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 (-0.691 kcal/mol/HA) ✓ Good fit quality (FQ -7.12) ✓ Strong H-bond network (11 bonds) ✗ Very high strain energy (71.2 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-26.247

kcal/mol

-0.691

kcal/mol/HA

Fit Quality

-7.12

FQ (Leeson)

HAC

heavy atoms

553

LogP

4.62

cLogP

Strain ΔE

71.2 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 71.2 kcal/mol

Interaction summary

Collapsible panels

H-bonds 11 Hydrophobic 24 π–π 4 Clashes 15 Severe clashes 0 ⚠ Hydrophobic exposure 38%

⚠️Partial hydrophobic solvent exposure

38% of hydrophobic surface appears solvent-exposed (10/26 atoms). Partial exposure is common but may limit selectivity and membrane permeability.

Non-polar atoms 26 Buried (contacted) 16 Exposed 10 LogP 4.62 H-bonds 11

Exposed fragments: phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)

Final rank	10.791120172075061	Score	-26.2473
Inter norm	-0.931632	Intra norm	0.239079
Top1000	no	Excluded	no
Contacts	17	H-bonds	11
Artifact reason	geometry warning; 15 clashes; 15 protein contact clashes; high strain Δ 79.3
Residues	A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS13;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;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	14	Native recall	0.74
Jaccard	0.64	RMSD	-
H-bond strict	3	Strict recall	0.50
H-bond same residue+role	2	Role recall	0.40
H-bond same residue	3	Residue recall	0.60

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
965	10.791120172075061	-0.931632	-26.2473	11	17	14	0.74	0.40	-	no	Current
964	10.094601244566498	-0.612018	-20.0227	8	15	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 -26.247kcal/mol

Ligand efficiency (LE) -0.6907kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -7.121

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

Heavy atom count 38HA

Physicochemical properties

Molecular weight 552.7Da

Lipinski: ≤ 500 Da

LogP (cLogP) 4.62

Lipinski: ≤ 5

Rotatable bonds 12

Conformational strain (MMFF94s)

Strain energy (ΔE) 71.18kcal/mol

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

Docked FF energy 56.24kcal/mol

Minimised FF energy -14.94kcal/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.

NMT-TY0951