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fix bonds and protonation for BRD4 ligand 5 #74

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fix bonds and protonation for BRD4 ligand 5 #74

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6ae6302
fix bonds and protonation for BRD4 ligand 5
GHeinzelmann Sep 29, 2021
e7dbe7e
remove chain identifier from ligand pdb
GHeinzelmann Sep 29, 2021
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102 changes: 49 additions & 53 deletions input_files/BRD4/mol2/ligand-5.mol2
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Original file line number Diff line number Diff line change
@@ -1,48 +1,46 @@
@<TRIPOS>MOLECULE
BRD4, Ligand 5
37 40 1 0 0
35 38 1 0 0
SMALL
Current Charge


@<TRIPOS>ATOM
1 CAS 2.1290 -0.9870 13.1590 C.ar 1 08H -0.067300
2 CAJ 2.3790 0.2880 13.6910 C.ar 1 08H -0.113000
3 CAP 2.9870 1.2310 12.8720 C.ar 1 08H 0.014400
4 ClAB 3.3180 2.8300 13.4830 Cl 1 08H -0.079400
5 CAH 3.3260 0.9880 11.5350 C.ar 1 08H -0.109000
6 CAI 3.0650 -0.2910 11.0120 C.ar 1 08H -0.141000
7 CAU 2.4600 -1.2450 11.8200 C.ar 1 08H 0.030800
8 NAV 2.2610 -2.4640 11.1890 N.pl3 1 08H -0.255800
9 CAR 1.8610 -2.7750 9.9270 C.2 1 08H 0.373800
10 CAA 1.4310 -1.8170 8.8000 C.3 1 08H -0.123400
11 NAM 1.8340 -4.1020 9.7850 N.2 1 08H -0.349000
12 NAN 2.2330 -4.6440 10.8780 N.2 1 08H -0.341000
13 CAT 2.4940 -3.6520 11.7600 C.2 1 08H 0.375800
14 CAK 2.8900 -3.8190 13.1940 C.3 1 08H 0.160500
15 NAL 1.7470 -3.2490 13.9570 N.3 1 08H -0.856200
16 CAO 1.5060 -1.9220 14.0440 C.3 1 08H 0.294100
17 CAQ 0.3490 -1.5560 14.8260 C.ar 1 08H -0.100300
18 CAF -0.3930 -0.4170 14.5250 C.ar 1 08H -0.111000
19 CAD -1.5570 -0.0930 15.2240 C.ar 1 08H -0.132500
20 CAC -2.0000 -0.8770 16.2860 C.ar 1 08H -0.121000
21 CAE -1.2580 -1.9990 16.5980 C.ar 1 08H -0.132500
22 CAG -0.1050 -2.3250 15.8900 C.ar 1 08H -0.111000
23 H 2.1190 0.5180 14.6630 H 1 08H 0.157000
24 H1 3.7540 1.7240 10.9520 H 1 08H 0.155000
25 H2 3.3200 -0.5180 10.0380 H 1 08H 0.152000
26 H3 1.1760 -2.3830 7.9290 H 1 08H 0.063033
27 H4 2.2370 -1.1520 8.5700 H 1 08H 0.063033
28 H5 0.5810 -1.2500 9.1190 H 1 08H 0.063033
29 H6 3.7920 -3.2820 13.4040 H 1 08H 0.064700
30 H7 3.0850 -4.8400 13.4490 H 1 08H 0.064700
31 H8 1.8580 -3.5770 14.9160 H 1 08H 0.398800
32 H9 2.3200 -1.5980 14.6580 H 1 08H 0.026700
33 H10 -0.0740 0.2040 13.7650 H 1 08H 0.140500
34 H11 -2.0980 0.7420 14.9490 H 1 08H 0.134500
35 H12 -2.8490 -0.6300 16.8180 H 1 08H 0.134000
