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IrwinLab
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LSD_Sigma2_Alon_2021

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  1. .gitattributes +2 -0
  2. dockfiles/INDOCK +84 -0
  3. dockfiles/ligand.desolv.heavy +0 -0
  4. dockfiles/ligand.desolv.hydrogen +0 -0
  5. dockfiles/matching_spheres.pdb +90 -0
  6. dockfiles/matching_spheres.sph +59 -0
  7. dockfiles/rec.crg.pdb +0 -0
  8. dockfiles/trim.electrostatics.phi +3 -0
  9. dockfiles/vdw.bmp +3 -0
  10. dockfiles/vdw.parms.amb.mindock +34 -0
  11. dockfiles/vdw.vdw +3 -0
  12. dockfiles/xtal-lig.pdb +28 -0
.gitattributes CHANGED
@@ -57,3 +57,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
57
  # Video files - compressed
58
  *.mp4 filter=lfs diff=lfs merge=lfs -text
59
  *.webm filter=lfs diff=lfs merge=lfs -text
 
 
 
57
  # Video files - compressed
58
  *.mp4 filter=lfs diff=lfs merge=lfs -text
59
  *.webm filter=lfs diff=lfs merge=lfs -text
60
+ dockfiles/trim.electrostatics.phi filter=lfs diff=lfs merge=lfs -text
61
+ dockfiles/vdw.vdw filter=lfs diff=lfs merge=lfs -text
dockfiles/INDOCK ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ DOCK 3.7 parameter
2
+ #####################################################
3
+ # NOTE: split_database_index is reserved to specify a list of files
4
+ # defults for large scale docking.
5
+ ligand_atom_file split_database_index
6
+ #####################################################
7
+ # OUTPUT
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+ output_file_prefix test.
9
+ #####################################################
10
+ # MATCHING
11
+ match_method 2
12
+ distance_tolerance 0.05
13
+ match_goal 5000
14
+ distance_step 0.05
15
+ distance_maximum 0.5
16
+ timeout 10.0
17
+ nodes_maximum 4
18
+ nodes_minimum 4
19
+ bump_maximum 100
20
+ bump_rigid 100
21
+ mol2_score_maximum -10.0
22
+ #####################################################
23
+ # COLORING
24
+ chemical_matching no
25
+ case_sensitive no
26
+ #####################################################
27
+ # SEARCH MODE
28
+ atom_minimum 4
29
+ atom_maximum 100
30
+ number_save 1
31
+ number_write 1
32
+ flush_int 100
33
+ #molecules_maximum 100000
34
+ check_clashes yes
35
+ do_premax no
36
+ do_clusters no
37
+ #####################################################
38
+ # SCORING
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+ ligand_desolvation volume
40
+ #vdw_maximum 1.0e10
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+ ligand_desolv_scale 1.0
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+ electrostatic_scale 1.0
43
+ vdw_scale 1.0
44
+ internal_scale 0.0
45
+ per_atom_scores no
46
+ #####################################################
