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 (-0.635 kcal/mol/HA) ✓ Good fit quality (FQ -6.35) ✓ Good H-bonds (4 bonds) ✗ Very high strain energy (25.0 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-21.591

kcal/mol

-0.635

kcal/mol/HA

Fit Quality

-6.35

FQ (Leeson)

HAC

heavy atoms

469

LogP

6.09

cLogP

Strain ΔE

25.0 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: excellent

Geometry reliability: low

Reason: clashes, strain 25.0 kcal/mol

Interaction summary

Collapsible panels

H-bonds 4 Hydrophobic 24 π–π 0 Clashes 16 Severe clashes 4

Final rank	60.839392709343095	Score	-21.5914
Inter norm	-0.674689	Intra norm	0.0396482
Top1000	no	Excluded	yes
Contacts	13	H-bonds	4
Artifact reason	excluded; geometry warning; 8 clashes; 4 protein clashes
Residues	A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:SER86;A:THR83;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	11	Native recall	0.55
Jaccard	0.50	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

No π–π interactions detected for this pose.

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
126	3.76153974804275	-0.572606	-18.2781	4	15	12	0.60	0.00	-	no	Open
107	4.608392209194758	-0.697437	-31.1136	6	15	10	0.50	0.20	-	no	Open
120	4.88083390201831	-0.618287	-12.9327	2	15	13	0.65	0.20	-	no	Open
106	54.40534654030967	-0.679324	-28.0681	2	14	9	0.45	0.20	-	yes	Open
105	55.063822370169085	-0.546972	-14.6064	2	14	12	0.60	0.00	-	yes	Open
115	55.49762728870236	-0.567065	-22.8514	2	13	10	0.50	0.20	-	yes	Open
117	55.838471522949696	-0.751618	-26.2902	5	18	16	0.80	0.60	-	yes	Open
132	55.97124546209148	-0.561467	-21.0215	3	16	12	0.60	0.40	-	yes	Open
113	56.18709186698408	-0.610423	-21.6937	3	14	13	0.65	0.20	-	yes	Open
114	56.547845980960915	-0.604287	-23.2831	3	13	10	0.50	0.20	-	yes	Open
103	56.68062173921869	-0.728509	-28.1932	5	14	9	0.45	0.20	-	yes	Open
104	57.51975088730978	-0.617623	-23.8075	5	15	10	0.50	0.20	-	yes	Open
119	57.54362080166637	-0.682162	-26.9501	3	13	10	0.50	0.20	-	yes	Open
129	57.76100134550365	-0.744251	-22.6842	6	13	11	0.55	0.00	-	yes	Open
111	57.89410888377062	-0.644457	-24.1267	3	10	7	0.35	0.00	-	yes	Open
102	57.951020020487334	-0.680567	-30.1506	4	14	9	0.45	0.20	-	yes	Open
125	58.02830192337697	-0.575862	-22.5964	3	12	10	0.50	0.20	-	yes	Open
121	58.601088903767646	-0.544948	-11.2572	3	15	11	0.55	0.00	-	yes	Open
128	59.323759473926565	-0.651	-22.3808	4	15	11	0.55	0.20	-	yes	Open
109	59.4253268095336	-0.576298	-21.4506	4	14	9	0.45	0.20	-	yes	Open
133	59.6930509318543	-0.547004	-16.2501	3	13	11	0.55	0.20	-	yes	Open
122	60.01993833953518	-0.682853	-26.933	4	12	10	0.50	0.00	-	yes	Open
108	60.53571199790079	-0.59657	-23.1784	5	15	10	0.50	0.20	-	yes	Open
131	60.682020093042475	-0.662537	-21.8339	4	13	11	0.55	0.00	-	yes	Open
112	60.75115576664222	-0.650718	-23.8733	3	14	10	0.50	0.20	-	yes	Open
130	60.839392709343095	-0.674689	-21.5914	4	13	11	0.55	0.00	-	yes	Current
110	61.70531528874464	-0.512111	-20.1501	5	17	15	0.75	0.00	-	yes	Open
124	62.87509160838793	-0.526629	-20.3304	3	14	8	0.40	0.00	-	yes	Open
123	63.5317439501212	-0.672527	-25.7271	6	15	10	0.50	0.20	-	yes	Open
127	63.57403462999861	-0.608687	-19.9006	3	16	11	0.55	0.20	-	yes	Open
116	63.61897050945813	-0.583937	-21.8596	5	18	16	0.80	0.40	-	yes	Open
118	65.52778879524574	-0.683965	-26.335	6	14	10	0.50	0.20	-	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 -21.591kcal/mol

Ligand efficiency (LE) -0.6350kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.354

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

Heavy atom count 34HA

Physicochemical properties

Molecular weight 468.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 6.09

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 25.03kcal/mol

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

Docked FF energy 71.44kcal/mol

Minimised FF energy 46.41kcal/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.

OHD_Leishmania_402