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 (-1.487 kcal/mol/HA) ✓ Good fit quality (FQ -12.91) ✓ Strong H-bond network (7 bonds) ✗ Very high strain energy (62.4 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-32.714

kcal/mol

-1.487

kcal/mol/HA

Fit Quality

-12.91

FQ (Leeson)

HAC

heavy atoms

313

LogP

-1.87

cLogP

Strain ΔE

62.4 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 62.4 kcal/mol

Interaction summary

Collapsible panels

H-bonds 7 Hydrophobic 13 π–π 2 Clashes 8 Severe clashes 2

Final rank	54.90253392845565	Score	-32.7137
Inter norm	-1.31928	Intra norm	-0.167709
Top1000	no	Excluded	yes
Contacts	15	H-bonds	7
Artifact reason	excluded; geometry warning; 4 clashes; 2 protein clashes
Residues	A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:SER207;A:SER95;A:TRP221;A:TYR174;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	14	Native recall	0.74
Jaccard	0.70	RMSD	-
H-bond strict	2	Strict recall	0.33
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
725	3.881764876434319	-1.33785	-34.4254	10	15	13	0.68	0.40	-	no	Open
717	4.363881452084701	-1.45296	-27.9395	7	14	14	0.74	0.60	-	no	Open
721	4.744809893168181	-1.28409	-31.1737	4	13	13	0.68	0.40	-	no	Open
713	52.25597153574474	-1.32351	-30.8251	6	12	11	0.58	0.60	-	no	Open
727	52.82554429742053	-1.37162	-30.9653	5	16	15	0.79	0.20	-	no	Open
722	52.901475344989514	-1.15628	-30.0541	10	15	14	0.74	0.40	-	no	Open
715	52.681550447846675	-1.40997	-33.9149	6	12	11	0.58	0.60	-	yes	Open
724	52.96105829878437	-1.30612	-32.8938	7	16	14	0.74	0.40	-	yes	Open
714	53.05253336422005	-1.24508	-31.8992	6	14	14	0.74	0.20	-	yes	Open
726	53.2539328674189	-1.33035	-29.904	7	16	14	0.74	0.40	-	yes	Open
719	54.00588526028555	-1.36162	-30.065	8	14	14	0.74	0.60	-	yes	Open
718	54.33639916166939	-1.2155	-30.6199	10	15	15	0.79	0.40	-	yes	Open
723	54.48952671147026	-1.37213	-32.3628	9	14	14	0.74	0.20	-	yes	Open
728	54.50548997474227	-1.26343	-31.9045	8	16	14	0.74	0.40	-	yes	Open
716	54.90253392845565	-1.31928	-32.7137	7	15	14	0.74	0.20	-	yes	Current
720	55.17790347223977	-1.36133	-31.8488	9	14	14	0.74	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 -32.714kcal/mol

Ligand efficiency (LE) -1.4870kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -12.910

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

Heavy atom count 22HA

Physicochemical properties

Molecular weight 313.2Da

Lipinski: ≤ 500 Da

LogP (cLogP) -1.87

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 62.38kcal/mol

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

Docked FF energy 82.27kcal/mol

Minimised FF energy 19.89kcal/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.

MK129