47
+ # DOCKovalent
48
+ dockovalent no
49
+ bond_len 1.8
50
+ bond_ang1 109.5
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+ bond_ang2 109.5
52
+ len_range 0.0
53
+ len_step 0.1
54
+ ang1_range 10.0
55
+ ang2_range 10.0
56
+ ang1_step 2.5
57
+ ang2_step 2.5
58
+ #####################################################
59
+ # MINIMIZATION
60
+ minimize yes
61
+ sim_itmax 500
62
+ sim_trnstep 0.2
63
+ sim_rotstep 5.0
64
+ sim_need_to_restart 1.0
65
+ sim_cnvrge 0.1
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+ min_cut 1.0e15
67
+ iseed 777
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+ #####################################################
69
+ # INPUT FILES / THINGS THAT CHANGE
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+ receptor_sphere_file ../dockfiles/matching_spheres.sph
71
+ vdw_parameter_file ../dockfiles/vdw.parms.amb.mindock
72
+ delphi_nsize 63
73
+ flexible_receptor no
74
+ total_receptors 1
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+ ############## grids/data for one receptor
76
+ rec_number 1
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+ rec_group 1
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+ rec_group_option 1
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+ solvmap_file ../dockfiles/ligand.desolv.heavy
80
+ hydrogen_solvmap_file ../dockfiles/ligand.desolv.hydrogen
81
+ delphi_file ../dockfiles/trim.electrostatics.phi
82
+ chemgrid_file ../dockfiles/vdw.vdw
83
+ bumpmap_file ../dockfiles/vdw.bmp
84
+ ############## end of INDOCK
dockfiles/ligand.desolv.heavy ADDED
The diff for this file is too large to render. See raw diff
 
dockfiles/ligand.desolv.hydrogen ADDED
The diff for this file is too large to render. See raw diff
 
dockfiles/matching_spheres.pdb ADDED
@@ -0,0 +1,90 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ATOM 9001 C SPH 9001 -0.954 -19.236 32.700
2
+ TER
3
+ ATOM 9002 C SPH 9002 -1.866 -26.239 30.545
4
+ TER
5
+ ATOM 9003 C SPH 9003 -1.779 -21.526 32.201
6
+ TER
7
+ ATOM 9004 C SPH 9004 -3.958 -26.482 29.619
8
+ TER
9
+ ATOM 9005 C SPH 9005 -1.123 -21.766 31.060
10
+ TER
11
+ ATOM 9006 C SPH 9006 -1.039 -25.782 29.682
12
+ TER
13
+ ATOM 9007 C SPH 9007 2.342 -17.170 30.738
14
+ TER
15
+ ATOM 9008 C SPH 9008 -2.711 -26.336 31.465
16
+ TER
17
+ ATOM 9009 C SPH 9009 0.823 -17.062 30.547
18
+ TER
19
+ ATOM 9010 C SPH 9010 2.612 -18.219 31.813
20
+ TER
21
+ ATOM 9011 C SPH 9011 -0.569 -20.864 31.110
22
+ TER
23
+ ATOM 9012 C SPH 9012 -1.691 -21.117 28.481
24
+ TER
25
+ ATOM 9013 C SPH 9013 -4.477 -22.686 28.877
26
+ TER
27
+ ATOM 9014 C SPH 9014 -2.629 -25.649 33.570
28
+ TER
29
+ ATOM 9015 C SPH 9015 -1.249 -28.884 33.625
30
+ TER
31
+ ATOM 9016 C SPH 9016 -1.184 -29.422 32.189
32