36 H13 -1.5650 -2.6080 17.3720 H 1 08H 0.134500
37 H14 0.4290 -3.1640 16.1640 H 1 08H 0.140500
1 CAS 2.1290 -0.9870 13.1590 C.ar 1 08H -0.176900
2 CAJ 2.3790 0.2880 13.6910 C.ar 1 08H -0.082000
3 CAP 2.9870 1.2310 12.8720 C.ar 1 08H 0.006400
4 ClAB 3.3180 2.8300 13.4830 Cl 1 08H -0.072400
5 CAH 3.3260 0.9880 11.5350 C.ar 1 08H -0.098000
6 CAI 3.0650 -0.2910 11.0120 C.ar 1 08H -0.140000
7 CAU 2.4600 -1.2450 11.8200 C.ar 1 08H 0.032800
8 NAV 2.2610 -2.4640 11.1890 N.pl3 1 08H -0.271800
9 CAR 1.8610 -2.7750 9.9270 C.2 1 08H 0.384800
10 CAA 1.4310 -1.8170 8.8000 C.3 1 08H -0.125400
11 NAM 1.8340 -4.1020 9.7850 N.2 1 08H -0.345000
12 NAN 2.2330 -4.6440 10.8780 N.2 1 08H -0.327000
13 CAT 2.4940 -3.6520 11.7600 C.2 1 08H 0.354800
14 CAK 2.8900 -3.8190 13.1940 C.3 1 08H 0.085500
15 NAL 1.7470 -3.2490 13.9570 N.2 1 08H -0.570900
16 CAO 1.5060 -1.9220 14.0440 C.2 1 08H 0.531500
17 CAQ 0.3490 -1.5560 14.8260 C.ar 1 08H -0.146900
18 CAF -0.3930 -0.4170 14.5250 C.ar 1 08H -0.099000
19 CAD -1.5570 -0.0930 15.2240 C.ar 1 08H -0.135000
20 CAC -2.0000 -0.8770 16.2860 C.ar 1 08H -0.115000
21 CAE -1.2580 -1.9990 16.5980 C.ar 1 08H -0.135000
22 CAG -0.1050 -2.3250 15.8900 C.ar 1 08H -0.099000
23 H 2.1190 0.5180 14.6630 H 1 08H 0.168000
24 H1 3.7540 1.7240 10.9520 H 1 08H 0.157000
25 H2 3.3200 -0.5180 10.0380 H 1 08H 0.154000
26 H3 1.1760 -2.3830 7.9290 H 1 08H 0.064700
27 H4 2.2370 -1.1520 8.5700 H 1 08H 0.064700
28 H5 0.5810 -1.2500 9.1190 H 1 08H 0.064700
29 H6 3.7920 -3.2820 13.4040 H 1 08H 0.089200
30 H7 3.0850 -4.8400 13.4490 H 1 08H 0.089200
31 H8 -0.0740 0.2040 13.7650 H 1 08H 0.142000
32 H9 -2.0980 0.7420 14.9490 H 1 08H 0.136500
33 H10 -2.8490 -0.6300 16.8180 H 1 08H 0.135000
34 H11 -1.5650 -2.6080 17.3720 H 1 08H 0.136500
35 H12 0.4290 -3.1640 16.1640 H 1 08H 0.142000
@<TRIPOS>BOND
1 1 2 ar
2 1 7 ar
Expand All @@ -69,20 +67,18 @@ Current Charge
23 14 15 1
24 14 29 1
25 14 30 1
26 15 16 1
27 15 31 1
28 16 17 1
29 16 32 1
30 17 18 ar
31 17 22 ar
32 18 19 ar
33 18 33 1
34 19 20 ar
35 19 34 1
36 20 21 ar
37 20 35 1
38 21 22 ar
39 21 36 1
40 22 37 1
26 15 16 2
27 16 17 1
28 17 18 ar
29 17 22 ar
30 18 19 ar
31 18 31 1
32 19 20 ar
33 19 32 1
34 20 21 ar
35 20 33 1
36 21 22 ar
37 21 34 1
38 22 35 1
@<TRIPOS>SUBSTRUCTURE
1 08H 1 TEMP 0 **** **** 0 ROOT
92 changes: 44 additions & 48 deletions input_files/BRD4/pdb/ligand-5.pdb
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
REMARK BRD4, Ligand 5
