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 (-0.522 kcal/mol/HA) ✓ Good fit quality (FQ -4.87) ✓ Strong H-bond network (6 bonds) ✗ Very high strain energy (29.7 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-14.091

kcal/mol

-0.522

kcal/mol/HA

Fit Quality

-4.87

FQ (Leeson)

HAC

heavy atoms

368

LogP

3.85

cLogP

Strain ΔE

29.7 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 29.7 kcal/mol

Interaction summary

Collapsible panels

H-bonds 6 Hydrophobic 20 π–π 1 Clashes 11 Severe clashes 2

Final rank	57.167598560916105	Score	-14.091
Inter norm	-0.76276	Intra norm	0.240871
Top1000	no	Excluded	yes
Contacts	16	H-bonds	6
Artifact reason	excluded; geometry warning; 9 clashes; 2 protein clashes
Residues	A:ALA32;A:ASP52;A:LEU94;A:LYS57;A:MET53;A:NDP301;A:PHE56;A:PHE91;A:PRO50;A:PRO88;A:THR54;A:TYR162;A:VAL156;A:VAL30;A:VAL31;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	0.71	RMSD	-
H-bond strict	2	Strict recall	0.29
H-bond same residue+role	2	Role recall	0.40
H-bond same residue	2	Residue recall	0.40

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
2608	3.698278565307773	-0.94739	-24.9655	5	17	15	0.75	0.60	-	no	Open
2612	3.70057410392316	-0.726303	-17.5994	2	16	11	0.55	0.40	-	no	Open
1182	4.362055859919374	-0.884136	-19.6065	2	18	1	0.05	0.00	-	no	Open
2604	4.419994708340056	-0.756398	-17.5123	4	12	11	0.55	0.40	-	no	Open
2605	5.008733444313428	-1.0097	-24.4552	6	16	15	0.75	0.80	-	no	Open
2609	5.410862809071742	-0.81119	-14.6132	4	16	14	0.70	0.00	-	no	Open
2601	5.436304521940765	-0.846938	-21.9185	4	18	13	0.65	0.20	-	no	Open
1191	5.365938897605203	-0.810506	-20.692	3	18	1	0.05	0.00	-	yes	Open
1186	5.479093802955195	-0.752228	-17.993	3	19	1	0.05	0.00	-	yes	Open
1188	5.537619678184513	-0.838075	-11.4512	2	19	1	0.05	0.00	-	yes	Open
1193	5.80687590716687	-0.872121	-23.5192	2	17	1	0.05	0.00	-	yes	Open
1181	6.097609180236347	-0.97482	-18.2139	3	18	1	0.05	0.00	-	yes	Open
1184	6.359659961901646	-0.680177	-18.9206	4	19	1	0.05	0.00	-	yes	Open
2603	6.5570386699385015	-0.844485	-25.0836	4	17	16	0.80	0.40	-	yes	Open
1192	6.812379661133425	-0.82684	-19.3107	4	17	1	0.05	0.00	-	yes	Open
2614	6.962520459224539	-0.791448	-23.0718	2	19	18	0.90	0.20	-	yes	Open
2613	7.157504635431177	-0.725153	-21.9182	5	16	12	0.60	0.20	-	yes	Open
2602	7.341619388530795	-0.848996	-18.6678	4	20	17	0.85	0.40	-	yes	Open
1183	8.492270677751259	-0.760172	-19.3597	2	18	1	0.05	0.00	-	yes	Open
1189	55.23594419180738	-0.940873	-10.675	1	17	1	0.05	0.00	-	yes	Open
2610	56.06968259624646	-0.867828	-22.4346	3	14	10	0.50	0.20	-	yes	Open
2606	56.54156088939767	-0.789539	-17.657	3	17	16	0.80	0.20	-	yes	Open
1185	57.03122331557638	-0.816234	-17.0131	3	19	1	0.05	0.00	-	yes	Open
2600	57.167598560916105	-0.76276	-14.091	6	16	15	0.75	0.40	-	yes	Current
1194	57.173033596652324	-0.678613	-16.6003	5	18	1	0.05	0.00	-	yes	Open
2611	57.57073127203884	-0.694403	-16.8255	3	13	11	0.55	0.20	-	yes	Open
1190	58.96388150318519	-0.763762	-11.9454	1	17	1	0.05	0.00	-	yes	Open
1180	60.5179075520816	-0.678169	-6.22749	6	17	1	0.05	0.00	-	yes	Open
2607	60.64472946672734	-0.749019	-18.5811	5	11	8	0.40	0.20	-	yes	Open
1187	63.88677328233778	-0.660785	-6.17783	5	16	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 -14.091kcal/mol

Ligand efficiency (LE) -0.5219kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.869

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

Heavy atom count 27HA

Physicochemical properties

Molecular weight 368.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.85

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 29.71kcal/mol

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

Docked FF energy 95.95kcal/mol

Minimised FF energy 66.24kcal/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.

Z104500108