Docking pose detail

Molecular metrics status: done

Cached molecular metrics are available for this pose.

Metrics cached · SASA missing

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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 (-0.790 kcal/mol/HA) ✓ Good fit quality (FQ -8.20) ✓ Good H-bonds (5 bonds) ✗ Very high strain energy (34.6 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-30.796

kcal/mol

-0.790

kcal/mol/HA

Fit Quality

-8.20

FQ (Leeson)

HAC

heavy atoms

563

LogP

5.57

cLogP

Strain ΔE

34.6 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 34.6 kcal/mol

Interaction summary

Collapsible panels

H-bonds 5 Hydrophobic 24 π–π 4 Clashes 9 Severe clashes 3 ⚠ Hydrophobic exposure 35%

⚠️Partial hydrophobic solvent exposure

36% of hydrophobic surface appears solvent-exposed (10/28 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 28 Buried (contacted) 18 Exposed 10 LogP 5.57 H-bonds 5

Exposed fragments: phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)

Final rank	10.263658085221024	Score	-30.7957
Inter norm	-0.677176	Intra norm	-0.112458
Top1000	no	Excluded	yes
Contacts	16	H-bonds	5
Artifact reason	excluded; geometry warning; 14 clashes; 3 protein clashes; high strain Δ 37.6
Residues	A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU209;A:LYS220;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;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	13	Native recall	0.68
Jaccard	0.59	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
1517	5.638791330156456	-0.667795	-27.1168	4	16	15	0.79	0.20	-	no	Open
1522	5.714183409418502	-0.685914	-32.1574	1	17	13	0.68	0.00	-	no	Open
1520	6.0613735494179375	-0.836047	-34.6794	4	19	15	0.79	0.00	-	no	Open
1521	7.392456645551796	-0.700733	-31.0763	4	14	14	0.74	0.20	-	no	Open
1515	6.714685739867728	-0.745681	-28.668	3	15	13	0.68	0.00	-	yes	Open
1516	8.391633141213417	-0.740138	-24.952	3	19	16	0.84	0.00	-	yes	Open
1519	10.263658085221024	-0.677176	-30.7957	5	16	13	0.68	0.40	-	yes	Current
1518	13.675639011320333	-0.49049	-14.0247	0	18	14	0.74	0.00	-	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 -30.796kcal/mol

Ligand efficiency (LE) -0.7896kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -8.195

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

Heavy atom count 39HA

Physicochemical properties

Molecular weight 563.1Da

Lipinski: ≤ 500 Da

LogP (cLogP) 5.57

Lipinski: ≤ 5

Rotatable bonds 8

Conformational strain (MMFF94s)

Strain energy (ΔE) 34.56kcal/mol

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

Docked FF energy 164.84kcal/mol

Minimised FF energy 130.28kcal/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.

Z49597823