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 ↗

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

✓ Excellent LE (-1.580 kcal/mol/HA) ✓ Good fit quality (FQ -14.16) ✓ Strong H-bond network (8 bonds) ✗ Very high strain energy (24.5 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-37.928

kcal/mol

-1.580

kcal/mol/HA

Fit Quality

-14.16

FQ (Leeson)

HAC

heavy atoms

326

LogP

1.84

cLogP

Strain ΔE

24.5 kcal/mol

SASA buried

computing…

Interaction summary

Collapsible panels

H-bonds 8 Hydrophobic 24 π–π 2 Clashes 4 Severe clashes 0

Final rank	3.4507517384190836	Score	-37.9275
Inter norm	-1.54266	Intra norm	-0.0376495
Top1000	no	Excluded	no
Contacts	17	H-bonds	8
Artifact reason	geometry warning; 11 clashes; 4 protein contact clashes; high strain Δ 32.9
Residues	A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:LEU263;A:LYS178;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	4	Strict recall	0.67
H-bond same residue+role	3	Role recall	0.60
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
208	2.8310249964429723	-1.10127	-26.7452	10	18	0	0.00	0.00	-	no	Open
209	2.9036950248110562	-1.07961	-24.8487	10	16	0	0.00	0.00	-	no	Open
248	3.044195362666372	-1.51122	-37.7581	8	16	13	0.68	0.60	-	no	Open
249	3.078881408016236	-1.43894	-36.0333	6	16	13	0.68	0.60	-	no	Open
250	3.4507517384190836	-1.54266	-37.9275	8	17	14	0.74	0.60	-	no	Current
210	3.6122169202787617	-1.00823	-24.9002	5	16	0	0.00	0.00	-	no	Open
250	4.7961851719185855	-0.986967	-24.5766	3	18	0	0.00	0.00	-	no	Open
252	4.879258263872926	-0.992095	-25.0548	6	18	0	0.00	0.00	-	no	Open
251	5.286565630587863	-0.979626	-24.3637	6	19	0	0.00	0.00	-	no	Open

Molecular metrics

FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.

✓ Metrics available

Scoring & efficiency

Docking score -37.928kcal/mol

Ligand efficiency (LE) -1.5803kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -14.163

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

Heavy atom count 24HA

Physicochemical properties

Molecular weight 326.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 1.84

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 24.52kcal/mol

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

Docked FF energy 48.59kcal/mol

Minimised FF energy 24.07kcal/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.

OHD_TB2022_41