Docking pose detail

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 (-1.172 kcal/mol/HA) ✓ Good fit quality (FQ -10.51) ✓ Good H-bonds (3 bonds) ✗ High strain energy (14.5 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-28.131

kcal/mol

-1.172

kcal/mol/HA

Fit Quality

-10.51

FQ (Leeson)

HAC

heavy atoms

320

LogP

2.52

cLogP

Strain ΔE

14.5 kcal/mol

SASA buried

computing…

Interaction summary

Collapsible panels

H-bonds 3 Hydrophobic 24 π–π 5 Clashes 5 Severe clashes 0

Final rank	2.5905657562689117	Score	-28.1313
Inter norm	-1.23636	Intra norm	0.064224
Top1000	no	Excluded	no
Contacts	15	H-bonds	3
Artifact reason	geometry warning; 9 clashes; 5 protein contact clashes; moderate strain Δ 16.3
Residues	A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;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	15	Native recall	0.79
Jaccard	0.79	RMSD	-
H-bond strict	0	Strict recall	0.00
H-bond same residue+role	1	Role recall	0.20
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
1296	2.5905657562689117	-1.23636	-28.1313	3	15	15	0.79	0.20	-	no	Current
1089	3.368035662733109	-1.2585	-28.7857	4	15	15	0.79	0.20	-	no	Open
1085	4.149909866343656	-1.41746	-31.6503	9	13	13	0.68	0.40	-	yes	Open
1293	5.301231772081614	-1.26725	-31.8799	9	9	7	0.37	0.40	-	yes	Open
1087	5.3798479439808595	-1.39599	-36.0359	9	15	15	0.79	0.40	-	yes	Open
1292	5.547320771564339	-1.27981	-28.4802	5	17	15	0.79	0.20	-	yes	Open
1084	6.848717318262922	-1.24381	-26.5271	5	16	12	0.63	0.40	-	yes	Open
1294	7.06015635216853	-1.39062	-35.0377	8	16	16	0.84	0.40	-	yes	Open
1086	8.03310281957473	-1.21009	-30.6743	5	15	11	0.58	0.40	-	yes	Open
1088	8.729945437549336	-1.28903	-29.2029	6	14	10	0.53	0.40	-	yes	Open
1295	8.837030827496049	-1.19167	-26.9921	7	15	11	0.58	0.60	-	yes	Open
1291	9.022622966208896	-1.43345	-31.4693	8	16	12	0.63	0.80	-	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 -28.131kcal/mol

Ligand efficiency (LE) -1.1721kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.505

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

Heavy atom count 24HA

Physicochemical properties

Molecular weight 320.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.52

Lipinski: ≤ 5

Rotatable bonds 3

Conformational strain (MMFF94s)

Strain energy (ΔE) 14.54kcal/mol

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

Docked FF energy 154.59kcal/mol

Minimised FF energy 140.05kcal/mol

SASA & burial (FreeSASA)

not yet run

SASA has not been computed yet for this pose. It will be calculated automatically the next time this pose is loaded if a receptor PDB path is stored.

Z57100312