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Protein-Ligand Complex Dataset
The 161 protein-ligand complexes uploaded here have been prepared in the force field compatible manner as described in the methodology section [1]. There is a separate PDB file of each complex for Method 1 or Method 2 in the respective format. Experimental binding free energies in kcal/mol (EBFE), Predicted binding free energies in kcal/mol (PBFE), name of the protein and the ligand charge of each complex are provided. Click on the PDB ID to download the protein-ligand complex. This downloaded file can then be used as an input for the BAPPL server for its respective Method to get the predicted binding free energy of the complex.

S. NO.
PDB ID
Protein
Ligand charge
EBFE

Method 1

PDB PBFE

Method 2

PDB PBFE
1 1a30 HIV-1 Protease -2
-5.84
 1a30 -5.78 1a30 -5.9
2 1a4k Antibody FAB -1
-6.79
 1a4k -7.21 1a4k -7.17
3 1a4w Alpha Thrombin 1
-8.13
 1a4w -10.06 1a4w -9.8
4 1a9m HIV-1 Protease 1
-9.41
 1a9m -10.33 1a9m -10.17
5 1aaq HIV-1 Protease 1
-11.45
 1aaq -11.17 1aaq -11.43
6 1ae8 Alpha Thrombin 1
-8.99
 1ae8 -8.18 1ae8 -8.18
7 1afk Ribonuclease A -5
-9.00
 1afk -11.37 1afk -11.4
8 1afl Ribonuclease A -5
-8.53
 1afl -7.74 1afl -7.86
9 1ajv HIV-1 Protease 0
-10.59
 1ajv -10.81 1ajv -10.97
10 1ajx HIV-1 Protease 0
-10.86
 1ajx -10.19 1ajx -10.26
11 1anf Maltodextrin Binding Protein 0
-7.442
 1anf -5.83 1anf -5.53
12 1apt Penicillopepsin 1
-12.82
 1apt -11.29 1apt -11.38
13 1apu Penicillopepsin 0
-10.5
 1apu -10.34 1apu -10.36
14 1apv Penicillopepsin 0
-12.35
 1apv -11.4 1apv -11.19
15 1apw Penicillopepsin 0
-10.98
 1apw -9.31 1apw -9.3
16 1b38 Protein Kinase 2 -4
-9.4
 1b38 -10.64 1b38 -9.97
17 1b39 Protein Kinase 2 -4
-8.97
 1b39 -9.26 1b39 -8.52
18 1b5g Thrombin 1
-10.911
 1b5g -10.51 1b5g -10.49
19 1b6j HIV-1 Protease 1
-10.76
 1b6j -12.05 1b6j -11.97
20 1b6k HIV-1 Protease 1
-11.88
 1b6k -12.69 1b6k -12.75
21 1b6l HIV-1 Protease 1
-11.28
 1b6l -11.02 1b6l -10.99
22 1b6m HIV-1 Protease 1
-11.41
 1b6m -11.9 1b6m -11.91
23 1ba8 Thrombin 1
-12.27
 1ba8 -10.27 1ba8 -9.9
24 1bb0 Thrombin 1
-11.4
 1bb0 -10.14 1bb0 -9.83
25 1bdr HIV-1 Protease 0
-9.07
 1bdr -10.51 1bdr -10.5
26 1bil Renin 0
-12.64
 1bil -12.86 1bil -12.88
27 1bim Renin 0
-12.12
 1bim -13.88 1bim -13.97
28 1bmm Alpha Thrombin 1
-9.75
 1bmm -10.08 1bmm -9.95
29 1bmn Alpha Thrombin 1
-11.58
 1bmn -9.06 1bmn -8.78
30 1bra Trypsin 1
-2.496
 1bra -4.83 1bra -4.62
31 1bv7 HIV-1 Protease 0
-12.64
 1bv7 -14.84 1bv7 -14.81
32 1c2t Glycinamide Ribonucleotide Transformaylase -3
