Docking pose detail

Molecular metrics status: done

Cached molecular metrics are available for this pose.

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

Molecular report

Full metrics ↗

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

✓ Excellent LE (-1.396 kcal/mol/HA) ✓ Good fit quality (FQ -11.68) ✓ Strong H-bond network (11 bonds) ✗ Very high strain energy (26.2 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-27.915

kcal/mol

-1.396

kcal/mol/HA

Fit Quality

-11.68

FQ (Leeson)

HAC

heavy atoms

297

LogP

-0.56

cLogP

Strain ΔE

26.2 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: excellent

Geometry reliability: low

Reason: geometry warning, clashes, strain 26.2 kcal/mol

Interaction summary

Collapsible panels

H-bonds 11 Hydrophobic 19 π–π 2 Clashes 9 Severe clashes 2

Final rank	6.482403506535664	Score	-27.9146
Inter norm	-1.40534	Intra norm	0.00961359
Top1000	no	Excluded	yes
Contacts	14	H-bonds	11
Artifact reason	excluded; geometry warning; 7 clashes; 2 protein clashes; high strain Δ 27.6
Residues	A:ALA32;A:ARG48;A:ASP52;A:GLY157;A:ILE45;A:MET53;A:NDP301;A:PHE56;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49

Protein summary

225 residues

Protein target	T03	Atoms	3428
Residues	225	Chains	2
Residue summary	LEU:380; ARG:360; VAL:272; LYS:264; ALA:240; GLU:240; PRO:224; PHE:180; THR:154; ILE:152; SER:132; TYR:126; GLN:119; ASN:98; GLY:84; NDP:74

Native ligand reference

★ reference

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

Name	3CL9	Contacts	20
Pose	Open native pose	H-bonds	9
IFP residues	A:ALA32; A:ARG97; A:ASP52; A:ILE45; A:LEU94; A:LYS57; A:MET53; A:NDP301; A:PHE56; A:PHE91; A:PRO88; A:SER86; A:THR180; A:THR54; A:THR83; A:TYR162; A:VAL156; A:VAL30; A:VAL31; A:VAL87
Current overlap	10	Native recall	0.50
Jaccard	0.42	RMSD	-
H-bond strict	4	Strict recall	0.57
H-bond same residue+role	4	Role recall	0.80
H-bond same residue	4	Residue recall	0.80

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
2852	3.8875326287475467	-1.25601	-23.6443	10	16	0	0.00	0.00	-	no	Open
2219	4.206658040262138	-1.35801	-25.8999	12	14	10	0.50	0.80	-	no	Open
2220	6.482403506535664	-1.40534	-27.9146	11	14	10	0.50	0.80	-	yes	Current

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -27.915kcal/mol

Ligand efficiency (LE) -1.3957kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.680

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

Heavy atom count 20HA

Physicochemical properties

Molecular weight 297.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) -0.56

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 26.16kcal/mol

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

Docked FF energy -3.00kcal/mol

Minimised FF energy -29.15kcal/mol

SASA & burial (FreeSASA)

not yet run

SASA has not been computed yet for this pose. Queue a background recompute to populate FreeSASA burial metrics without blocking the page.

NMT-TY0581