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 (-0.421 kcal/mol/HA) ✓ Good fit quality (FQ -4.18) ✓ Strong H-bond network (7 bonds) ✗ Very high strain energy (93.6 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-13.900

kcal/mol

-0.421

kcal/mol/HA

Fit Quality

-4.18

FQ (Leeson)

HAC

heavy atoms

515

LogP

3.54

cLogP

Strain ΔE

93.6 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 93.6 kcal/mol

Interaction summary

Collapsible panels

H-bonds 7 Hydrophobic 24 π–π 4 Clashes 24 Severe clashes 4

Final rank	21.01681068023511	Score	-13.9002
Inter norm	-0.585086	Intra norm	0.161593
Top1000	no	Excluded	yes
Contacts	19	H-bonds	7
Artifact reason	excluded; geometry warning; 16 clashes; 4 protein clashes; high strain Δ 95.9
Residues	A:ALA34;A:ARG100;A:ARG59;A:ASP54;A:GLN56;A:HIS182;A:ILE47;A:LEU90;A:LEU97;A:MET55;A:NDP301;A:PHE233;A:PHE58;A:PHE94;A:PRO52;A:THR184;A:TYR57;A:VAL32;A:VAL33

Protein summary

223 residues

Protein target	T06	Atoms	3452
Residues	223	Chains	1
Residue summary	ARG:408; VAL:352; LYS:308; LEU:304; PRO:238; ILE:209; GLU:195; THR:182; SER:176; ALA:160; PHE:140; ASN:126; GLY:126; ASP:108; GLN:85; NDP:74

Native ligand reference

★ reference

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

Name	8RHT	Contacts	21
Pose	Open native pose	H-bonds	6
IFP residues	A:ALA34; A:ASP54; A:HIS182; A:ILE160; A:ILE47; A:LEU90; A:LEU97; A:MET55; A:NDP301; A:PHE233; A:PHE58; A:PHE94; A:PRO91; A:SER89; A:THR184; A:THR86; A:TRP49; A:TYR166; A:TYR57; A:VAL32; A:VAL33
Current overlap	15	Native recall	0.71
Jaccard	0.60	RMSD	-
H-bond strict	2	Strict recall	0.40
H-bond same residue+role	2	Role recall	0.50
H-bond same residue	2	Residue recall	0.50

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
621	11.843070215384966	-0.501684	-6.82749	7	15	0	0.00	0.00	-	no	Open
755	12.510265020795174	-0.800221	-21.0844	10	21	17	0.81	0.50	-	no	Open
756	12.517436311880019	-0.777335	-21.6609	8	21	17	0.81	0.50	-	no	Open
622	9.861134013194741	-0.672092	-16.4283	2	16	0	0.00	0.00	-	yes	Open
620	13.04205183813502	-0.46004	-7.50613	2	12	0	0.00	0.00	-	yes	Open
619	13.541734180477112	-0.546125	-13.0402	8	14	0	0.00	0.00	-	yes	Open
757	16.859934548743205	-0.640926	-17.5797	6	20	16	0.76	0.50	-	yes	Open
754	21.01681068023511	-0.585086	-13.9002	7	19	15	0.71	0.50	-	yes	Current

Molecular metrics

FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -13.900kcal/mol

Ligand efficiency (LE) -0.4212kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -4.179

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

Heavy atom count 33HA

Physicochemical properties

Molecular weight 514.9Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.54

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 93.57kcal/mol

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

Docked FF energy 118.06kcal/mol

Minimised FF energy 24.49kcal/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.

NMT-TY0518