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 ↗

Weak Marginal quality. Consider only alongside better-scoring alternatives.

✓ Excellent LE (-1.339 kcal/mol/HA) ✓ Good fit quality (FQ -11.62) ✓ Strong H-bond network (13 bonds) ✗ High strain energy (15.5 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-29.451

kcal/mol

-1.339

kcal/mol/HA

Fit Quality

-11.62

FQ (Leeson)

HAC

heavy atoms

322

LogP

0.40

cLogP

Strain ΔE

15.5 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 15.5 kcal/mol

Interaction summary

Collapsible panels

H-bonds 13 Hydrophobic 13 π–π 2 Clashes 12 Severe clashes 1

Final rank	6.257196281895082	Score	-29.4506
Inter norm	-1.42843	Intra norm	0.089773
Top1000	no	Excluded	yes
Contacts	10	H-bonds	13
Artifact reason	excluded; geometry warning; 9 clashes; 1 protein clash; high strain Δ 21.4
Residues	A:ALA96;A:ARG14;A:ASP161;A:LYS178;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174;A:TYR98

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	9	Native recall	0.47
Jaccard	0.45	RMSD	-
H-bond strict	5	Strict recall	0.83
H-bond same residue+role	4	Role recall	0.80
H-bond same residue	4	Residue recall	0.80

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
855	3.601377635446771	-1.46166	-29.9963	9	16	15	0.79	0.60	-	no	Open
641	4.368820087684692	-0.994229	-19.6345	7	13	0	0.00	0.00	-	no	Open
640	4.695549526805484	-1.10744	-22.7076	7	13	0	0.00	0.00	-	yes	Open
856	4.7629460374865324	-1.39857	-27.5234	8	16	15	0.79	0.60	-	yes	Open
642	5.144648952571811	-1.24137	-25.3727	6	13	0	0.00	0.00	-	yes	Open
854	6.257196281895082	-1.42843	-29.4506	13	10	9	0.47	0.80	-	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 -29.451kcal/mol

Ligand efficiency (LE) -1.3387kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -11.622

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

Heavy atom count 22HA

Physicochemical properties

Molecular weight 322.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 0.40

Lipinski: ≤ 5

Rotatable bonds 4

Conformational strain (MMFF94s)

Strain energy (ΔE) 15.54kcal/mol

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

Docked FF energy -5.84kcal/mol

Minimised FF energy -21.39kcal/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-TY0562