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, protein contact clashes

Interaction summary

Collapsible panels

H-bonds 1 Hydrophobic 24 π–π 1 Clashes 5 Severe clashes 0 ⚠ Hydrophobic exposure 39%

⚠️Partial hydrophobic solvent exposure

39% of hydrophobic surface appears solvent-exposed (11/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 28 Buried (contacted) 17 Exposed 11 LogP 1.89 H-bonds 1

Exposed fragments: phenyl (5/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)

Final rank	5.887912759674269	Score	-19.6733
Inter norm	-0.582376	Intra norm	0.00375012
Top1000	no	Excluded	no
Contacts	18	H-bonds	1
Artifact reason	geometry warning; 7 clashes; 5 protein contact clashes; high strain Δ 65.3
Residues	A:NDP301;B:ALA32;B:ARG48;B:ASP52;B:ILE45;B:LEU94;B:MET53;B:PHE56;B:SER44;B:SER86;B:THR83;B:TRP47;B:TYR162;B:VAL156;B:VAL30;B:VAL31;B:VAL49;B:VAL87

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	14	Native recall	0.67
Jaccard	0.56	RMSD	-
H-bond strict	0	Strict recall	0.00
H-bond same residue+role	0	Role recall	0.00
H-bond same residue	0	Residue recall	0.00

Hydrogen bonds

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

π–π interactions

Native π–π recall is disabled because no explicit native π–π reference was stored.

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
943	5.155740312203035	-0.682995	-21.9922	2	17	13	0.62	0.00	-	no	Open
954	5.581895086827499	-0.627151	-21.4642	1	19	17	0.81	0.00	-	no	Open
947	5.887912759674269	-0.582376	-19.6733	1	18	14	0.67	0.00	-	no	Current
946	6.34114894282035	-0.77439	-24.7957	2	17	13	0.62	0.00	-	no	Open
950	8.455004243492803	-0.723579	-19.9954	3	19	14	0.67	0.17	-	no	Open
952	8.6497207242308	-0.61874	-18.3952	2	15	12	0.57	0.17	-	no	Open
941	54.06703272536614	-0.633146	-18.0235	1	19	16	0.76	0.00	-	yes	Open
942	54.16920974889726	-0.561114	-17.485	3	14	10	0.48	0.17	-	yes	Open
945	55.21993551730869	-0.75376	-23.3692	1	19	15	0.71	0.00	-	yes	Open
949	55.231542952680904	-0.607383	-17.9901	3	20	15	0.71	0.17	-	yes	Open
948	56.06005616487332	-0.585058	-18.5735	3	14	10	0.48	0.17	-	yes	Open
944	56.24903751535288	-0.574172	-19.2804	2	13	10	0.48	0.17	-	yes	Open
951	56.76915910678876	-0.594088	-16.7777	2	14	12	0.57	0.17	-	yes	Open
953	59.26608234783549	-0.652314	-21.017	3	19	15	0.71	0.00	-	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.

ulfkktlib_3721