REMARK BRD4, Ligand 5
ATOM 1 CAS 08H 1 2.129 -0.987 13.159 1.00 0.00 C
ATOM 2 CAJ 08H 1 2.379 0.288 13.691 1.00 0.00 C
ATOM 3 CAP 08H 1 2.987 1.231 12.872 1.00 0.00 C
ATOM 4 ClAB 08H 1 3.318 2.830 13.483 1.00 0.00 CL
ATOM 4 ClAB 08H 1 3.318 2.830 13.483 1.00 0.00 Cl
ATOM 5 CAH 08H 1 3.326 0.988 11.535 1.00 0.00 C
ATOM 6 CAI 08H 1 3.065 -0.291 11.012 1.00 0.00 C
ATOM 7 CAU 08H 1 2.460 -1.245 11.820 1.00 0.00 C
Expand All @@ -29,49 +29,45 @@ ATOM 27 H4 08H 1 2.237 -1.152 8.570 1.00 0.00 H
ATOM 28 H5 08H 1 0.581 -1.250 9.119 1.00 0.00 H
ATOM 29 H6 08H 1 3.792 -3.282 13.404 1.00 0.00 H
ATOM 30 H7 08H 1 3.085 -4.840 13.449 1.00 0.00 H
ATOM 31 H8 08H 1 1.858 -3.577 14.916 1.00 0.00 H
ATOM 32 H9 08H 1 2.320 -1.598 14.658 1.00 0.00 H
ATOM 33 H10 08H 1 -0.074 0.204 13.765 1.00 0.00 H
ATOM 34 H11 08H 1 -2.098 0.742 14.949 1.00 0.00 H
ATOM 35 H12 08H 1 -2.849 -0.630 16.818 1.00 0.00 H
ATOM 36 H13 08H 1 -1.565 -2.608 17.372 1.00 0.00 H
ATOM 37 H14 08H 1 0.429 -3.164 16.164 1.00 0.00 H
TER 38 08H 1
CONECT 1 2 7 16
CONECT 2 1 3 23
CONECT 3 2 4 5
CONECT 4 3
CONECT 5 3 6 24
CONECT 6 5 7 25
CONECT 7 1 6 8
CONECT 8 7 9 13
CONECT 9 8 10 11
CONECT 10 9 26 27 28
CONECT 11 9 12
CONECT 12 11 13
CONECT 13 8 12 14
CONECT 14 13 15 29 30
CONECT 15 14 16 31
CONECT 16 1 15 17 32
CONECT 17 16 18 22
CONECT 18 17 19 33
CONECT 19 18 20 34
CONECT 20 19 21 35
CONECT 21 20 22 36
CONECT 22 17 21 37
CONECT 23 2
CONECT 24 5
CONECT 25 6
CONECT 26 10
CONECT 27 10
CONECT 28 10
CONECT 29 14
CONECT 30 14
CONECT 31 15
CONECT 32 16
CONECT 33 18
CONECT 34 19
CONECT 35 20
CONECT 36 21
CONECT 37 22
END
ATOM 31 H8 08H 1 -0.074 0.204 13.765 1.00 0.00 H
ATOM 32 H9 08H 1 -2.098 0.742 14.949 1.00 0.00 H
ATOM 33 H10 08H 1 -2.849 -0.630 16.818 1.00 0.00 H
ATOM 34 H11 08H 1 -1.565 -2.608 17.372 1.00 0.00 H
ATOM 35 H12 08H 1 0.429 -3.164 16.164 1.00 0.00 H
TER 36 08H 1
CONECT 1 2 7 16
CONECT 2 1 3 23
CONECT 3 2 4 5
CONECT 4 3
CONECT 5 3 6 24
CONECT 6 5 7 25
CONECT 7 1 6 8
CONECT 8 7 9 13
CONECT 9 8 10 11
CONECT 10 9 26 27 28
CONECT 11 9 12
CONECT 12 11 13
CONECT 13 8 12 14
CONECT 14 13 15 29 30
CONECT 15 14 16
CONECT 16 1 15 17
CONECT 17 16 18 22
CONECT 18 17 19 31
CONECT 19 18 20 32
CONECT 20 19 21 33
CONECT 21 20 22 34
CONECT 22 17 21 35
CONECT 23 2
CONECT 24 5
CONECT 25 6
CONECT 26 10
CONECT 27 10
CONECT 28 10
CONECT 29 14
CONECT 30 14
CONECT 31 18
CONECT 32 19
CONECT 33 20
CONECT 34 21
CONECT 35 22
END
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