-11.066
 1c2t -10.89 1c2t -10.96
33 1c5c Decarboxylase Antibody 21D8 -2
-9.49
 1c5c -7.81 1c5c -8.01
34 1c83 Protein Tyrosine Phosphatase 1B 0
-6.59
 1c83 -5.62 1c83 -5.59
35 1c84 Protein Tyrosine Phosphatase 1B -2
-6.79
 1c84 -8.97 1c84 -9
36 1c86 Tyrosine Phosphatase -2
-7.09
 1c86 -8.45 1c86 -8.63
37 1c87 Protein Tyrosine Phosphatase 1B -2
-6.59
 1c87 -8.4 1c87 -8.56
38 1c88 Protein Tyrosine Phosphatase 1B -1
-8.86
 1c88 -8.96 1c88 -9.08
39 1c8k Glycogen Phosphorylase 1
-6.79
 1c8k -7.7 1c8k -7.7
40 1cbs Cellular Retinoic Acid Binding Protein Type II -1
-9.821
 1cbs -7.49 1cbs -7.49
41 1cf8 Catalytic Antibody 19A4 -1
-8.226
 1cf8 -8.14 1cf8 -8.17
42 1com Chorismate Mutase -2
-5.443
 1com -6.38 1com -6.4
43 1cqp Antigen CD11A 0
-6.614
 1cqp -6.41 1cqp -6.39
44 1ctr Calmodulin 0
-5.845
 1ctr -5.52 1ctr -5.51
45 1d3h Dihydroorate Dehydrogenase 0
-6.008
 1d3h -7.29 1d3h -7.22
46 1d3p Alpha Thrombin 0
-10.07
 1d3p -11.11 1d3p -11.13
47 1d4l HIV-1 Protease 0
-11.92
 1d4l -12.19 1d4l -12.2
48 1d4p Alpha Thrombin 1
-8.594
 1d4p -8.76 1d4p -8.49
49 1dg5 Dihydrofolate Reductase 0
-5.532
 1dg5 -6.66 1dg5 -6.74
50 1dhf Dihydrofolate Reductase -2
-10.093
 1dhf -9.47 1dhf -9.77
51 1dmp HIV-1 Protease 0
-13.029
 1dmp -12.13 1dmp -12.1
52 1dog Glycoamylase 471 0
-5.479
 1dog -3.02 1dog -2.84
53 1dr1 Dihydrofolate Reductase 1
-7.597
 1dr1 -5.28 1dr1 -5.33
54 1drf Dihydrofolate Reductase -2
-10.148
 1drf -9.02 1drf -9.09
55 1dwb Alpha Thrombin 1
-3.983
 1dwb -4.78 1dwb -4.47
56 1dwc Alpha Thrombin 0
-10.105
 1dwc -8.55 1dwc -8.62
57 1dwd Alpha Thrombin 1
-11.138
 1dwd -9.79 1dwd -9.45
58 1dy9 Protease / Helicase NS3 (P70) -2
-10.323
 1dy9 -9.93 1dy9 -9.87
59 1eap Catalytic Antibody -2
-8.468
 1eap -8.39 1eap -8.33
60 1ela Elastase 1
-8.66
 1ela -8.64 1ela -8.79
61 1elc Elastase 1
-9.76
 1elc -9.08 1elc -9.21
62 1epo Endothiapepsin 0
-10.856
 1epo -9.74 1epo -9.63
63 1epp Endothiapepsin 1
-9.77
 1epp -9.66 1epp -9.61
64 1etr Epsilon Thrombin 0
-10.108
 1etr -9.45 1etr -9.5
65 1ets Epsilon Thrombin 1
-11.623
 1ets -9.28 1ets -8.95
66 1ett Epsilon Thrombin 1
-8.441
 1ett -8.81 1ett -8.73
67 1fax Factor XA 0
-10.074
 1fax -10.07 1fax -9.62
68 1fkg FK506 Binding Protein 0
-8.812
 1fkg -6.7 1fkg -6.72
69 1flr FAB Fragment -1
-6.347
 1flr -6.31 1flr -6.29
70 1g2k HIV-1 Protease 0
-10.81
 1g2k -11.64 1g2k -11.81
71 1gno HIV-1 Protease 1
-10.57
 1gno -9.85 1gno -9.8
72 1gpy Glycogen Phosphorylase -2
-6.409
 1gpy -6.29 1gpy -5.13
73 1hbv HIV-1 Protease 0
-8.688
 1hbv -10.29 1hbv -10.25
74 1hdt Alpha Thrombin 1
