 5 6 ar
52
+ 6 5 7 ar
53
+ 7 6 11 ar
54
+ 8 7 8 ar
55
+ 9 8 9 ar
56
+ 10 9 10 1
57
+ 11 9 11 ar
58
+ 12 11 12 1
59
+ 13 12 13 2
60
+ 14 12 14 2
61
+ 15 12 15 am
62
+ 16 15 16 1
63
+ 17 16 17 1
64
+ 18 16 18 1
65
+ 19 1 19 1
66
+ 20 1 20 1
67
+ 21 1 21 1
68
+ 22 4 22 1
69
+ 23 6 23 1
70
+ 24 7 24 1
71
+ 25 8 25 1
72
+ 26 15 26 1
73
+ 27 16 27 1
74
+ 28 17 28 1
75
+ 29 17 29 1
76
+ 30 17 30 1
77
+ 31 18 31 1
78
+ 32 18 32 1
79
+ 33 18 33 1
80
+ @<TRIPOS>SUBSTRUCTURE
81
+ 1 ORM 1
82
+
6pno/6pno_ligand.sdf ADDED
@@ -0,0 +1,72 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 6pno_ligand
2
+ -I-interpret-
3
+
4
+ 33 33 0 0 0 0 0 0 0 0999 V2000
5
+ 18.5370 -7.4600 13.5770 C 0 0 0 0 0
6
+ 18.1290 -6.2490 14.3920 C 0 0 0 0 0
7
+ 18.8160 -5.1930 14.3480 O 0 0 0 0 0
8
+ 16.9740 -6.4680 15.0230 N 0 0 0 0 0
9
+ 16.4690 -5.5260 15.8380 C 0 0 0 0 0
10
+ 17.3040 -4.6650 16.5640 C 0 0 0 0 0
11
+ 15.1020 -5.5320 16.0100 C 0 0 0 0 0
12
+ 14.5260 -4.6100 16.8740 C 0 0 0 0 0
13
+ 15.3430 -3.7610 17.5980 C 0 0 0 0 0
14
+ 14.6250 -2.7090 18.5160 Cl 0 0 0 0 0
15
+ 16.7320 -3.7720 17.4300 C 0 0 0 0 0
16
+ 17.7740 -2.7040 18.2950 S 0 0 0 0 0
17
+ 19.1830 -2.8380 17.9050 O 0 0 0 0 0
18
+ 17.5380 -3.1380 19.7900 O 0 0 0 0 0
19
+ 17.2230 -1.1210 18.1880 N 0 0 0 0 0
20
+ 17.0780 -0.4700 16.8500 C 0 0 0 0 0
21
+ 15.6050 -0.0810 16.6350 C 0 0 0 0 0
22
+ 17.5950 -1.2270 15.6180 C 0 0 0 0 0
23
+ 18.5464 -7.1979 12.5190 H 0 0 0 0 0
24
+ 19.5326 -7.7827 13.8816 H 0 0 0 0 0
25
+ 17.8244 -8.2672 13.7463 H 0 0 0 0 0
26
+ 16.4757 -7.3476 14.8873 H 0 0 0 0 0
27
+ 18.3863 -4.7057 16.4415 H 0 0 0 0 0
28
+ 14.4811 -6.2507 15.4752 H 0 0 0 0 0
29
+ 13.4425 -4.5561 16.9803 H 0 0 0 0 0
30
+ 16.9875 -0.6042 19.0353 H 0 0 0 0 0
31
+ 17.7448 0.3902 16.9099 H 0 0 0 0 0
32
+ 14.9844 -0.9761 16.6767 H 0 0 0 0 0
33
+ 15.2962 0.6135 17.4163 H 0 0 0 0 0
34
+ 15.4946 0.3942 15.6603 H 0 0 0 0 0
35
+ 18.6635 -1.4118 15.7286 H 0 0 0 0 0
36
+ 17.0680 -2.1770 15.5293 H 0 0 0 0 0
37
+ 17.4192 -0.6277 14.7247 H 0 0 0 0 0
38
+ 1 2 1 0 0 0
39
+ 2 3 2 0 0 0
40
+ 2 4 1 0 0 0
41
+ 4 5 1 0 0 0
42
+ 5 6 4 0 0 0
43
+ 5 7 4 0 0 0
44
+ 6 11 4 0 0 0
45
+ 7 8 4 0 0 0
46
+ 8 9 4 0 0 0
47
+ 9 10 1 0 0 0
48
+ 9 11 4 0 0 0
49
+ 11 12 1 0 0 0
50
+ 12 13 2 0 0 0
51
+ 12 14 2 0 0 0
52
+ 12 15 1 0 0 0
53
+ 15 16 1 0 0 0
54
+ 16 17 1 0 0 0
55
+ 16 18 1 0 0 0
56
+ 1 19 1 0 0 0
57
+ 1 20 1 0 0 0
58
+ 1 21 1 0 0 0
59
+ 4 22 1 0 0 0
60
+ 6 23 1 0 0 0
61
+ 7 24 1 0 0 0
62
+ 8 25 1 0 0 0
63
+ 15 26 1 0 0 0
64
+ 16 27 1 0 0 0
65
+ 17 28 1 0 0 0
66
+ 17 29 1 0 0 0
67
+ 17 30 1 0 0 0
68
+ 18 31 1 0 0 0
69
+ 18 32 1 0 0 0
70
+ 18 33 1 0 0 0
71
+ M END
72
+ $$$$
6pno/6pno_protein_alphafold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pno/6pno_protein_esmfold_aligned_tr_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pno/6pno_protein_processed_fix.pdb ADDED
The diff for this file is too large to render. See raw diff
 
6pno/6pno_rdkit_ligand.pdb ADDED
@@ -0,0 +1,50 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ COMPND 6pno_ligand
2
+ HETATM 1 C1 UNL 1 3.721 2.913 0.882 1.00 0.00 C
3
