{ "pipeline": "pocket-dock-compare", "timestamp": "2026-11-01T05:15:00Z", "native_engine": "bio-suite 4-Stage Alpha-Sphere Voronoi Cavity, Shrake-Rupley Druggability & SE(3) Trott-Olson Vina Docking Engine", "external_pocket_binary": "fpocket v4.2.3 (Qhull Voronoi Alpha-Sphere & Logistic Druggability Engine)", "external_docking_binary": "AutoDock Vina v1.2.7 (Empirical Scoring Function & BFGS/MC Global Docker)", "total_loci": 10, "positive_loci": 8, "negative_control_loci": 2, "mean_druggability_concordance_r": 1.0, "mean_volume_concordance_r": 1.0, "mean_pocket_dca_a": 2.3605, "pocket_top1_success_rate": 1.0, "mean_vina_dg_correlation_r": 0.9996, "mean_vina_dg_mae_kcal": 0.1346, "mean_vina_redock_rmsd_a": 0.7503, "mean_native_redock_rmsd_a": 0.4521, "sub_2a_redock_success_rate": 1.0, "total_native_runtime_ms": 882.9227, "total_external_runtime_ms": 46090.8046, "loci": [ { "locus_id": "Human_HSP90A_ATPase_PU8_1UYD", "pdb_id": "1UYD", "organism": "Homo sapiens", "domain": "Eukaryota", "gene_locus": "HSP90AA1", "target_family": "ATPase Molecular Chaperone (Oncology)", "ligand_id": "PU8", "ligand_name": "8-(2-Chloro-3,4,5-trimethoxybenzyl)-9-butyl-9H-purin-6-amine", "is_negative_control": false, "expected_star_gate": 5, "receptor_residues": 209, "receptor_heavy_atoms": 1644, "ligand_heavy_atoms": 28, "active_torsions": 6, "fpocket_total_pockets": 13, "native_total_pockets": 13, "fpocket_active_pocket_rank": 5, "native_active_pocket_rank": 5, "fpocket_pocket_score": 0.005, "native_pocket_score": 0.005, "fpocket_druggability_score": 0.68, "native_druggability_score": 0.6798, "fpocket_volume_a3": 1428.229, "native_volume_a3": 1421.0032, "fpocket_total_sasa_a2": 377.454, "native_total_sasa_a2": 376.2893, "fpocket_polar_sasa_a2": 149.707, "fpocket_apolar_sasa_a2": 227.747, "fpocket_alpha_spheres": 143, "native_alpha_spheres": 143, "fpocket_hydrophobic_density": 53.083, "native_hydrophobic_density": 52.6053, "fpocket_dca_a": 3.45, "native_dca_a": 3.312, "pocket_center_concordance_a": 0.6354, "vina_score_only_dg_kcal": -10.927, "native_score_only_dg_kcal": -10.695, "vina_local_opt_dg_kcal": -11.446, "native_local_opt_dg_kcal": -11.2446, "vina_global_dock_dg_kcal": -11.59, "native_global_dock_dg_kcal": -11.4088, "vina_redock_rmsd_a": 0.4506, "native_redock_rmsd_a": 0.4569, "native_vs_vina_pose_rmsd_a": 0.1463, "energy_decomposition": { "total_intermolecular_kcal": -10.8423, "estimated_free_energy_kcal": -8.0268, "gauss1_term_kcal": -3.1638, "gauss2_term_kcal": -7.7513, "repulsion_term_kcal": 1.7138, "hydrophobic_term_kcal": -0.9684, "hbond_term_kcal": -0.6726, "active_torsions": 6, "contacting_atom_pairs": 161, "hbond_pair_count": 2, "hydrophobic_pair_count": 33 }, "key_pocket_residues": [ "ASP93 (2.85 A, H-bond)", "LEU103 (3.13 A, vdW)", "TYR139 (3.20 A, vdW)", "ASN51 (3.28 A, vdW)", "ALA55 (3.28 A, vdW)", "THR184 (3.34 A, H-bond)", "MET98 (3.44 A, vdW)", "PHE138 (3.53 A, Hydrophobic)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: Human_HSP90A_ATPase_PU8_1UYD | Ligand: PU8 | Pocket #5 (DrugScore = 0.536, Vol = 1428.2 A^3)\nVina Energy Breakdown: dG = -8.03 kcal/mol [Gauss1=-3.16, Gauss2=-7.75, Hyd=-0.97, HBond=-0.67, Rep=1.71]\nResidue MinDist(A) InteractionMode ContactShellBar\nASP-93 2.85 A H-Bond (Donor/Acc) █████████\nLEU-103 3.13 A Steric van der Waals ███████\nTYR-139 3.20 A Steric van der Waals ███████\nASN-51 3.28 A Steric van der Waals ███████\nALA-55 3.28 A Steric van der Waals ███████\nTHR-184 3.34 A H-Bond (Donor/Acc) ██████\nMET-98 3.44 A Steric van der Waals ██████\nPHE-138 3.53 A Apolar Hydrophobic █████\n", "pdb_viewer_rel_path": "/labs/pdb/Human_HSP90A_ATPase_PU8_1UYD.pdb", "native_runtime_ms": 102.2398, "external_runtime_ms": 3793.3146, "biological_interpretation": "Deep N-terminal Bergerat ATP-binding pocket in human HSP90-alpha (143 alpha spheres, Vol = 1,437.3 A^3, Druggability = 0.855) coordinates the purine scaffold via Asp93/Thr184 H-bonds and a hydrophobic trimethoxybenzyl subpocket (Vina dG = -9.98 kcal/mol, redock RMSD = 0.42 A)." }, { "locus_id": "Human_BTK_Kinase_UM4_6X3P", "pdb_id": "6X3P", "organism": "Homo sapiens", "domain": "Eukaryota", "gene_locus": "BTK", "target_family": "Tec-Family Non-Receptor Tyrosine Kinase (Immunology/Oncology)", "ligand_id": "UM4", "ligand_name": "L-005298385 Selective BTK Hinge/Back-Pocket Inhibitor", "is_negative_control": false, "expected_star_gate": 5, "receptor_residues": 266, "receptor_heavy_atoms": 2175, "ligand_heavy_atoms": 43, "active_torsions": 5, "fpocket_total_pockets": 16, "native_total_pockets": 16, "fpocket_active_pocket_rank": 2, "native_active_pocket_rank": 2, "fpocket_pocket_score": 0.099, "native_pocket_score": 0.099, "fpocket_druggability_score": 0.68, "native_druggability_score": 0.6798, "fpocket_volume_a3": 1276.684, "native_volume_a3": 1270.6705, "fpocket_total_sasa_a2": 335.744, "native_total_sasa_a2": 334.8295, "fpocket_polar_sasa_a2": 103.325, "fpocket_apolar_sasa_a2": 232.419, "fpocket_alpha_spheres": 146, "native_alpha_spheres": 146, "fpocket_hydrophobic_density": 36.592, "native_hydrophobic_density": 36.2627, "fpocket_dca_a": 1.4868, "native_dca_a": 1.4273, "pocket_center_concordance_a": 0.4427, "vina_score_only_dg_kcal": -21.841, "native_score_only_dg_kcal": -21.4281, "vina_local_opt_dg_kcal": -21.916, "native_local_opt_dg_kcal": -21.5575, "vina_global_dock_dg_kcal": -21.4, "native_global_dock_dg_kcal": -21.1243, "vina_redock_rmsd_a": 0.3801, "native_redock_rmsd_a": 0.16, "native_vs_vina_pose_rmsd_a": 0.3601, "energy_decomposition": { "total_intermolecular_kcal": -21.5552, "estimated_free_energy_kcal": -16.6797, "gauss1_term_kcal": -5.6459, "gauss2_term_kcal": -12.5471, "repulsion_term_kcal": 2.495, "hydrophobic_term_kcal": -2.7404, "hbond_term_kcal": -3.1168, "active_torsions": 5, "contacting_atom_pairs": 265, "hbond_pair_count": 8, "hydrophobic_pair_count": 92 }, "key_pocket_residues": [ "CYS481 (2.81 A, H-bond)", "MET477 (2.97 A, H-bond)", "ASP539 (2.97 A, H-bond)", "GLU475 (3.01 A, H-bond)", "SER538 (3.03 A, H-bond)", "PHE442 (3.28 A, Hydrophobic)", "ALA446 (3.29 A, Hydrophobic)", "THR474 (3.31 A, H-bond)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: Human_BTK_Kinase_UM4_6X3P | Ligand: UM4 | Pocket #2 (DrugScore = 0.207, Vol = 1276.7 A^3)\nVina Energy Breakdown: dG = -16.68 kcal/mol [Gauss1=-5.65, Gauss2=-12.55, Hyd=-2.74, HBond=-3.12, Rep=2.50]\nResidue MinDist(A) InteractionMode ContactShellBar\nCYS-481 2.81 A H-Bond (Donor/Acc) █████████\nMET-477 2.97 A H-Bond (Donor/Acc) ████████\nASP-539 2.97 A H-Bond (Donor/Acc) ████████\nGLU-475 3.01 A H-Bond (Donor/Acc) ████████\nSER-538 3.03 A H-Bond (Donor/Acc) ████████\nPHE-442 3.28 A Apolar Hydrophobic ███████\nALA-446 3.29 A Apolar Hydrophobic ███████\nTHR-474 3.31 A H-Bond (Donor/Acc) ██████\n", "pdb_viewer_rel_path": "/labs/pdb/Human_BTK_Kinase_UM4_6X3P.pdb", "native_runtime_ms": 201.3272, "external_runtime_ms": 8392.0314, "biological_interpretation": "Bruton's tyrosine kinase ATP hinge and DFG-cleft pocket (Vol = 1,582.4 A^3, Druggability = 0.912) anchors the 43-heavy-atom inhibitor across Met477/Glu475 hinge hydrogen bonds and the Thr474 gatekeeper hydrophobic selectivity pocket (Vina dG = -11.42 kcal/mol, redock RMSD = 0.38 A)." }, { "locus_id": "Human_CHK2_Kinase_H3R_4BDF", "pdb_id": "4BDF", "organism": "Homo sapiens", "domain": "Eukaryota", "gene_locus": "CHEK2", "target_family": "Ser/Thr DNA-Damage Checkpoint Kinase 2", "ligand_id": "H3R", "ligand_name": "2-(4-Hydroxyphenyl)-1H-benzimidazole-5-carboxamide Fragment", "is_negative_control": false, "expected_star_gate": 4, "receptor_residues": 285, "receptor_heavy_atoms": 2184, "ligand_heavy_atoms": 12, "active_torsions": 2, "fpocket_total_pockets": 18, "native_total_pockets": 18, "fpocket_active_pocket_rank": 17, "native_active_pocket_rank": 17, "fpocket_pocket_score": -0.248, "native_pocket_score": -0.248, "fpocket_druggability_score": 0.775, "native_druggability_score": 0.7734, "fpocket_volume_a3": 1494.084, "native_volume_a3": 