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 ↗

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

✓ Excellent LE (-0.700 kcal/mol/HA) ✓ Good fit quality (FQ -6.53) ✗ Very high strain energy (41.2 kcal/mol) ✗ No H-bonds detected ✗ Geometry warnings ℹ SASA not computed

Score

-18.897

kcal/mol

-0.700

kcal/mol/HA

Fit Quality

-6.53

FQ (Leeson)

HAC

heavy atoms

469

LogP

2.26

cLogP

Strain ΔE

41.2 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, strain 41.2 kcal/mol

Interaction summary

Collapsible panels

H-bonds 0 Hydrophobic 24 π–π 5 Clashes 11 Severe clashes 5

Final rank	61.13584018952961	Score	-18.8967
Inter norm	-0.73289	Intra norm	0.0330135
Top1000	no	Excluded	yes
Contacts	14	H-bonds	0
Artifact reason	excluded; hard geometry fail; 1 severe clash; 5 protein clashes
Residues	A:ARG14;A:CYS168;A:GLY205;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;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	14	Native recall	0.74
Jaccard	0.74	RMSD	-
H-bond strict	0	Strict recall	0.00
H-bond same residue+role	0	Role recall	0.00
H-bond same residue	0	Residue recall	0.00

Hydrogen bonds

No hydrogen bonds detected for this pose.

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
2161	6.917569230340829	-0.677705	-12.1203	2	15	12	0.63	0.40	-	no	Open
2155	7.899546141926001	-1.07273	-15.3798	5	18	15	0.79	0.40	-	no	Open
2157	6.03062642477628	-1.18799	-31.7817	4	18	17	0.89	0.40	-	yes	Open
2156	6.697056661987551	-0.547966	-15.8339	1	16	14	0.74	0.20	-	yes	Open
2166	7.330413635105748	-1.05907	-27.5008	3	14	13	0.68	0.40	-	yes	Open
2165	7.762706348493656	-1.14752	-30.4346	3	15	14	0.74	0.40	-	yes	Open
2163	7.842158737858947	-1.3195	-20.6756	7	19	15	0.79	0.60	-	yes	Open
2162	8.079704318159484	-0.935728	-26.8049	6	17	14	0.74	0.20	-	yes	Open
2169	8.235870195014677	-0.757522	-22.9356	3	15	13	0.68	0.40	-	yes	Open
2168	8.658214255951851	-0.82964	-22.7117	4	19	13	0.68	0.00	-	yes	Open
2159	8.77311855838003	-0.914467	-17.6085	6	18	14	0.74	0.40	-	yes	Open
2167	9.124989107565245	-0.907893	-13.7272	6	18	14	0.74	0.40	-	yes	Open
2164	57.90606817536138	-0.679572	-18.1945	3	16	13	0.68	0.20	-	yes	Open
2160	58.33860967177957	-0.693043	-16.1475	3	15	12	0.63	0.20	-	yes	Open
2170	61.13584018952961	-0.73289	-18.8967	0	14	14	0.74	0.00	-	yes	Current
2158	64.48402522992136	-0.626452	-16.9171	3	15	14	0.74	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 -18.897kcal/mol

Ligand efficiency (LE) -0.6999kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -6.530

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

Heavy atom count 27HA

Physicochemical properties

Molecular weight 469.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.26

Lipinski: ≤ 5

Rotatable bonds 7

Conformational strain (MMFF94s)

Strain energy (ΔE) 41.17kcal/mol

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

Docked FF energy 134.79kcal/mol

Minimised FF energy 93.61kcal/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.

Z56929378