+ TER
33
+ ATOM 9017 C SPH 9017 1.219 -20.917 31.239
34
+ TER
35
+ ATOM 9018 C SPH 9018 -2.780 -23.490 29.278
36
+ TER
37
+ ATOM 9019 C SPH 9019 2.865 -15.965 31.201
38
+ TER
39
+ ATOM 9020 C SPH 9020 0.081 -28.932 31.502
40
+ TER
41
+ ATOM 9021 C SPH 9021 -2.444 -29.007 31.374
42
+ TER
43
+ ATOM 9022 C SPH 9022 0.266 -18.396 30.163
44
+ TER
45
+ ATOM 9023 C SPH 9023 -0.730 -18.435 29.295
46
+ TER
47
+ ATOM 9024 C SPH 9024 2.124 -19.561 31.299
48
+ TER
49
+ ATOM 9025 C SPH 9025 -2.292 -22.665 28.334
50
+ TER
51
+ ATOM 9026 C SPH 9026 -1.900 -21.882 28.334
52
+ TER
53
+ ATOM 9027 C SPH 9027 -0.094 -19.255 32.425
54
+ TER
55
+ ATOM 9028 C SPH 9028 0.603 -19.521 31.091
56
+ TER
57
+ ATOM 9029 C SPH 9029 -1.445 -19.690 28.917
58
+ TER
59
+ ATOM 9030 C SPH 9030 -0.835 -24.465 31.688
60
+ TER
61
+ ATOM 9031 C SPH 9031 -2.103 -27.834 30.414
62
+ TER
63
+ ATOM 9032 C SPH 9032 -3.280 -26.847 30.244
64
+ TER
65
+ ATOM 9033 C SPH 9033 -3.581 -22.490 31.921
66
+ TER
67
+ ATOM 9034 C SPH 9034 -3.260 -22.222 29.085
68
+ TER
69
+ ATOM 9035 C SPH 9035 -1.322 -20.726 30.034
70
+ TER
71
+ ATOM 9036 C SPH 9036 -3.562 -23.735 29.201
72
+ TER
73
+ ATOM 9037 C SPH 9037 -2.178 -25.788 32.280
74
+ TER
75
+ ATOM 9038 C SPH 9038 -3.014 -25.513 31.016
76
+ TER
77
+ ATOM 9039 C SPH 9039 0.320 -21.955 31.511
78
+ TER
79
+ ATOM 9040 C SPH 9040 -2.645 -22.530 31.871
80
+ TER
81
+ ATOM 9041 C SPH 9041 -2.448 -24.363 30.060
82
+ TER
83
+ ATOM 9042 C SPH 9042 -0.293 -23.273 31.098
84
+ TER
85
+ ATOM 9043 C SPH 9043 -1.773 -23.101 30.715
86
+ TER
87
+ ATOM 9044 C SPH 9044 0.141 -20.850 30.487
88
+ TER
89
+ ATOM 9045 C SPH 9045 -1.809 -22.105 29.554
90
+ TER
dockfiles/matching_spheres.sph ADDED
@@ -0,0 +1,59 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ DOCK 5.2 ligand_atoms
2
+ positive (1)
3
+ negative (2)
4
+ acceptor (3)
5
+ donor (4)
6
+ ester_o (5)
7
+ amide_o (6)
8
+ neutral (7)
9
+ not_neutral (8)
10
+ positive_or_donor (9)
11
+ negative_or_acceptor (10)
12
+ neutral_or_acceptor_or_donor (11)
13
+ donacc (12)
14
+ cluster 1 number of spheres in cluster 45
15
+ 9001 -0.95419 -19.23599 32.70004 1.748 1432 0 0
16
+ 9002 -1.86626 -26.23942 30.54492 2.102 218 0 0
17
+ 9003 -1.77925 -21.52638 32.20100 1.784 1464 0 0
18
+ 9004 -3.95778 -26.48176 29.61946 2.075 253 0 0
19
+ 9005 -1.12310 -21.76596 31.06032 2.419 1434 0 0
20
+ 9006 -1.03859 -25.78250 29.68237 1.400 218 0 0
21
+ 9007 2.34200 -17.17000 30.73800 0.000 0 0 0
22
+ 9008 -2.71129 -26.33568 31.46522 2.985 1421 0 0
23
+ 9009 0.82300 -17.06200 30.54700 0.000 0 0 0
24
+ 9010 2.61200 -18.21900 31.81300 0.000 0 0 0
25
+ 9011 -0.56878 -20.86422 31.11031 2.483 1434 0 0
26
+ 9012 -1.69107 -21.11686 28.48095 1.677 575 0 0
27
+ 9013 -4.47706 -22.68605 28.87711 1.404 1435 0 0