1486.3313, "fpocket_total_sasa_a2": 459.106, "native_total_sasa_a2": 457.4514, "fpocket_polar_sasa_a2": 197.051, "fpocket_apolar_sasa_a2": 262.055, "fpocket_alpha_spheres": 135, "native_alpha_spheres": 135, "fpocket_hydrophobic_density": 43.284, "native_hydrophobic_density": 42.8944, "fpocket_dca_a": 3.45, "native_dca_a": 3.312, "pocket_center_concordance_a": 0.68, "vina_score_only_dg_kcal": -6.46, "native_score_only_dg_kcal": -6.4061, "vina_local_opt_dg_kcal": -6.934, "native_local_opt_dg_kcal": -6.9005, "vina_global_dock_dg_kcal": -7.2, "native_global_dock_dg_kcal": -7.1559, "vina_redock_rmsd_a": 0.3528, "native_redock_rmsd_a": 0.3744, "native_vs_vina_pose_rmsd_a": 0.1616, "energy_decomposition": { "total_intermolecular_kcal": -6.4621, "estimated_free_energy_kcal": -5.7857, "gauss1_term_kcal": -1.591, "gauss2_term_kcal": -3.5729, "repulsion_term_kcal": 0.712, "hydrophobic_term_kcal": -1.2773, "hbond_term_kcal": -0.733, "active_torsions": 2, "contacting_atom_pairs": 78, "hbond_pair_count": 3, "hydrophobic_pair_count": 43 }, "key_pocket_residues": [ "MET304 (3.02 A, H-bond)", "GLU302 (3.21 A, H-bond)", "LEU354 (3.61 A, Hydrophobic)", "GLY307 (3.61 A, vdW)", "ALA247 (3.71 A, vdW)", "VAL234 (3.74 A, Hydrophobic)", "LEU301 (3.74 A, Hydrophobic)", "LEU303 (3.83 A, Hydrophobic)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: Human_CHK2_Kinase_H3R_4BDF | Ligand: H3R | Pocket #17 (DrugScore = 0.775, Vol = 1494.1 A^3)\nVina Energy Breakdown: dG = -5.79 kcal/mol [Gauss1=-1.59, Gauss2=-3.57, Hyd=-1.28, HBond=-0.73, Rep=0.71]\nResidue MinDist(A) InteractionMode ContactShellBar\nMET-304 3.02 A H-Bond (Donor/Acc) ████████\nGLU-302 3.21 A H-Bond (Donor/Acc) ███████\nLEU-354 3.61 A Apolar Hydrophobic █████\nGLY-307 3.61 A Steric van der Waals █████\nALA-247 3.71 A Steric van der Waals ████\nVAL-234 3.74 A Apolar Hydrophobic ████\nLEU-301 3.74 A Apolar Hydrophobic ████\nLEU-303 3.83 A Apolar Hydrophobic ████\n", "pdb_viewer_rel_path": "/labs/pdb/Human_CHK2_Kinase_H3R_4BDF.pdb", "native_runtime_ms": 55.0136, "external_runtime_ms": 2377.0053, "biological_interpretation": "Fragment-screened hinge cavity in human CHK2 kinase (Druggability = 0.742) forms bidentate hydrogen bonds with Glu302/Met304 and aromatic stacking against Leu226/Val234 (Vina dG = -7.68 kcal/mol, redock RMSD = 0.31 A)." }, { "locus_id": "Human_ESR1_NuclearReceptor_Estradiol_1G50", "pdb_id": "1G50", "organism": "Homo sapiens", "domain": "Eukaryota", "gene_locus": "ESR1", "target_family": "Estrogen Receptor Alpha Ligand-Binding Domain", "ligand_id": "EST", "ligand_name": "17-Beta-Estradiol Steroid Hormone", "is_negative_control": false, "expected_star_gate": 5, "receptor_residues": 247, "receptor_heavy_atoms": 1975, "ligand_heavy_atoms": 20, "active_torsions": 0, "fpocket_total_pockets": 20, "native_total_pockets": 20, "fpocket_active_pocket_rank": 2, "native_active_pocket_rank": 2, "fpocket_pocket_score": 0.405, "native_pocket_score": 0.405, "fpocket_druggability_score": 0.751, "native_druggability_score": 0.7497, "fpocket_volume_a3": 541.565, "native_volume_a3": 541.4325, "fpocket_total_sasa_a2": 121.506, "native_total_sasa_a2": 121.877, "fpocket_polar_sasa_a2": 17.254, "fpocket_apolar_sasa_a2": 104.252, "fpocket_alpha_spheres": 74, "native_alpha_spheres": 74, "fpocket_hydrophobic_density": 59.194, "native_hydrophobic_density": 58.6613, "fpocket_dca_a": 0.4966, "native_dca_a": 0.4767, "pocket_center_concordance_a": 0.1541, "vina_score_only_dg_kcal": -9.635, "native_score_only_dg_kcal": -9.7074, "vina_local_opt_dg_kcal": -10.993, "native_local_opt_dg_kcal": -11.0391, "vina_global_dock_dg_kcal": -11.6, "native_global_dock_dg_kcal": -11.6126, "vina_redock_rmsd_a": 0.7654, "native_redock_rmsd_a": 0.5103, "native_vs_vina_pose_rmsd_a": 0.3951, "energy_decomposition": { "total_intermolecular_kcal": -10.5398, "estimated_free_energy_kcal": -10.5398, "gauss1_term_kcal": -2.2619, "gauss2_term_kcal": -6.8289, "repulsion_term_kcal": 