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 ↗

Promising Reasonable quality metrics. Warrants further investigation.

✓ Excellent LE (-1.114 kcal/mol/HA) ✓ Good fit quality (FQ -9.83) ✓ Good H-bonds (4 bonds) ✗ Moderate strain (9.6 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-25.626

kcal/mol

-1.114

kcal/mol/HA

Fit Quality

-9.83

FQ (Leeson)

HAC

heavy atoms

327

LogP

2.58

cLogP

Strain ΔE

9.6 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: mixed

Ligand efficiency: excellent

Geometry reliability: low

Reason: geometry warning, clashes

Interaction summary

Collapsible panels

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

Final rank	4.4161784023178585	Score	-25.6257
Inter norm	-1.22636	Intra norm	0.112203
Top1000	no	Excluded	yes
Contacts	15	H-bonds	4
Artifact reason	excluded; geometry warning; 6 clashes; 1 protein clash; moderate strain Δ 12.5
Residues	A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:LEU263;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:SER95;A:TRP221;A:TYR174;A:VAL164;A:VAL206

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	10	Native recall	0.53
Jaccard	0.42	RMSD	-
H-bond strict	1	Strict recall	0.17
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

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
2024	2.589170647778713	-1.50349	-30.0368	5	16	12	0.63	0.40	-	no	Open
3614	2.7533982013798304	-1.03289	-23.426	4	15	0	0.00	0.00	-	no	Open
2026	3.3612364493700033	-1.51582	-30.1977	5	16	12	0.63	0.40	-	no	Open
2023	4.4161784023178585	-1.22636	-25.6257	4	15	10	0.53	0.20	-	yes	Current
3613	7.769415734387132	-0.921047	-19.4407	5	13	0	0.00	0.00	-	yes	Open
2025	7.8505538540969715	-1.20824	-25.6127	3	16	12	0.63	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 -25.626kcal/mol

Ligand efficiency (LE) -1.1142kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.833

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

Heavy atom count 23HA

Physicochemical properties

Molecular weight 327.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.58

Lipinski: ≤ 5

Rotatable bonds 6

Conformational strain (MMFF94s)

Strain energy (ΔE) 9.55kcal/mol

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

Docked FF energy 99.07kcal/mol

Minimised FF energy 89.52kcal/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.

Z29395300