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 (-1.081 kcal/mol/HA) ✓ Good fit quality (FQ -9.96) ✓ Good H-bonds (3 bonds) ✗ Very high strain energy (58.1 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-28.108

kcal/mol

-1.081

kcal/mol/HA

Fit Quality

-9.96

FQ (Leeson)

HAC

heavy atoms

390

LogP

3.96

cLogP

Strain ΔE

58.1 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, strain 58.1 kcal/mol

Interaction summary

Collapsible panels

H-bonds 3 Hydrophobic 24 π–π 5 Clashes 17 Severe clashes 0

Final rank	8.401677015332918	Score	-28.1075
Inter norm	-1.15471	Intra norm	0.0736565
Top1000	no	Excluded	no
Contacts	18	H-bonds	3
Artifact reason	geometry warning; 7 clashes; 17 protein contact clashes; high strain Δ 59.3
Residues	A:ARG14;A:CYS168;A:GLN166;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206;D:HIS267

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	14	Native recall	0.74
Jaccard	0.61	RMSD	-
H-bond strict	1	Strict recall	0.17
H-bond same residue+role	1	Role recall	0.20
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
2338	5.617341264788754	-0.888273	-21.6534	4	18	0	0.00	0.00	-	no	Open
872	8.401677015332918	-1.15471	-28.1075	3	18	14	0.74	0.20	-	no	Current
2337	8.851922685093875	-0.997696	-26.8941	7	18	0	0.00	0.00	-	yes	Open
871	14.272550090415217	-1.02829	-27.3452	8	18	14	0.74	0.40	-	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 -28.108kcal/mol

Ligand efficiency (LE) -1.0811kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -9.960

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

Heavy atom count 26HA

Physicochemical properties

Molecular weight 390.5Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.96

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 58.14kcal/mol

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

Docked FF energy 84.34kcal/mol

Minimised FF energy 26.20kcal/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.

GemmaOHDUnisi_18