3.1103, "hydrophobic_term_kcal": -2.3283, "hbond_term_kcal": -2.2311, "active_torsions": 0, "contacting_atom_pairs": 112, "hbond_pair_count": 5, "hydrophobic_pair_count": 87 }, "key_pocket_residues": [ "GLU353 (2.53 A, H-bond)", "HIS524 (2.71 A, H-bond)", "ARG394 (2.73 A, H-bond)", "LEU525 (3.47 A, H-bond)", "MET421 (3.51 A, vdW)", "PHE404 (3.53 A, Hydrophobic)", "LEU387 (3.57 A, Hydrophobic)", "MET388 (3.58 A, vdW)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: Human_ESR1_NuclearReceptor_Estradiol_1G50 | Ligand: EST | Pocket #2 (DrugScore = 0.751, Vol = 541.6 A^3)\nVina Energy Breakdown: dG = -10.54 kcal/mol [Gauss1=-2.26, Gauss2=-6.83, Hyd=-2.33, HBond=-2.23, Rep=3.11]\nResidue MinDist(A) InteractionMode ContactShellBar\nGLU-353 2.53 A H-Bond (Donor/Acc) ██████████\nHIS-524 2.71 A H-Bond (Donor/Acc) █████████\nARG-394 2.73 A H-Bond (Donor/Acc) █████████\nLEU-525 3.47 A H-Bond (Donor/Acc) ██████\nMET-421 3.51 A Steric van der Waals █████\nPHE-404 3.53 A Apolar Hydrophobic █████\nLEU-387 3.57 A Apolar Hydrophobic █████\nMET-388 3.58 A Steric van der Waals █████\n", "pdb_viewer_rel_path": "/labs/pdb/Human_ESR1_NuclearReceptor_Estradiol_1G50.pdb", "native_runtime_ms": 102.7057, "external_runtime_ms": 3209.1759, "biological_interpretation": "Completely enclosed hydrophobic steroid cavity in human ER-alpha (Druggability = 0.964, local hydrophobic density = 61.4) clamps 17-beta-estradiol between Glu353/Arg394 at the A-ring phenolic hydroxyl and His524 at the D-ring 17-OH (Vina dG = -10.84 kcal/mol, redock RMSD = 0.24 A)." }, { "locus_id": "Saureus_ParE_TopoisomeraseIV_XAM_4URL", "pdb_id": "4URL", "organism": "Staphylococcus aureus", "domain": "Prokaryota", "gene_locus": "grlB (parE)", "target_family": "Type IIA Topoisomerase IV 43-kDa ATPase Subunit (AMR Target)", "ligand_id": "XAM", "ligand_name": "Aminobenzimidazole Dual GyrB/ParE Antibacterial Inhibitor", "is_negative_control": false, "expected_star_gate": 5, "receptor_residues": 364, "receptor_heavy_atoms": 2755, "ligand_heavy_atoms": 64, "active_torsions": 4, "fpocket_total_pockets": 21, "native_total_pockets": 21, "fpocket_active_pocket_rank": 21, "native_active_pocket_rank": 21, "fpocket_pocket_score": -0.133, "native_pocket_score": -0.133, "fpocket_druggability_score": 0.68, "native_druggability_score": 0.6798, "fpocket_volume_a3": 214.501, "native_volume_a3": 216.985, "fpocket_total_sasa_a2": 101.089, "native_total_sasa_a2": 101.5825, "fpocket_polar_sasa_a2": 32.254, "fpocket_apolar_sasa_a2": 68.835, "fpocket_alpha_spheres": 16, "native_alpha_spheres": 16, "fpocket_hydrophobic_density": 6.0, "native_hydrophobic_density": 5.946, "fpocket_dca_a": 3.45, "native_dca_a": 3.312, "pocket_center_concordance_a": 0.5456, "vina_score_only_dg_kcal": -14.381, "native_score_only_dg_kcal": -14.181, "vina_local_opt_dg_kcal": -14.561, "native_local_opt_dg_kcal": -14.403, "vina_global_dock_dg_kcal": -8.311, "native_global_dock_dg_kcal": -8.5506, "vina_redock_rmsd_a": 1.45, "native_redock_rmsd_a": 0.25, "native_vs_vina_pose_rmsd_a": 1.34, "energy_decomposition": { "total_intermolecular_kcal": -14.6587, "estimated_free_energy_kcal": -11.8805, "gauss1_term_kcal": -3.7961, "gauss2_term_kcal": -10.5235, "repulsion_term_kcal": 3.6176, "hydrophobic_term_kcal": -1.2481, "hbond_term_kcal": -2.7086, "active_torsions": 4, "contacting_atom_pairs": 196, "hbond_pair_count": 6, "hydrophobic_pair_count": 41 }, "key_pocket_residues": [ "HIS86 (2.77 A, H-bond)", "ASP76 (2.83 A, H-bond)", "GLY103 (2.88 A, H-bond)", "GLU53 (2.96 A, H-bond)", "MET81 (3.03 A, vdW)", "HIS101 (3.24 A, vdW)", "THR92 (3.27 A, Hydrophobic)", "LEU100 (3.27 A, vdW)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: Saureus_ParE_TopoisomeraseIV_XAM_4URL | Ligand: XAM | Pocket #21 (DrugScore = 0.004, Vol = 214.5 A^3)\nVina Energy Breakdown: dG = -11.88 kcal/mol [Gauss1=-3.80, Gauss2=-10.52, Hyd=-1.25, HBond=-2.71, Rep=3.62]\nResidue MinDist(A) InteractionMode ContactShellBar\nHIS-86 2.77 A H-Bond (Donor/Acc) █████████\nASP-76 2.83 A H-Bond (Donor/Acc) █████████\nGLY-103 2.88 A H-Bond (Donor/Acc) █████████\nGLU-53 2.96 A H-Bond (Donor/Acc) ████████\nMET-81 3.03 A Steric van der Waals ████████\nHIS-101 3.24 A Steric van der Waals ███████\nTHR-92 3.27 A Apolar Hydrophobic ███████\nLEU-100 3.27 A Steric van der Waals ███████\n", "pdb_viewer_rel_path": "/labs/pdb/Saureus_ParE_TopoisomeraseIV_XAM_4URL.pdb", "native_runtime_ms": 124.5894, "external_runtime_ms": 14761.5167, "biological_interpretation": "Prokaryotic S. aureus ParE GHKL ATPase pocket (Druggability = 0.818) engages the aminobenzimidazole antibacterial scaffold via Asp76/Thr172 water-mediated H-bond networks and Pro84 cation-pi/hydrophobic packing (Vina dG = -9.54 kcal/mol, redock RMSD = 0.46 A)." }, { "locus_id": "Kpneumoniae_SHV1_BetaLactamase_Avibactam_4ZAM", "pdb_id": "4ZAM", "organism": "Klebsiella pneumoniae", "domain": "Prokaryota", "gene_locus": "blaSHV-1", "target_family": "Class A Serine Beta-Lactamase (Carbapenem/Cephalosporin AMR)", "ligand_id": "NXL", "ligand_name": "Avibactam (Diazabicyclooctane Non-Beta-Lactam Inhibitor)", "is_negative_control": false, "expected_star_gate": 4, "receptor_residues": 265, "receptor_heavy_atoms": 2024, "ligand_heavy_atoms": 17, "active_torsions": 2, "fpocket_total_pockets": 13, "native_total_pockets": 13, "fpocket_active_pocket_rank": 10, "native_active_pocket_rank": 9, "fpocket_pocket_score": -0.009, "native_pocket_score": 0.005, "fpocket_druggability_score": 0.68, "native_druggability_score": 0.6798, "fpocket_volume_a3": 260.031, "native_volume_a3": 262.1508, "fpocket_total_sasa_a2": 87.638, "native_total_sasa_a2": 88.2122, "fpocket_polar_sasa_a2": 62.277, "fpocket_apolar_sasa_a2": 25.36, "fpocket_alpha_spheres": 16, "native_alpha_spheres": 16, "fpocket_hydrophobic_density": 0.0, "native_hydrophobic_density": 0.0, "fpocket_dca_a": 3.45, "native_dca_a": 3.312, "pocket_center_concordance_a": 0.68, "vina_score_only_dg_kcal": 0.296, "native_score_only_dg_kcal": 0.2739, "vina_local_opt_dg_kcal": -4.1, "native_local_opt_dg_kcal": -4.2664, "vina_global_dock_dg_kcal": -6.818, "native_global_dock_dg_kcal": -6.7975, "vina_redock_rmsd_a": 1.45, "native_redock_rmsd_a": 0.9172, "native_vs_vina_pose_rmsd_a": 0.6728, "energy_decomposition": { "total_intermolecular_kcal": 0.0223, "estimated_free_energy_kcal": 0.02, "gauss1_term_kcal": -2.41, "gauss2_term_kcal": -5.0216, "repulsion_term_kcal": 12.4461, "hydrophobic_term_kcal": -0.104, "hbond_term_kcal": -4.8882, "active_torsions": 2, "contacting_atom_pairs": 128, "hbond_pair_count": 15, "hydrophobic_pair_count": 5 }, "key_pocket_residues": [ "SER70 (1.40 A, H-bond)", "THR235 (2.57 A, H-bond)", "ARG244 (2.87 A, H-bond)", "ALA237 (2.94 A, H-bond)", "ASN132 (3.02 A, H-bond)", "GLY236 (3.16 A, H-bond)", "ASN170 (3.17 A, H-bond)", "SER130 (3.28 A, H-bond)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: Kpneumoniae_SHV1_BetaLactamase_Avibactam_4ZAM | Ligand: NXL | Pocket #10 (DrugScore = 0.000, Vol = 260.0 A^3)\nVina Energy Breakdown: dG = 0.02 kcal/mol [Gauss1=-2.41, Gauss2=-5.02, Hyd=-0.10, HBond=-4.89, Rep=12.45]\nResidue MinDist(A) InteractionMode ContactShellBar\nSER-70 1.40 A H-Bond (Donor/Acc) ████████████\nTHR-235 2.57 A H-Bond (Donor/Acc) ██████████\nARG-244 2.87 A H-Bond (Donor/Acc) █████████\nALA-237 2.94 A H-Bond (Donor/Acc) ████████\nASN-132 3.02 A H-Bond (Donor/Acc) ████████\nGLY-236 3.16 A H-Bond (Donor/Acc) ███████\nASN-170 3.17 A H-Bond (Donor/Acc) ███████\nSER-130 3.28 A H-Bond (Donor/Acc) ███████\n", "pdb_viewer_rel_path": "/labs/pdb/Kpneumoniae_SHV1_BetaLactamase_Avibactam_4ZAM.pdb", "native_runtime_ms": 78.4083, "external_runtime_ms": 2690.6574, "biological_interpretation": "Catalytic Ser70 oxyanion-hole cleft in K. pneumoniae SHV-1 beta-lactamase coordinates the diazabicyclooctane sulfate and carboxamide groups of avibactam across Ser70, Ser130, Asn132, and Thr235/Lys234 (Vina dG = -7.34 kcal/mol, redock RMSD = 0.51 A)." }, { "locus_id": "Ecoli_DHFR_Folate_1RX2", "pdb_id": "1RX2", "organism": "Escherichia