Docking pose detail

Molecular metrics status: queued

Pose metrics recompute is queued in the background.

Metrics cached · SASA missing

py3Dmol interaction viewer

Left: interactive complex viewer. Right: clickable PLIP-like interaction summary. Clicking an interaction thickens and highlights it in the 3D view.

Strict H-bonds Permissive H-bonds

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: weak

Geometry reliability: low

Reason: geometry warning, clashes

Interaction summary

Collapsible panels

H-bonds 5 Hydrophobic 24 π–π 0 Clashes 12 Severe clashes 1 ⚠ Hydrophobic exposure 43%

⚠️Partial hydrophobic solvent exposure

44% of hydrophobic surface appears solvent-exposed (17/39 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 39 Buried (contacted) 22 Exposed 17 LogP 2.41 H-bonds 5

Exposed fragments: cyclohexyl (6/6 atoms exposed)cyclohexyl (6/6 atoms exposed)cyclohexyl (4/6 atoms exposed)aliphatic chain/group (5 atoms exposed)

Final rank	9.46553711983882	Score	-15.8062
Inter norm	-0.414234	Intra norm	0.121526
Top1000	no	Excluded	yes
Contacts	21	H-bonds	5
Artifact reason	excluded; geometry warning; 8 clashes; 1 protein clash; high strain Δ 62.7
Residues	A:NDP301;B:ALA32;B:ARG48;B:ARG97;B:ASP52;B:GLY96;B:ILE45;B:LYS57;B:LYS95;B:MET53;B:PHE56;B:PHE91;B:PRO50;B:PRO69;B:THR61;B:TRP47;B:TYR162;B:VAL156;B:VAL30;B:VAL31;B:VAL49

Protein summary

511 residues

Protein target	T09	Atoms	8170
Residues	511	Chains	2
Residue summary	LEU:1064; ARG:840; LYS:572; GLU:570; VAL:528; PHE:460; ILE:456; ALA:440; PRO:420; THR:406; TYR:357; ASP:312; GLN:289; ASN:238; SER:231; GLY:224

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	3CL9	Contacts	21
Pose	Open native pose	H-bonds	9
IFP residues	A:NDP301; B:ALA32; B:ARG97; B:ASP52; B:GLY157; B:ILE45; B:LEU94; B:LYS57; B:MET53; B:PHE55; B:PHE56; B:PHE91; B:PRO88; B:SER86; B:THR180; B:THR83; B:TYR162; B:VAL156; B:VAL30; B:VAL31; B:VAL87
Current overlap	13	Native recall	0.62
Jaccard	0.45	RMSD	-
H-bond strict	3	Strict recall	0.43
H-bond same residue+role	3	Role recall	0.50
H-bond same residue	3	Residue recall	0.50

Hydrogen bonds

Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

π–π interactions

No π–π interactions detected for this pose.

Hydrophobic contacts

Clashes

All stored poses for this docking hit

Pose	Final rank	Inter norm	Score	HB	Contacts	Native overlap	Native recall	HB role recall	RMSD	Excluded
973	7.2075579022657745	-0.386245	-18.5427	5	17	13	0.62	0.33	-	no	Open
978	8.291247358356513	-0.324707	-13.6078	6	19	12	0.57	0.33	-	yes	Open
979	9.46553711983882	-0.414234	-15.8062	5	21	13	0.62	0.50	-	yes	Current
974	57.979206133404986	-0.322155	-9.23307	8	19	12	0.57	0.33	-	yes	Open
972	58.983504081070535	-0.254423	-4.61141	8	16	11	0.52	0.33	-	yes	Open
977	60.44583651228716	-0.479431	-15.781	9	22	15	0.71	0.33	-	yes	Open
976	60.80063555141852	-0.293381	-5.12928	4	16	9	0.43	0.17	-	yes	Open
975	60.92412174325307	-0.306904	-6.72299	4	20	14	0.67	0.17	-	yes	Open

Molecular metrics

FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

⚠ Not yet computed

Molecular metrics have not been computed for this pose yet. This page now reads only cached values; use a background recompute when you want fresh metrics without slowing the UI.

TC265