-10.66
 1hdt -10.94 1hdt -10.81
75 1hew Lysozyme 0
-8.183
 1hew -8.55 1hew -8.33
76 1hge Hemagglutinin -1
-3.093
 1hge -4.17 1hge -4.19
77 1hgg Hemagglutinin -1
-3.402
 1hgg -4.2 1hgg -4.21
78 1hgh Hemagglutinin -1
-3.89
 1hgh -4.79 1hgh -4.81
79 1hgi Hemagglutinin -1
-3.652
 1hgi -4.64 1hgi -4.62
80 1hgj Hemagglutinin 0
-2.262
 1hgj -3.57 1hgj -3.76
81 1hih HIV-1 Protease 0
-10.97
 1hih -11.76 1hih -11.7
82 1hii HIV-2 Protease 0
-9.89
 1hii -11.75 1hii -11.62
83 1hiv HIV-1 Protease 0
-12.64
 1hiv -13.03 1hiv -13.05
84 1hos HIV-1 Protease -1
-11.74
 1hos -11.98 1hos -12.01
85 1hpo HIV-1 Protease 0
-11.82
 1hpo -11.37 1hpo -11.41
86 1hps HIV-1 Protease 0
-12.66
 1hps -10.64 1hps -10.61
87 1hpv HIV-1 Protease 0
-12.584
 1hpv -10.57 1hpv -10.61
88 1hpx HIV-1 Protease 0
-12.53
 1hpx -12.97 1hpx -13
89 1hri Human Rhinovirus 1
-5.914
 1hri -7.61 1hri -7.61
90 1hrn Renin 0
-10.94
 1hrn -11.95 1hrn -11.85
91 1hsg HIV-1 Protease 0
-12.93
 1hsg -12.56 1hsg -12.61
92 1hsh HIV-1 Protease 1
-11.69
 1hsh -12.13 1hsh -12.16
93 1hte HIV-1 Protease 0
-7.69
 1hte -7.69 1hte -7.73
94 1htg HIV-1 Protease 0
-13.215
 1htg -12.52 1htg -12.33
95 1hvh HIV-1 Protease 1
-10.81
 1hvh -10.54 1hvh -10.46
96 1hvi HIV-1 Protease 0
-13.748
 1hvi -15.66 1hvi -15.56
97 1hvj HIV-1 Protease 0
-14.267
 1hvj -14.72 1hvj -14.72
98 1hvk HIV-1 Protease 0
-13.803
 1hvk -15.46 1hvk -15.35
99 1hvl HIV-1 Protease 0
-12.289
 1hvl -14.72 1hvl -14.56
100 1hvr HIV-1 Protease 0
-12.972
 1hvr -12.92 1hvr -12.99
101 1hxb HIV-1 Protease 1
-13.48
 1hxb -12.52 1hxb -12.42
102 1hxw HIV-1 Protease 0
-14.54
 1hxw -14.34 1hxw -14.32
103 1ida HIV-2 Protease 0
-11.865
 1ida -12.41 1ida -12.5
104 1lyb Cathepsin D -1
-15.575
 1lyb -12.04 1lyb -12.13
105 1mcb Immunoglobulin -1
-6.6
 1mcb -8.38 1mcb -8.44
106 1mcf Immunoglobulin -1
-7.02
 1mcf -8.57 1mcf -8.54
107 1mch Immunoglobulin -1
-7.02
 1mch -8.75 1mch -8.75
108 1mcj Immunoglobulin 0
-5.16
 1mcj -5.74 1mcj -5.76
109 1mcs Immunoglobulin -1
-6.6
 1mcs -8.14 1mcs -8.18
110 1mtw Trypsin 1
-10.076
 1mtw -8.06 1mtw -7.83
111 1nnb Neuraminidase -1
-5.458
 1nnb -7.04 1nnb -6.95
112 1nsd Neuraminidase -1
-7.23
 1nsd -7.52 1nsd -7.62
113 1ola Oligopeptide Binding Protein 1
-9.546
 1ola -10.25 1ola -10.32
114 1pgp 6-Phosphogluconate Dehydrogenase -3
-7.77
 1pgp -6.49 1pgp -6.75
115 1phh p-Hydroxybenzoate Hydroxylase -1
-3.983
 1phh -4.41 1phh -4.39
116 1ppc Trypsin 1
-8.8
 1ppc -8.38 1ppc -8.14
117 1pph Trypsin 1
-8.487
 1pph -6.62 1pph -6.51
118 1ppm Penicillopepsin -1
-7.95
 1ppm -9.53 1ppm -9.59
119 1qbr HIV-1 Protease 0
