Docking pose detail

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

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.526 kcal/mol/HA) ✓ Good fit quality (FQ -5.22) ✗ High strain energy (14.4 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-17.361

kcal/mol

-0.526

kcal/mol/HA

Fit Quality

-5.22

FQ (Leeson)

HAC

heavy atoms

434

LogP

4.80

cLogP

Strain ΔE

14.4 kcal/mol

SASA buried

computing…

Interaction summary

Collapsible panels

H-bonds 0 Hydrophobic 24 π–π 2 Clashes 3 Severe clashes 0

Final rank	3.0967688271430647	Score	-17.3608
Inter norm	-0.578839	Intra norm	0.0527546
Top1000	no	Excluded	no
Contacts	15	H-bonds	0
Artifact reason	geometry warning; 12 clashes; 3 protein contact clashes; moderate strain Δ 15.8
Residues	A:NDP301;B:ALA32;B:ARG97;B:ASP52;B:LEU94;B:LYS95;B:MET53;B:PHE56;B:PHE91;B:PRO88;B:TYR162;B:VAL156;B:VAL30;B:VAL31;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	0.64	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

No hydrogen bonds detected for this pose.

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
2458	3.0967688271430647	-0.578839	-17.3608	0	15	14	0.67	0.00	-	no	Current
2459	4.473191079411137	-0.84762	-23.9977	4	17	14	0.67	0.17	-	no	Open
2461	4.898745234910512	-0.845516	-26.4438	5	16	13	0.62	0.17	-	no	Open
2460	5.960396340711199	-0.539191	-15.9802	0	15	13	0.62	0.00	-	no	Open
2462	8.223360214093578	-0.623479	-22.9327	4	12	11	0.52	0.17	-	yes	Open
2463	8.756840373709856	-0.869106	-21.8212	6	17	12	0.57	0.17	-	yes	Open

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -17.361kcal/mol

Ligand efficiency (LE) -0.5261kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.220

LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe

Heavy atom count 33HA

Physicochemical properties

Molecular weight 434.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.80

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 14.36kcal/mol

< 5 good · 5–10 marginal · > 10 problematic

Docked FF energy 82.22kcal/mol

Minimised FF energy 67.86kcal/mol

SASA & burial (FreeSASA)

not yet run

SASA has not been computed yet for this pose. It will be calculated automatically the next time this pose is loaded if a receptor PDB path is stored.

Z57388199