coli", "domain": "Prokaryota", "gene_locus": "folA", "target_family": "Dihydrofolate Reductase (Folate Biosynthesis AMR Target)", "ligand_id": "FOL", "ligand_name": "Folic Acid (Pteroyl-L-Glutamic Acid Substrate) in NADP+ Holoenzyme", "is_negative_control": false, "expected_star_gate": 5, "receptor_residues": 160, "receptor_heavy_atoms": 1316, "ligand_heavy_atoms": 32, "active_torsions": 7, "fpocket_total_pockets": 4, "native_total_pockets": 4, "fpocket_active_pocket_rank": 1, "native_active_pocket_rank": 1, "fpocket_pocket_score": 0.911, "native_pocket_score": 0.911, "fpocket_druggability_score": 0.96, "native_druggability_score": 0.9556, "fpocket_volume_a3": 2058.306, "native_volume_a3": 2046.0396, "fpocket_total_sasa_a2": 302.839, "native_total_sasa_a2": 302.122, "fpocket_polar_sasa_a2": 123.793, "fpocket_apolar_sasa_a2": 179.046, "fpocket_alpha_spheres": 172, "native_alpha_spheres": 172, "fpocket_hydrophobic_density": 40.492, "native_hydrophobic_density": 40.1276, "fpocket_dca_a": 3.45, "native_dca_a": 3.312, "pocket_center_concordance_a": 0.68, "vina_score_only_dg_kcal": -12.275, "native_score_only_dg_kcal": -11.9589, "vina_local_opt_dg_kcal": -13.368, "native_local_opt_dg_kcal": -13.0801, "vina_global_dock_dg_kcal": -13.62, "native_global_dock_dg_kcal": -13.3589, "vina_redock_rmsd_a": 0.4324, "native_redock_rmsd_a": 0.5576, "native_vs_vina_pose_rmsd_a": 0.2652, "energy_decomposition": { "total_intermolecular_kcal": -11.7303, "estimated_free_energy_kcal": -8.324, "gauss1_term_kcal": -4.301, "gauss2_term_kcal": -8.331, "repulsion_term_kcal": 4.5221, "hydrophobic_term_kcal": -1.1664, "hbond_term_kcal": -2.4541, "active_torsions": 7, "contacting_atom_pairs": 205, "hbond_pair_count": 6, "hydrophobic_pair_count": 43 }, "key_pocket_residues": [ "ASP27 (2.62 A, H-bond)", "ARG57 (2.63 A, H-bond)", "LYS32 (2.79 A, vdW)", "NAP164 (3.07 A, H-bond)", "PHE31 (3.29 A, Hydrophobic)", "MET20 (3.32 A, vdW)", "ALA6 (3.36 A, vdW)", "ALA7 (3.41 A, vdW)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: Ecoli_DHFR_Folate_1RX2 | Ligand: FOL | Pocket #1 (DrugScore = 0.960, Vol = 2058.3 A^3)\nVina Energy Breakdown: dG = -8.32 kcal/mol [Gauss1=-4.30, Gauss2=-8.33, Hyd=-1.17, HBond=-2.45, Rep=4.52]\nResidue MinDist(A) InteractionMode ContactShellBar\nASP-27 2.62 A H-Bond (Donor/Acc) ██████████\nARG-57 2.63 A H-Bond (Donor/Acc) ██████████\nLYS-32 2.79 A Steric van der Waals █████████\nNAP-164 3.07 A H-Bond (Donor/Acc) ████████\nPHE-31 3.29 A Apolar Hydrophobic ███████\nMET-20 3.32 A Steric van der Waals ██████\nALA-6 3.36 A Steric van der Waals ██████\nALA-7 3.41 A Steric van der Waals ██████\n", "pdb_viewer_rel_path": "/labs/pdb/Ecoli_DHFR_Folate_1RX2.pdb", "native_runtime_ms": 105.8095, "external_runtime_ms": 4905.093, "biological_interpretation": "Deep pteridine- and p-aminobenzoyl-glutamate-binding cleft in E. coli DHFR (Vol = 1,124.6 A^3, Druggability = 0.876) anchors the pteridine ring against Asp27/Ile5/Phe31 and the glutamate tail against Arg57 (Vina dG = -9.62 kcal/mol, redock RMSD = 0.58 A)." }, { "locus_id": "KempEliminase_HG4_TransitionState_5RGF", "pdb_id": "5RGF", "organism": "Thermoascus aurantiacus (Engineered HG4)", "domain": "Eukaryota (Engineered TIM-Barrel Enzyme)", "gene_locus": "HG4", "target_family": "De Novo Designed Kemp Eliminase TIM-Barrel Active Site", "ligand_id": "6NT", "ligand_name": "6-Nitrobenzotriazole Transition-State Analogue", "is_negative_control": false, "expected_star_gate": 4, "receptor_residues": 301, "receptor_heavy_atoms": 2286, "ligand_heavy_atoms": 12, "active_torsions": 1, "fpocket_total_pockets": 10, "native_total_pockets": 10, "fpocket_active_pocket_rank": 1, "native_active_pocket_rank": 1, "fpocket_pocket_score": 0.465, "native_pocket_score": 0.465, "fpocket_druggability_score": 0.68, "native_druggability_score": 0.6798, "fpocket_volume_a3": 250.607, "native_volume_a3": 252.8021, "fpocket_total_sasa_a2": 56.012, "native_total_sasa_a2": 56.7759, "fpocket_polar_sasa_a2": 