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 ↗

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

✓ Excellent LE (-0.652 kcal/mol/HA) ✓ Good fit quality (FQ -6.53) ✓ Strong H-bond network (6 bonds) ✗ Very high strain energy (20.2 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-22.174

kcal/mol

-0.652

kcal/mol/HA

Fit Quality

-6.53

FQ (Leeson)

HAC

heavy atoms

469

LogP

6.09

cLogP

Strain ΔE

20.2 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: mixed

Ligand efficiency: excellent

Geometry reliability: low

Reason: clashes, strain 20.2 kcal/mol

Interaction summary

Collapsible panels

H-bonds 6 Hydrophobic 24 π–π 0 Clashes 18 Severe clashes 5

Final rank	62.57019389964971	Score	-22.1742
Inter norm	-0.643455	Intra norm	-0.00872857
Top1000	no	Excluded	yes
Contacts	14	H-bonds	6
Artifact reason	excluded; geometry warning; 9 clashes; 5 protein clashes
Residues	A:ARG97;A:ILE45;A:LEU94;A:LYS57;A:LYS95;A:MET53;A:PHE56;A:PHE91;A:PRO88;A:PRO93;A:SER44;A:SER86;A:TRP47;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	10	Native recall	0.50
Jaccard	0.42	RMSD	-
H-bond strict	2	Strict recall	0.29
H-bond same residue+role	1	Role recall	0.20
H-bond same residue	1	Residue recall	0.20

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
149	4.047887373005908	-0.516486	-11.8157	3	17	14	0.70	0.20	-	no	Open
139	4.6906090570936625	-0.536831	-20.3994	1	13	12	0.60	0.00	-	no	Open
138	4.905994859984899	-0.670494	-25.3015	3	14	13	0.65	0.00	-	no	Open
146	55.934610089911295	-0.692774	-28.1437	2	15	12	0.60	0.40	-	yes	Open
147	56.34771883473068	-0.662448	-25.4322	6	14	10	0.50	0.20	-	yes	Open
162	56.62391442875628	-0.717188	-23.2962	2	15	12	0.60	0.40	-	yes	Open
165	56.83816213032371	-0.423343	-13.6193	1	13	10	0.50	0.20	-	yes	Open
164	56.91895318372833	-0.478031	-16.6032	4	14	10	0.50	0.00	-	yes	Open
154	57.49057397971445	-0.529726	-15.5765	1	12	11	0.55	0.20	-	yes	Open
156	58.08227678003993	-0.603221	-18.1906	3	15	12	0.60	0.00	-	yes	Open
153	58.1636401838264	-0.663917	-19.2432	3	14	10	0.50	0.20	-	yes	Open
136	58.16980378343325	-0.541617	-17.9995	2	13	10	0.50	0.20	-	yes	Open
148	58.49369130164978	-0.668917	-16.4172	5	15	11	0.55	0.00	-	yes	Open
143	58.660006986060054	-0.570562	-16.5023	3	10	7	0.35	0.00	-	yes	Open
163	59.0878907084202	-0.664975	-20.652	2	16	12	0.60	0.40	-	yes	Open
142	59.094678165216415	-0.565546	-17.9421	5	15	13	0.65	0.40	-	yes	Open
152	59.3801101008321	-0.435136	-11.2897	1	13	12	0.60	0.20	-	yes	Open
157	59.52489744825776	-0.641126	-19.7267	4	15	12	0.60	0.20	-	yes	Open
134	59.52538836541424	-0.60988	-18.0373	2	15	10	0.50	0.20	-	yes	Open
144	59.54156759009728	-0.714736	-24.7405	2	18	16	0.80	0.40	-	yes	Open
145	59.648307015439585	-0.850289	-29.6049	6	18	16	0.80	0.60	-	yes	Open
161	59.9493871750495	-0.599115	-22.7478	3	11	7	0.35	0.00	-	yes	Open
158	60.096423249525046	-0.669938	-22.0738	4	15	12	0.60	0.00	-	yes	Open
155	60.94206863996566	-0.506885	-15.7875	3	12	10	0.50	0.00	-	yes	Open
141	61.112863273097126	-0.638477	-17.772	5	15	9	0.45	0.20	-	yes	Open
140	61.1613288437999	-0.6849	-20.9883	3	15	12	0.60	0.00	-	yes	Open
150	61.54574321719964	-0.558044	-16.2437	2	15	9	0.45	0.20	-	yes	Open
160	61.91170107784806	-0.587773	-19.4037	7	18	16	0.80	0.40	-	yes	Open
135	62.57019389964971	-0.643455	-22.1742	6	14	10	0.50	0.20	-	yes	Current
159	63.879713236990455	-0.653579	-22.5869	6	14	12	0.60	0.00	-	yes	Open
137	64.04549139782667	-0.518843	-18.6066	7	14	10	0.50	0.20	-	yes	Open
151	64.20454014191088	-0.573451	-18.4287	4	13	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 -22.174kcal/mol

Ligand efficiency (LE) -0.6522kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.526

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) 20.19kcal/mol

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

Docked FF energy 58.71kcal/mol

Minimised FF energy 38.52kcal/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_403