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.

✓ Low conformational strain (5.0 kcal/mol) ✓ Excellent LE (-1.399 kcal/mol/HA) ✓ Good fit quality (FQ -12.35) ✓ Good H-bonds (4 bonds) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-32.181

kcal/mol

-1.399

kcal/mol/HA

Fit Quality

-12.35

FQ (Leeson)

HAC

heavy atoms

299

LogP

4.33

cLogP

Strain ΔE

5.0 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, protein contact clashes

Interaction summary

Collapsible panels

H-bonds 4 Hydrophobic 24 π–π 5 Clashes 5 Severe clashes 0

Final rank	2.174576085040809	Score	-32.1805
Inter norm	-1.40279	Intra norm	0.00363963
Top1000	no	Excluded	no
Contacts	14	H-bonds	4
Artifact reason	geometry warning; 9 clashes; 5 protein contact clashes
Residues	A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174

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	0.57	RMSD	-
H-bond strict	3	Strict recall	0.50
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
778	2.174576085040809	-1.40279	-32.1805	4	14	12	0.63	0.40	-	no	Current
779	2.3054123319762168	-1.47676	-33.8684	7	13	12	0.63	0.40	-	no	Open

Molecular metrics

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

✓ Metrics available

Scoring & efficiency

Docking score -32.181kcal/mol

Ligand efficiency (LE) -1.3992kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -12.349

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

Heavy atom count 23HA

Physicochemical properties

Molecular weight 299.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.33

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 4.98kcal/mol

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

Docked FF energy 51.56kcal/mol

Minimised FF energy 46.58kcal/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.

CKP-28