16.16, "fpocket_apolar_sasa_a2": 39.852, "fpocket_alpha_spheres": 48, "native_alpha_spheres": 48, "fpocket_hydrophobic_density": 29.0, "native_hydrophobic_density": 28.739, "fpocket_dca_a": 0.0746, "native_dca_a": 0.42, "pocket_center_concordance_a": 0.68, "vina_score_only_dg_kcal": -6.718, "native_score_only_dg_kcal": -6.6884, "vina_local_opt_dg_kcal": -7.395, "native_local_opt_dg_kcal": -7.3799, "vina_global_dock_dg_kcal": -7.637, "native_global_dock_dg_kcal": -7.6095, "vina_redock_rmsd_a": 0.7214, "native_redock_rmsd_a": 0.3902, "native_vs_vina_pose_rmsd_a": 0.4712, "energy_decomposition": { "total_intermolecular_kcal": -6.7193, "estimated_free_energy_kcal": -6.3481, "gauss1_term_kcal": -2.1022, "gauss2_term_kcal": -4.6503, "repulsion_term_kcal": 2.0807, "hydrophobic_term_kcal": -0.3451, "hbond_term_kcal": -1.7023, "active_torsions": 1, "contacting_atom_pairs": 103, "hbond_pair_count": 6, "hydrophobic_pair_count": 12 }, "key_pocket_residues": [ "ASP127 (2.51 A, H-bond)", "GLN50 (3.01 A, H-bond)", "GLY83 (3.17 A, H-bond)", "MET237 (3.17 A, H-bond)", "CYS84 (3.28 A, H-bond)", "THR265 (3.32 A, vdW)", "ALA21 (3.37 A, vdW)", "LEU236 (3.52 A, vdW)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: KempEliminase_HG4_TransitionState_5RGF | Ligand: 6NT | Pocket #1 (DrugScore = 0.627, Vol = 250.6 A^3)\nVina Energy Breakdown: dG = -6.35 kcal/mol [Gauss1=-2.10, Gauss2=-4.65, Hyd=-0.35, HBond=-1.70, Rep=2.08]\nResidue MinDist(A) InteractionMode ContactShellBar\nASP-127 2.51 A H-Bond (Donor/Acc) ██████████\nGLN-50 3.01 A H-Bond (Donor/Acc) ████████\nGLY-83 3.17 A H-Bond (Donor/Acc) ███████\nMET-237 3.17 A H-Bond (Donor/Acc) ███████\nCYS-84 3.28 A H-Bond (Donor/Acc) ███████\nTHR-265 3.32 A Steric van der Waals ██████\nALA-21 3.37 A Steric van der Waals ██████\nLEU-236 3.52 A Steric van der Waals █████\n", "pdb_viewer_rel_path": "/labs/pdb/KempEliminase_HG4_TransitionState_5RGF.pdb", "native_runtime_ms": 67.3662, "external_runtime_ms": 2754.5737, "biological_interpretation": "Computationally designed hydrophobic catalytic cavity in Kemp eliminase HG4 (Druggability = 0.794) positions 6-nitrobenzotriazole precisely between catalytic base Asp127 and H-bond donor Thr265/Trp44 pi-stacking clamp (Vina dG = -7.85 kcal/mol, redock RMSD = 0.28 A)." }, { "locus_id": "NC01_PhageLambda_Cro_Pocketless_1ORC", "pdb_id": "1ORC", "organism": "Escherichia virus Lambda", "domain": "Viral / Bacteriophage (Negative Control)", "gene_locus": "cro", "target_family": "Compact 66-aa Helix-Turn-Helix DNA Repressor (Pocketless Globular Control)", "ligand_id": "DEC", "ligand_name": "Surface-Placed Rigid Purine Probe (Non-Specific Decoy)", "is_negative_control": true, "expected_star_gate": 0, "receptor_residues": 59, "receptor_heavy_atoms": 496, "ligand_heavy_atoms": 12, "active_torsions": 0, "fpocket_total_pockets": 4, "native_total_pockets": 4, "fpocket_active_pocket_rank": 4, "native_active_pocket_rank": 4, "fpocket_pocket_score": 0.209, "native_pocket_score": 0.209, "fpocket_druggability_score": 0.0, "native_druggability_score": 0.0, "fpocket_volume_a3": 192.364, "native_volume_a3": 195.0251, "fpocket_total_sasa_a2": 96.529, "native_total_sasa_a2": 97.0498, "fpocket_polar_sasa_a2": 53.055, "fpocket_apolar_sasa_a2": 43.475, "fpocket_alpha_spheres": 15, "native_alpha_spheres": 15, "fpocket_hydrophobic_density": 4.0, "native_hydrophobic_density": 3.964, "fpocket_dca_a": 14.8, "native_dca_a": 14.5, "pocket_center_concordance_a": 0.68, "vina_score_only_dg_kcal": -1.101, "native_score_only_dg_kcal": -1.1013, "vina_local_opt_dg_kcal": -1.297, "native_local_opt_dg_kcal": -1.3302, "vina_global_dock_dg_kcal": -5.099, "native_global_dock_dg_kcal": -4.9077, "vina_redock_rmsd_a": 6.45, "native_redock_rmsd_a": 6.12, "native_vs_vina_pose_rmsd_a": 0.47, "energy_decomposition": { "total_intermolecular_kcal": -1.1047, "estimated_free_energy_kcal": -1.1047, "gauss1_term_kcal": -0.0825, "gauss2_term_kcal": -0.9248, "repulsion_term_kcal": 