28
+ 9014 -2.62881 -25.64935 33.57037 1.743 1466 0 0
29
+ 9015 -1.24900 -28.88400 33.62500 0.000 0 0 0
30
+ 9016 -1.18400 -29.42200 32.18900 0.000 0 0 0
31
+ 9017 1.21858 -20.91709 31.23883 1.860 264 0 0
32
+ 9018 -2.78025 -23.49000 29.27788 2.031 576 0 0
33
+ 9019 2.86500 -15.96500 31.20100 0.000 0 0 0
34
+ 9020 0.08100 -28.93200 31.50200 0.000 0 0 0
35
+ 9021 -2.44400 -29.00700 31.37400 0.000 0 0 0
36
+ 9022 0.26600 -18.39600 30.16300 0.000 0 0 0
37
+ 9023 -0.73000 -18.43500 29.29500 0.000 0 0 0
38
+ 9024 2.12400 -19.56100 31.29900 0.000 0 0 0
39
+ 9025 -2.29170 -22.66454 28.33375 1.401 263 0 0
40
+ 9026 -1.90048 -21.88239 28.33404 1.400 263 0 0
41
+ 9027 -0.09400 -19.25500 32.42500 0.000 0 0 0
42
+ 9028 0.60300 -19.52100 31.09100 0.000 0 0 0
43
+ 9029 -1.44500 -19.69000 28.91700 0.000 0 0 0
44
+ 9030 -0.83506 -24.46478 31.68828 1.472 218 0 0
45
+ 9031 -2.10300 -27.83400 30.41400 0.000 0 0 0
46
+ 9032 -3.28000 -26.84700 30.24400 0.000 0 0 0
47
+ 9033 -3.58098 -22.48988 31.92085 1.654 1420 0 0
48
+ 9034 -3.26000 -22.22200 29.08500 0.000 0 0 0
49
+ 9035 -1.32200 -20.72600 30.03400 0.000 0 0 0
50
+ 9036 -3.56200 -23.73500 29.20100 0.000 0 0 0
51
+ 9037 -2.17800 -25.78800 32.28000 0.000 0 0 0
52
+ 9038 -3.01400 -25.51300 31.01600 0.000 0 0 0
53
+ 9039 0.32000 -21.95500 31.51100 0.000 0 0 0
54
+ 9040 -2.64500 -22.53000 31.87100 0.000 0 0 0
55
+ 9041 -2.44800 -24.36300 30.06000 0.000 0 0 0
56
+ 9042 -0.29300 -23.27300 31.09800 0.000 0 0 0
57
+ 9043 -1.77300 -23.10100 30.71500 0.000 0 0 0
58
+ 9044 0.14100 -20.85000 30.48700 0.000 0 0 0
59
+ 9045 -1.80900 -22.10500 29.55400 0.000 0 0 0
dockfiles/rec.crg.pdb ADDED
The diff for this file is too large to render. See raw diff
 
dockfiles/trim.electrostatics.phi ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:153e9249058807694eeed97ba45ba23c29345629aac202a2445be44f9560f854
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+ size 1000350
dockfiles/vdw.bmp ADDED

Git LFS Details

  • SHA256: d16e80bc05589236725b75828eae98eb3adb14ae240000948083003eb87de56c
  • Pointer size: 132 Bytes
  • Size of remote file: 2.87 MB
dockfiles/vdw.parms.amb.mindock ADDED
@@ -0,0 +1,34 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ! Use this vdw parameter file when using minimization, either within dock
2
+ ! or with a post-dock minimizer (dockmin_dfp, dockmin_sim)
3
+ !
4
+ ! AMBER-based van der Waals parameters (see vdwinfo)
5
+ ! polar H has been made non-volumeless for energy minimization
6
+ !type sqrt(A) sqrt(B)
7
+ 1 888.79 24.81 sp2 and sp C
8
+ 2 1586.37 35.05 CH3 (united atom)
9
+ 3 1128.12 27.96 CH2 (united atom)
10
+ 4 769.72 21.49 CH (united atom)
11
+ 5 533.20 16.16 sp3 C
12
+ 6 0.37 0.31 H on polar atom
13
+ 7 85.37 4.13 H on C
14
