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 (-0.571 kcal/mol/HA) ✓ Good fit quality (FQ -5.76) ✓ Strong H-bond network (8 bonds) ✗ Very high strain energy (37.3 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-19.988

kcal/mol

-0.571

kcal/mol/HA

Fit Quality

-5.76

FQ (Leeson)

HAC

heavy atoms

481

LogP

-0.59

cLogP

Strain ΔE

37.3 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 37.3 kcal/mol

Interaction summary

Collapsible panels

H-bonds 8 Hydrophobic 24 π–π 2 Clashes 10 Severe clashes 2

Final rank	9.674745267475345	Score	-19.9878
Inter norm	-0.790283	Intra norm	0.219204
Top1000	no	Excluded	yes
Contacts	18	H-bonds	8
Artifact reason	excluded; geometry warning; 17 clashes; 2 protein clashes; high strain Δ 36.6
Residues	A:ALA10;A:ARG29;A:ASP22;A:GLU31;A:GLY117;A:GLY21;A:ILE8;A:LEU23;A:LEU28;A:NAP201;A:PHE32;A:PHE35;A:PRO27;A:SER60;A:TRP25;A:TYR122;A:VAL116;A:VAL9

Protein summary

200 residues

Protein target	T02	Atoms	3128
Residues	200	Chains	2
Residue summary	LYS:374; LEU:361; GLU:240; VAL:224; ARG:192; PHE:180; ILE:171; PRO:168; ASN:140; SER:132; TYR:126; GLN:119; ASP:108; MET:102; THR:98; GLY:91

Native ligand reference

★ reference

Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.

Name	5SD8	Contacts	21
Pose	Open native pose	H-bonds	5
IFP residues	A:ALA10; A:ASN65; A:ASP22; A:GLN36; A:GLU31; A:GLY117; A:GLY21; A:ILE61; A:ILE8; A:LEU23; A:LEU68; A:NAP201; A:PHE32; A:PHE35; A:PRO62; A:SER60; A:THR137; A:THR57; A:TYR122; A:VAL116; A:VAL9
Current overlap	14	Native recall	0.67
Jaccard	0.56	RMSD	-
H-bond strict	3	Strict recall	0.60
H-bond same residue+role	3	Role recall	0.60
H-bond same residue	3	Residue recall	0.60

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
66	6.938548188579787	-0.808005	-24.1866	5	18	14	0.67	0.40	-	no	Open
69	9.188319575486904	-0.759759	-20.925	13	22	17	0.81	0.80	-	yes	Open
68	9.674745267475345	-0.790283	-19.9878	8	18	14	0.67	0.60	-	yes	Current
70	9.767739220053992	-0.812027	-31.9556	8	22	17	0.81	0.60	-	yes	Open
67	10.947027023285257	-0.740443	-21.4498	8	22	19	0.90	0.20	-	yes	Open
71	11.267955533191873	-0.766528	-24.5835	5	18	13	0.62	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 -19.988kcal/mol

Ligand efficiency (LE) -0.5711kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.760

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

Heavy atom count 35HA

Physicochemical properties

Molecular weight 480.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) -0.59

Lipinski: ≤ 5

Rotatable bonds 9

Conformational strain (MMFF94s)

Strain energy (ΔE) 37.34kcal/mol

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

Docked FF energy 150.12kcal/mol

Minimised FF energy 112.78kcal/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_134