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.

✓ Good LE (-0.314 kcal/mol/HA) ✓ Good fit quality (FQ -2.93) ✗ Very high strain energy (24.4 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ℹ SASA not computed

Score

-8.471

kcal/mol

-0.314

kcal/mol/HA

Fit Quality

-2.93

FQ (Leeson)

HAC

heavy atoms

383

LogP

2.61

cLogP

Strain ΔE

24.4 kcal/mol

SASA buried

computing…

Overall: Promising but geometrically suspicious

Binding evidence: strong

Native-like contacts: strong

Ligand efficiency: good

Geometry reliability: low

Reason: geometry warning, clashes, strain 24.4 kcal/mol

Interaction summary

Collapsible panels

H-bonds 0 Hydrophobic 24 π–π 3 Clashes 12 Severe clashes 3

Final rank	59.2856226558447	Score	-8.47096
Inter norm	-0.653765	Intra norm	0.340026
Top1000	no	Excluded	yes
Contacts	15	H-bonds	0
Artifact reason	excluded; geometry warning; 12 clashes; 3 protein clashes
Residues	A:ARG14;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;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	12	Native recall	0.63
Jaccard	0.55	RMSD	-
H-bond strict	0	Strict recall	0.00
H-bond same residue+role	0	Role recall	0.00
H-bond same residue	0	Residue recall	0.00

Hydrogen bonds

No hydrogen bonds detected for this pose.

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
481	3.1737613548484154	-0.493619	-12.9818	1	10	7	0.37	0.00	-	no	Open
484	3.7234326921177825	-0.665802	-16.9576	1	14	10	0.53	0.00	-	no	Open
486	4.481598924812605	-0.509817	-13.2568	1	10	7	0.37	0.00	-	yes	Open
482	55.89286417755465	-1.10364	-27.8269	1	16	14	0.74	0.20	-	yes	Open
487	56.08568514471958	-0.989031	-19.792	0	13	11	0.58	0.00	-	yes	Open
480	56.301599164878965	-0.97797	-24.7874	0	19	15	0.79	0.00	-	yes	Open
485	59.186968359509606	-1.06195	-21.2343	0	14	12	0.63	0.00	-	yes	Open
483	59.2856226558447	-0.653765	-8.47096	0	15	12	0.63	0.00	-	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 -8.471kcal/mol

Ligand efficiency (LE) -0.3137kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -2.927

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

Heavy atom count 27HA

Physicochemical properties

Molecular weight 383.0Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.61

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 24.43kcal/mol

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

Docked FF energy 143.85kcal/mol

Minimised FF energy 119.42kcal/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.

OSA_Lib_160