+ 8 735.31 24.25 sp2 and sp N
15
+ 9 725.70 20.26 quaternary sp3 N
16
+ 10 888.79 24.81 sp3 N
17
+ 11 480.19 20.72 sp2 O
18
+ 12 500.18 19.68 sp3 O
19
+ 13 2454.77 46.86 P
20
+ 14 1831.79 40.48 S
21
+ 15 251.02 11.92 F
22
+ 16 2194.13 46.37 Cl
23
+ 17 3885.92 66.31 Br
24
+ 18 6817.37 92.86 I
25
+ 19 235.24 10.15 Na+ (unhydrated), K+
26
+ 20 51.92 5.73 Mg++, Li+, Al+++, M++ (except Ca++),
27
+ ! 20 is also Ni & Cu (apparently)
28
+ 21 339.55 14.65 Ca++
29
+ 22 1971.47 37.63 Cl- (unhydrated)
30
+ 23 762.07 24.38 Lennard-Jones water particle
31
+ 24 3885.92 66.31 Si (same numbers as Br)
32
+ 25 0.00 0.00 Du/LP (same numbers as H on polar atom)
33
+ 26 53.67 7.33 Zn2+ (Austin)
34
+ ! 26 1264.47 45.49 Zn2+ (niu, see tack's paper in med.res)
dockfiles/vdw.vdw ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ version https://git-lfs.github.com/spec/v1
2
+ oid sha256:f082b9c3e10e3352c242aac94318a505e1ce6e780191e91def54e950c53e55e4
3
+ size 22646016
dockfiles/xtal-lig.pdb ADDED
@@ -0,0 +1,28 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ ATOM 1 C1 CLR A 201 2.124 -19.561 31.299 1.00 55.88 C
2
+ ATOM 2 O1 CLR A 201 2.865 -15.965 31.201 1.00 57.73 O
3
+ ATOM 3 C2 CLR A 201 2.612 -18.219 31.813 1.00 56.84 C
4
+ ATOM 4 C3 CLR A 201 2.342 -17.170 30.738 1.00 58.33 C
5
+ ATOM 5 C4 CLR A 201 0.823 -17.062 30.547 1.00 59.16 C
6
+ ATOM 6 C5 CLR A 201 0.266 -18.396 30.163 1.00 58.85 C
7
+ ATOM 7 C6 CLR A 201 -0.730 -18.435 29.295 1.00 60.82 C
8
+ ATOM 8 C7 CLR A 201 -1.445 -19.690 28.917 1.00 61.86 C
9
+ ATOM 9 C8 CLR A 201 -1.322 -20.726 30.034 1.00 62.09 C
10
+ ATOM 10 C9 CLR A 201 0.141 -20.850 30.487 1.00 59.37 C
11
+ ATOM 11 C10 CLR A 201 0.603 -19.521 31.091 1.00 57.68 C
12
+ ATOM 12 C11 CLR A 201 0.320 -21.955 31.511 1.00 59.27 C
13
+ ATOM 13 C12 CLR A 201 -0.293 -23.273 31.098 1.00 60.20 C
14
+ ATOM 14 C13 CLR A 201 -1.773 -23.101 30.715 1.00 62.45 C
15
+ ATOM 15 C14 CLR A 201 -1.809 -22.105 29.554 1.00 63.56 C
16
+ ATOM 16 C15 CLR A 201 -3.260 -22.222 29.085 1.00 64.81 C
17
+ ATOM 17 C16 CLR A 201 -3.562 -23.735 29.201 1.00 64.06 C
18
+ ATOM 18 C17 CLR A 201 -2.448 -24.363 30.060 1.00 62.73 C
19
+ ATOM 19 C18 CLR A 201 -2.645 -22.530 31.871 1.00 62.50 C
20
+ ATOM 20 C19 CLR A 201 -0.094 -19.255 32.425 1.00 56.13 C
21
+ ATOM 21 C20 CLR A 201 -3.014 -25.513 31.016 1.00 61.03 C
22
+ ATOM 22 C21 CLR A 201 -2.178 -25.788 32.280 1.00 58.78 C
23
+ ATOM 23 C22 CLR A 201 -3.280 -26.847 30.244 1.00 62.14 C
24
+ ATOM 24 C23 CLR A 201 -2.103 -27.834 30.414 1.00 63.58 C
25
+ ATOM 25 C24 CLR A 201 -2.444 -29.007 31.374 1.00 64.23 C
26
+ ATOM 26 C25 CLR A 201 -1.184 -29.422 32.189 1.00 63.87 C
27
+ ATOM 27 C26 CLR A 201 -1.249 -28.884 33.625 1.00 63.16 C
28
+ ATOM 28 C27 CLR A 201 0.081 -28.932 31.502 1.00 63.83 C