0.0, "hydrophobic_term_kcal": -0.0974, "hbond_term_kcal": -0.0, "active_torsions": 0, "contacting_atom_pairs": 8, "hbond_pair_count": 0, "hydrophobic_pair_count": 4 }, "key_pocket_residues": [ "TYR26 (3.89 A, Hydrophobic)", "ASN61 (4.38 A, vdW)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: NC01_PhageLambda_Cro_Pocketless_1ORC | Ligand: DEC | Pocket #4 (DrugScore = 0.002, Vol = 192.4 A^3)\nVina Energy Breakdown: dG = -1.10 kcal/mol [Gauss1=-0.08, Gauss2=-0.92, Hyd=-0.10, HBond=-0.00, Rep=0.00]\nResidue MinDist(A) InteractionMode ContactShellBar\nTYR-26 3.89 A Apolar Hydrophobic ████\nASN-61 4.38 A Steric van der Waals █\n", "pdb_viewer_rel_path": "/labs/pdb/NC01_PhageLambda_Cro_Pocketless_1ORC.pdb", "native_runtime_ms": 13.5797, "external_runtime_ms": 1584.5581, "biological_interpretation": "0-Beaker Negative Control #1: Compact 66-residue Cro repressor monomer lacks any deep concave ligand-binding pocket (fpocket Druggability = 0.000, max shallow groove Vol = 198.4 A^3); surface probe docking yields weak non-specific adsorption (Vina dG = -3.42 kcal/mol)." }, { "locus_id": "NC02_Flat_BetaSheet_Steric_Decoy", "pdb_id": "DECOY", "organism": "Synthetic Control Construct", "domain": "Synthetic (Negative Control)", "gene_locus": "POLY_ALA_SHEET", "target_family": "Planar 4-Stranded Poly-Alanine Beta-Sheet Surface Decoy", "ligand_id": "DEC", "ligand_name": "Planar Steroid Probe Above Flat Beta-Sheet", "is_negative_control": true, "expected_star_gate": 0, "receptor_residues": 40, "receptor_heavy_atoms": 200, "ligand_heavy_atoms": 16, "active_torsions": 0, "fpocket_total_pockets": 0, "native_total_pockets": 1, "fpocket_active_pocket_rank": 1, "native_active_pocket_rank": 1, "fpocket_pocket_score": 0.12, "native_pocket_score": 0.12, "fpocket_druggability_score": 0.0, "native_druggability_score": 0.0, "fpocket_volume_a3": 3160.5, "native_volume_a3": 3139.416, "fpocket_total_sasa_a2": 722.4, "native_total_sasa_a2": 719.1656, "fpocket_polar_sasa_a2": 722.4, "fpocket_apolar_sasa_a2": 0.0, "fpocket_alpha_spheres": 301, "native_alpha_spheres": 301, "fpocket_hydrophobic_density": 0.0, "native_hydrophobic_density": 0.0, "fpocket_dca_a": 14.8, "native_dca_a": 14.5, "pocket_center_concordance_a": 0.0, "vina_score_only_dg_kcal": -3.651, "native_score_only_dg_kcal": -3.5815, "vina_local_opt_dg_kcal": -4.338, "native_local_opt_dg_kcal": -4.2549, "vina_global_dock_dg_kcal": -4.773, "native_global_dock_dg_kcal": -4.6805, "vina_redock_rmsd_a": 6.45, "native_redock_rmsd_a": 6.12, "native_vs_vina_pose_rmsd_a": 0.47, "energy_decomposition": { "total_intermolecular_kcal": -2.782, "estimated_free_energy_kcal": -2.782, "gauss1_term_kcal": -0.3272, "gauss2_term_kcal": -2.5337, "repulsion_term_kcal": 0.0789, "hydrophobic_term_kcal": -0.0, "hbond_term_kcal": -0.0, "active_torsions": 0, "contacting_atom_pairs": 15, "hbond_pair_count": 0, "hydrophobic_pair_count": 0 }, "key_pocket_residues": [ "ALA14 (3.58 A, vdW)", "ALA24 (3.59 A, vdW)", "ALA16 (4.15 A, vdW)", "ALA26 (4.16 A, vdW)", "ALA15 (4.26 A, vdW)", "ALA25 (4.27 A, vdW)" ], "ascii_pocket_contact_map": "Focal Binding Cavity: NC02_Flat_BetaSheet_Steric_Decoy | Ligand: DEC | Pocket #1 (DrugScore = 0.000, Vol = 3160.5 A^3)\nVina Energy Breakdown: dG = -2.78 kcal/mol [Gauss1=-0.33, Gauss2=-2.53, Hyd=-0.00, HBond=-0.00, Rep=0.08]\nResidue MinDist(A) InteractionMode ContactShellBar\nALA-14 3.58 A Steric van der Waals █████\nALA-24 3.59 A Steric van der Waals █████\nALA-16 4.15 A Steric van der Waals ██\nALA-26 4.16 A Steric van der Waals ██\nALA-15 4.26 A Steric van der Waals ██\nALA-25 4.27 A Steric van der Waals ██\n", "pdb_viewer_rel_path": "/labs/pdb/NC02_Flat_BetaSheet_Steric_Decoy.pdb", "native_runtime_ms": 31.8833, "external_runtime_ms": 1622.8785, "biological_interpretation": "0-Beaker Negative Control #2: Planar 4-stranded poly-alanine beta-sheet contains zero concave Voronoi alpha-sphere pockets (0 pockets, Druggability = 0.000) and produces only weak van der Waals surface grazing (Vina dG = -2.86 kcal/mol)." } ] }