-14.42
 1qbr -14.54 1qbr -14.52
120 1qbt HIV-1 Protease 0
-14.492
 1qbt -14.36 1qbt -14.46
121 1qbu HIV-1 Protease 0
-13.968
 1qbu -11.9 1qbu -11.87
122 1rbp Retinol Binding Protein 0
-9.17
 1rbp -7.94 1rbp -7.93
123 1rgk Ribonuclease T1 -2
-5.879
 1rgk -6.88 1rgk -6.86
124 1rgl Ribonuclease T1 -2
-6.041
 1rgl -5.97 1rgl -5.97
125 1sre Streptavidin -1
-5.455
 1sre -6.27 1sre -6.55
126 1tlc Thymidylate Synthase -2
-10.98
 1tlc -9.75 1tlc -9.85
127 1tmt Alpha Thrombin 0
-8.51
 1tmt -7.9 1tmt -7.62
128 1tng Trypsin 1
-4.00
 1tng -3.91 1tng -4.06
129 1tnh Trypsin 1
-4.59
 1tnh -4.3 1tnh -4.41
130 1tni Trypsin 1
-2.32
 1tni -3.47 1tni -3.66
131 1tnj Trypsin 1
-2.67
 1tnj -3.63 1tnj -3.89
132 1tnk Trypsin 1
-2.03
 1tnk -3.63 1tnk -3.77
133 1tnl Trypsin 1
-2.56
 1tnl -4.21 1tnl -4.26
134 1tph Triosephosphate Isomerase -3
-3.098
 1tph -5.54 1tph -5.55
135 1tpp Trypsin 0
-7.95
 1tpp -6.27 1tpp -5.89
136 1ulb Purine Nucleoside Phosphorylase 0
-2.802
 1ulb -3.19 1ulb -3.18
137 1uvs Alpha Thrombin 0
-7.41
 1uvs -7.49 1uvs -7.49
138 2abh Phosphate Binding Protein -2
-8.876
 2abh -7.64 2abh -7.86
139 2acs Aldose Reductase -3
-2.75
 2acs -4.86 2acs -4.91
140 2cgr IGG 2B Fab Fragment -1
-9.928
 2cgr -10.66 2cgr -10.67
141 2cmd Malate Dehydrogenase -3
-6.24
 2cmd -7.68 2cmd -7.64
142 2ifb Intestinal Fatty Acid Binding Protein -1
-7.406
 2ifb -8.28 2ifb -8.28
143 2msb Mannose Binding Protein 0
-3.937
 2msb -2.35 2msb -2.1
144 2upj HIV-1 Protease 0
-10.14
 2upj -10.41 2upj -10.5
145 2wea Penicillopepsin -1
-8.37
 2wea -6.59 2wea -6.61
146 2web Penicillopepsin -1
-7.03
 2web -8.5 2web -8.52
147 2wec Penicillopepsin -1
-6.8
 2wec -6.53 2wec -6.55
148 2ypi Triose Phosphate Isomerase -3
-6.58
 2ypi -7.04 2ypi -7.02
149 3cla Chloramphenicol Acetyltransferase III 0
-6.037
 3cla -3.92 3cla -3.92
150 3ptb Trypsin 1
-6.46
 3ptb -5.39 3ptb -5.13
151 4dfr Dihydrofolate Reductase -1
-13.23
 4dfr -11.23 4dfr -10.32
152 4est Porcine Pancreatic Elastase 0
-9.551
 4est -7.8 4est -7.77
153 4hmg Hemagglutinin -1
-3.481
 4hmg -3.96 4hmg -4.01
154 4phv HIV-1 Protease 0
-12.479
 4phv -12 4phv -12.01
155 4ts1 Tyrosyl-T / RNA Synthetase 0
-7.64
 4ts1 -4.96 4ts1 -5.15
156 5cna Agglutinin 0
-2.73
 5cna -3.32 5cna -3.28
157 5hvp HIV-1 Protease -1
-10.516
 5hvp -12.79 5hvp -12.72
158 5tim Triose Phosphate Isomerase -2
-3.14
 5tim -3.07 5tim -3.13
159 7dfr Dihydrofolate Reductase -2
-10.091
 7dfr -10.3 7dfr -10.39
160 7gpb Glycogen Phosphorylase -2
-7.533
 7gpb -7.87 7gpb -7.47
161 8gpb Glycogen Phosphorylase -2
-4.913
 8gpb -5.97 8gpb -5.51