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 (-0.629 kcal/mol/HA) ✓ Good fit quality (FQ -6.53) ✗ Very high strain energy (39.1 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-24.549

kcal/mol

-0.629

kcal/mol/HA

Fit Quality

-6.53

FQ (Leeson)

HAC

heavy atoms

531

LogP

2.06

cLogP

Strain ΔE

39.1 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 39.1 kcal/mol

Interaction summary

Collapsible panels

H-bonds 1 Hydrophobic 24 π–π 2 Clashes 9 Severe clashes 1

Final rank	56.99791562961044	Score	-24.5493
Inter norm	-0.602026	Intra norm	-0.0274423
Top1000	no	Excluded	yes
Contacts	19	H-bonds	1
Artifact reason	excluded; geometry warning; 16 clashes; 1 protein clash
Residues	A:ARG48;A:ARG97;A:ASP52;A:ILE45;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO88;A:SER44;A:TRP47;A:TYR162;A:VAL156;A:VAL30;A:VAL31;A:VAL49;A:VAL87

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	15	Native recall	0.75
Jaccard	0.62	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
1464	5.509428730143796	-0.520867	-18.1928	1	13	11	0.55	0.00	-	no	Open
1458	5.680785857086903	-0.645089	-22.2439	1	22	19	0.95	0.00	-	no	Open
1453	5.824604941715309	-0.611265	-25.1778	1	18	14	0.70	0.00	-	no	Open
1443	6.192221961796047	-0.544979	-19.814	0	18	14	0.70	0.00	-	no	Open
1450	6.542215858383177	-0.594891	-21.356	1	14	13	0.65	0.00	-	no	Open
1436	6.585521153572293	-0.601086	-23.7052	1	16	13	0.65	0.00	-	no	Open
1451	6.745848121216568	-0.620787	-23.6819	1	18	14	0.70	0.20	-	no	Open
1457	6.750049931059524	-0.584669	-19.7929	1	18	13	0.65	0.20	-	no	Open
1442	6.915275108844973	-0.5894	-21.9221	0	23	19	0.95	0.00	-	no	Open
1445	7.467922329302385	-0.611287	-28.3225	1	19	15	0.75	0.00	-	no	Open
1440	7.925582739183767	-0.582872	-18.6448	2	17	16	0.80	0.20	-	no	Open
1434	7.973215159568482	-0.670617	-26.0583	1	17	15	0.75	0.00	-	no	Open
1462	54.911815638581345	-0.631992	-23.0558	2	20	15	0.75	0.20	-	no	Open
1447	54.92202282109854	-0.656758	-23.4547	1	16	10	0.50	0.00	-	no	Open
1446	55.671480662259455	-0.660942	-25.8678	1	20	16	0.80	0.00	-	no	Open
1454	55.71965575447093	-0.699568	-22.4107	2	21	17	0.85	0.00	-	no	Open
1439	55.79529845962102	-0.608856	-22.5847	1	14	11	0.55	0.00	-	no	Open
1437	56.184201001024284	-0.677468	-25.6051	1	17	14	0.70	0.00	-	no	Open
1444	56.37668543205625	-0.634386	-24.2291	2	19	16	0.80	0.00	-	no	Open
1435	56.37787864162716	-0.565775	-22.4017	0	19	14	0.70	0.00	-	no	Open
1455	56.43667434023049	-0.660754	-24.7567	2	14	11	0.55	0.00	-	no	Open
1459	56.94476587995384	-0.652046	-20.2903	0	20	16	0.80	0.00	-	no	Open
1448	56.118991582453795	-0.64767	-19.6065	1	18	17	0.85	0.00	-	yes	Open
1438	56.591203625332795	-0.609921	-24.5171	0	22	18	0.90	0.00	-	yes	Open
1452	56.65348080484486	-0.644473	-23.6805	1	19	16	0.80	0.00	-	yes	Open
1461	56.99791562961044	-0.602026	-24.5493	1	19	15	0.75	0.00	-	yes	Current
1449	57.169229237197	-0.534231	-20.9104	1	12	10	0.50	0.20	-	yes	Open
1433	57.53727433053105	-0.579637	-20.6982	1	17	16	0.80	0.20	-	yes	Open
1463	58.24847081336015	-0.595229	-21.1435	1	18	17	0.85	0.20	-	yes	Open
1460	58.57599012331262	-0.594365	-22.5919	1	18	16	0.80	0.00	-	yes	Open
1441	59.22001908332825	-0.600628	-23.3048	1	14	11	0.55	0.20	-	yes	Open
1456	60.634029765538855	-0.582856	-14.7654	2	14	11	0.55	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 -24.549kcal/mol

Ligand efficiency (LE) -0.6295kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.533

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

Heavy atom count 39HA

Physicochemical properties

Molecular weight 530.8Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.06

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 39.07kcal/mol

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

Docked FF energy 209.70kcal/mol

Minimised FF energy 170.63kcal/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.

OSA_Lib_223