Docking pose detail

Molecular metrics status: done

Cached molecular metrics are available for this pose.

Metrics cached · SASA missing

py3Dmol interaction viewer

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Strict H-bonds Permissive H-bonds

Molecular report

Full metrics ↗

Reject Multiple quality flags — this pose should be deprioritised or discarded.

✓ Excellent LE (-0.840 kcal/mol/HA) ✓ Good fit quality (FQ -8.40) ✓ Strong H-bond network (7 bonds) ✗ Very high strain energy (24.1 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-28.543

kcal/mol

-0.840

kcal/mol/HA

Fit Quality

-8.40

FQ (Leeson)

HAC

heavy atoms

490

LogP

2.10

cLogP

Strain ΔE

24.1 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 24.1 kcal/mol

Interaction summary

Collapsible panels

H-bonds 7 Hydrophobic 24 π–π 3 Clashes 11 Severe clashes 0 ⚠ Hydrophobic exposure 37%

⚠️Partial hydrophobic solvent exposure

38% of hydrophobic surface appears solvent-exposed (9/24 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 24 Buried (contacted) 15 Exposed 9 LogP 2.1 H-bonds 7

Exposed fragments: phenyl (5/6 atoms exposed)phenyl (3/5 atoms exposed)aliphatic chain/group (3 atoms exposed)

Final rank	6.5752281328867355	Score	-28.5431
Inter norm	-1.00078	Intra norm	0.140043
Top1000	no	Excluded	no
Contacts	14	H-bonds	7
Artifact reason	geometry warning; 12 clashes; 11 protein contact clashes; high strain Δ 38.7
Residues	A:ARG14;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS13;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER37;A:TRP221;A:VAL206

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	12	Native recall	0.63
Jaccard	0.57	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
423	6.235444614885987	-0.921178	-28.5461	4	13	11	0.58	0.20	-	no	Open
424	6.5752281328867355	-1.00078	-28.5431	7	14	12	0.63	0.40	-	no	Current
468	6.827904118123914	-0.746868	-24.6373	1	17	0	0.00	0.00	-	no	Open
601	7.401065038593859	-0.779113	-26.4587	2	20	0	0.00	0.00	-	no	Open
600	6.751124317430976	-0.70137	-19.2185	4	18	0	0.00	0.00	-	yes	Open
602	7.494104916731109	-0.827691	-22.9203	4	18	0	0.00	0.00	-	yes	Open
467	8.007040405112697	-0.677413	-17.4227	1	17	0	0.00	0.00	-	yes	Open
420	8.66704616002394	-0.810841	-22.9533	4	16	15	0.79	0.20	-	yes	Open
421	9.458859204989842	-0.907133	-29.9858	3	19	14	0.74	0.00	-	yes	Open
422	10.017601772255048	-0.907876	-25.4826	10	16	13	0.68	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 -28.543kcal/mol

Ligand efficiency (LE) -0.8395kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.400

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

Heavy atom count 34HA

Physicochemical properties

Molecular weight 489.6Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.10

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 24.06kcal/mol

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

Docked FF energy 110.16kcal/mol

Minimised FF energy 86.10kcal/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_151