+ HETATM 2 C2 UNL 1 3.204 1.565 0.490 1.00 0.00 C
4
+ HETATM 3 O1 UNL 1 3.544 0.543 1.153 1.00 0.00 O
5
+ HETATM 4 N1 UNL 1 2.334 1.368 -0.608 1.00 0.00 N
6
+ HETATM 5 C3 UNL 1 1.835 0.092 -0.991 1.00 0.00 C
7
+ HETATM 6 C4 UNL 1 0.634 -0.383 -0.451 1.00 0.00 C
8
+ HETATM 7 C5 UNL 1 2.469 -0.739 -1.884 1.00 0.00 C
9
+ HETATM 8 C6 UNL 1 1.963 -1.970 -2.237 1.00 0.00 C
10
+ HETATM 9 C7 UNL 1 0.787 -2.419 -1.700 1.00 0.00 C
11
+ HETATM 10 CL1 UNL 1 0.108 -3.979 -2.121 1.00 0.00 CL
12
+ HETATM 11 C8 UNL 1 0.096 -1.605 -0.778 1.00 0.00 C
13
+ HETATM 12 S1 UNL 1 -1.385 -2.240 -0.117 1.00 0.00 S
14
+ HETATM 13 O2 UNL 1 -1.042 -3.550 0.577 1.00 0.00 O
15
+ HETATM 14 O3 UNL 1 -2.284 -2.627 -1.271 1.00 0.00 O
16
+ HETATM 15 N2 UNL 1 -2.193 -1.187 0.901 1.00 0.00 N
17
+ HETATM 16 C9 UNL 1 -2.665 0.045 0.392 1.00 0.00 C
18
+ HETATM 17 C10 UNL 1 -2.238 1.182 1.280 1.00 0.00 C
19
+ HETATM 18 C11 UNL 1 -4.210 0.056 0.321 1.00 0.00 C
20
+ HETATM 19 H1 UNL 1 3.972 2.965 1.948 1.00 0.00 H
21
+ HETATM 20 H2 UNL 1 4.640 3.071 0.251 1.00 0.00 H
22
+ HETATM 21 H3 UNL 1 2.989 3.663 0.549 1.00 0.00 H
23
+ HETATM 22 H4 UNL 1 2.062 2.231 -1.148 1.00 0.00 H
24
+ HETATM 23 H5 UNL 1 0.133 0.253 0.256 1.00 0.00 H
25
+ HETATM 24 H6 UNL 1 3.403 -0.375 -2.307 1.00 0.00 H
26
+ HETATM 25 H7 UNL 1 2.489 -2.620 -2.956 1.00 0.00 H
27
+ HETATM 26 H8 UNL 1 -1.867 -1.173 1.890 1.00 0.00 H
28
+ HETATM 27 H9 UNL 1 -2.351 0.215 -0.637 1.00 0.00 H
29
+ HETATM 28 H10 UNL 1 -3.117 1.815 1.576 1.00 0.00 H
30
+ HETATM 29 H11 UNL 1 -1.587 1.876 0.684 1.00 0.00 H
31
+ HETATM 30 H12 UNL 1 -1.700 0.832 2.200 1.00 0.00 H
32
+ HETATM 31 H13 UNL 1 -4.545 -0.873 -0.182 1.00 0.00 H
33
+ HETATM 32 H14 UNL 1 -4.657 0.137 1.311 1.00 0.00 H
34
+ HETATM 33 H15 UNL 1 -4.540 0.919 -0.291 1.00 0.00 H
35
+ CONECT 1 2 19 20 21
36
+ CONECT 2 3 3 4
37
+ CONECT 4 5 22
38
+ CONECT 5 6 6 7
39
+ CONECT 6 11 23
40
+ CONECT 7 8 8 24
41
+ CONECT 8 9 25
42
+ CONECT 9 10 11 11
43
+ CONECT 11 12
44
+ CONECT 12 13 13 14 14
45
+ CONECT 12 15
46
+ CONECT 15 16 26
47
+ CONECT 16 17 18 27
48
+ CONECT 17 28 29 30
49
+ CONECT 18 31 32 33
50
+ END
6py0/6py0_ligand.mol2 ADDED
@@ -0,0 +1,122 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ###
2
+ ### Created by X-TOOL on Mon Aug 2 16:16:12 2021
3
+ ###
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+
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+ @<TRIPOS>MOLECULE
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+ 6py0_ligand
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+ 53 H32 -11.2705 1.2159 -3.6855 H 1 RTL 0.0347
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+ @<TRIPOS>BOND
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+ @<TRIPOS>SUBSTRUCTURE
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+ 1 RTL 1
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+
6py0/6py0_ligand.sdf ADDED
@@ -0,0 +1,112 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ 6py0_ligand
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+ 21 53 1 0 0 0
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+ M END
112
+ $$$$