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 (-0.789 kcal/mol/HA) ✓ Good fit quality (FQ -8.02) ✓ Strong H-bond network (9 bonds) ✗ High strain energy (14.8 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-28.410

kcal/mol

-0.789

kcal/mol/HA

Fit Quality

-8.02

FQ (Leeson)

HAC

heavy atoms

487

LogP

4.95

cLogP

Strain ΔE

14.8 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 14.8 kcal/mol

Interaction summary

Collapsible panels

H-bonds 9 Hydrophobic 24 π–π 4 Clashes 6 Severe clashes 1

Final rank	6.527573863183832	Score	-28.41
Inter norm	-0.935701	Intra norm	0.146535
Top1000	no	Excluded	yes
Contacts	13	H-bonds	9
Artifact reason	excluded; geometry warning; 18 clashes; 1 protein clash; high strain Δ 21.2
Residues	A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO99;A:SER95;A:TRP221;A:TYR98

Protein summary

275 residues

Protein target	T07	Atoms	3932
Residues	275	Chains	3
Residue summary	LEU:437; VAL:433; ALA:361; ARG:288; ILE:266; GLU:210; LYS:198; SER:198; ASN:182; THR:154; GLN:153; PHE:140; PRO:140; TYR:126; GLY:112; HIS:103

Native ligand reference

★ reference

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

Name	TbPTR1_cW_6RX6_Ready	Contacts	19
Pose	Open native pose	H-bonds	6
IFP residues	A:ARG14; A:ASP161; A:CYS168; A:GLY205; A:LEU208; A:LEU209; A:LYS178; A:MET213; A:NAP301; A:PHE171; A:PHE97; A:PRO210; A:PRO99; A:SER207; A:SER95; A:TRP221; A:TYR174; A:TYR98; A:VAL206
Current overlap	11	Native recall	0.58
Jaccard	0.52	RMSD	-
H-bond strict	2	Strict recall	0.33
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
1954	4.172182705475963	-0.687195	-20.29	3	17	0	0.00	0.00	-	no	Open
1953	5.989464138450463	-0.705968	-21.027	3	18	0	0.00	0.00	-	no	Open
990	6.442977655601891	-0.721187	-22.5888	7	13	0	0.00	0.00	-	no	Open
631	6.444321292213236	-0.84285	-27.2267	5	14	12	0.63	0.40	-	no	Open
630	6.527573863183832	-0.935701	-28.41	9	13	11	0.58	0.40	-	yes	Current
989	7.925280221930736	-0.676757	-20.4246	7	18	0	0.00	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 -28.410kcal/mol

Ligand efficiency (LE) -0.7892kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.021

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

Heavy atom count 36HA

Physicochemical properties

Molecular weight 486.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.95

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 14.77kcal/mol

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

Docked FF energy 108.85kcal/mol

Minimised FF energy 94.08kcal/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.

TC343