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 ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.417 kcal/mol/HA) ✓ Good fit quality (FQ -11.86) ✓ Strong H-bond network (10 bonds) ✗ High strain energy (17.6 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-28.334

kcal/mol

-1.417

kcal/mol/HA

Fit Quality

-11.86

FQ (Leeson)

HAC

heavy atoms

313

LogP

0.81

cLogP

Strain ΔE

17.6 kcal/mol

SASA buried

computing…

Interaction summary

Collapsible panels

H-bonds 10 Hydrophobic 19 π–π 2 Clashes 6 Severe clashes 0

Final rank	3.067803694016666	Score	-28.3343
Inter norm	-1.4959	Intra norm	0.0791829
Top1000	no	Excluded	no
Contacts	14	H-bonds	10
Artifact reason	geometry warning; 7 clashes; 6 protein contact clashes; high strain Δ 29.1
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
741	2.4431014686266868	-1.15426	-21.7801	8	16	1	0.05	0.00	-	no	Open
2827	2.8528809983601167	-1.28962	-25.9234	9	16	0	0.00	0.00	-	no	Open
740	2.9118932102520394	-1.1627	-22.7243	10	17	1	0.05	0.00	-	no	Open
2203	3.067803694016666	-1.4959	-28.3343	10	14	10	0.50	0.80	-	no	Current
742	3.5843619745137447	-1.12529	-21.3684	7	15	1	0.05	0.00	-	no	Open
2829	3.699553722845288	-1.11771	-20.3646	8	14	0	0.00	0.00	-	no	Open
2828	3.8785774657049177	-1.1001	-20.2857	5	16	0	0.00	0.00	-	no	Open
743	3.803476724397061	-1.12629	-21.9808	9	16	1	0.05	0.00	-	yes	Open
744	4.220272913274842	-1.04358	-20.4885	8	17	1	0.05	0.00	-	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 -28.334kcal/mol

Ligand efficiency (LE) -1.4167kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.855

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

Heavy atom count 20HA

Physicochemical properties

Molecular weight 313.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.81

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 17.57kcal/mol

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

Docked FF energy 1.67kcal/mol

Minimised FF energy -15.90kcal/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.

NMT-TY0409