Docking pose detail

Molecular metrics status: done

Cached molecular metrics are available for this pose.

Metrics cached · SASA missing

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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 (-0.755 kcal/mol/HA) ✓ Good fit quality (FQ -7.49) ✓ Good H-bonds (5 bonds) ✗ Very high strain energy (33.8 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-24.904

kcal/mol

-0.755

kcal/mol/HA

Fit Quality

-7.49

FQ (Leeson)

HAC

heavy atoms

471

LogP

-0.41

cLogP

Strain ΔE

33.8 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 33.8 kcal/mol

Interaction summary

Collapsible panels

H-bonds 5 Hydrophobic 12 π–π 1 Clashes 13 Severe clashes 2 ⚠ Hydrophobic exposure 45%

⚠️Partial hydrophobic solvent exposure

46% of hydrophobic surface appears solvent-exposed (11/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 24 Buried (contacted) 13 Exposed 11 LogP -0.41 H-bonds 5

Exposed fragments: phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)

Final rank	58.20044515834379	Score	-24.9045
Inter norm	-0.968374	Intra norm	0.213691
Top1000	no	Excluded	yes
Contacts	18	H-bonds	5
Artifact reason	excluded; geometry warning; 13 clashes; 2 protein clashes
Residues	A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS13;A:NAP301;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:TYR98;A:VAL206;A:VAL211

Protein summary

258 residues

Protein target	T08	Atoms	3881
Residues	258	Chains	2
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	15	Native recall	0.79
Jaccard	0.68	RMSD	-
H-bond strict	2	Strict recall	0.33
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
343	3.812752552123337	-0.994563	-31.4469	6	18	14	0.74	0.20	-	no	Open
344	3.8705243401228744	-0.870754	-28.115	3	16	14	0.74	0.00	-	no	Open
347	4.356298300693849	-0.965998	-30.8745	4	17	15	0.79	0.20	-	no	Open
351	4.379586910799428	-0.969195	-33.0114	5	18	14	0.74	0.20	-	no	Open
477	4.389746743148744	-0.489235	-15.7609	5	11	0	0.00	0.00	-	no	Open
478	5.101064648093625	-0.509403	-14.2208	2	11	0	0.00	0.00	-	no	Open
350	5.142267070290366	-0.96498	-30.1462	3	19	15	0.79	0.00	-	no	Open
355	5.247370235052955	-0.612381	-15.2624	4	12	0	0.00	0.00	-	no	Open
359	5.360352943942462	-0.72041	-23.1843	6	14	0	0.00	0.00	-	no	Open
475	5.774198577861414	-0.456512	-12.9251	2	11	0	0.00	0.00	-	no	Open
479	7.694967007527174	-0.538491	-14.0072	4	11	0	0.00	0.00	-	no	Open
348	4.878707951509122	-0.934625	-31.8094	5	17	13	0.68	0.20	-	yes	Open
342	5.833367815917855	-0.896866	-28.1377	5	17	14	0.74	0.20	-	yes	Open
354	5.847562371311991	-0.65567	-18.9976	4	14	0	0.00	0.00	-	yes	Open
349	5.970706771991042	-0.817193	-27.7005	4	16	14	0.74	0.20	-	yes	Open
358	6.943685250944132	-0.64618	-20.4915	6	15	0	0.00	0.00	-	yes	Open
476	6.961132261695528	-0.607793	-18.0138	5	9	0	0.00	0.00	-	yes	Open
474	7.064209232112513	-0.595766	-18.7824	5	13	0	0.00	0.00	-	yes	Open
357	7.121210526073309	-0.510579	-13.6016	3	13	0	0.00	0.00	-	yes	Open
481	7.430854451805857	-0.476256	-13.496	4	13	0	0.00	0.00	-	yes	Open
345	9.797896602715781	-0.983616	-28.2511	8	18	13	0.68	0.40	-	yes	Open
480	56.557544805031874	-0.456017	-12.0125	3	10	0	0.00	0.00	-	yes	Open
356	56.71320713716938	-0.565556	-15.5944	4	15	0	0.00	0.00	-	yes	Open
346	58.20044515834379	-0.968374	-24.9045	5	18	15	0.79	0.40	-	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 -24.904kcal/mol

Ligand efficiency (LE) -0.7547kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.488

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

Heavy atom count 33HA

Physicochemical properties

Molecular weight 470.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) -0.41

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 33.77kcal/mol

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

Docked FF energy 203.12kcal/mol

Minimised FF energy 169.36kcal/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.

KB_HAT_8