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 (-0.565 kcal/mol/HA) ✓ Good fit quality (FQ -5.13) ✓ Strong H-bond network (10 bonds) ✗ High strain energy (17.2 kcal/mol) ✗ Geometry warnings ✗ Protein contact clashes ℹ SASA not computed

Score

-14.117

kcal/mol

-0.565

kcal/mol/HA

Fit Quality

-5.13

FQ (Leeson)

HAC

heavy atoms

344

LogP

2.08

cLogP

Strain ΔE

17.2 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 17.2 kcal/mol

Interaction summary

Collapsible panels

H-bonds 10 Hydrophobic 24 π–π 1 Clashes 18 Severe clashes 0

Final rank	6.940391670352547	Score	-14.1169
Inter norm	-0.617226	Intra norm	0.05255
Top1000	no	Excluded	no
Contacts	15	H-bonds	10
Artifact reason	geometry warning; 8 clashes; 18 protein contact clashes; moderate strain Δ 17.3
Residues	A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;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	0.70	RMSD	-
H-bond strict	4	Strict recall	0.67
H-bond same residue+role	3	Role recall	0.60
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
253	6.940391670352547	-0.617226	-14.1169	10	15	14	0.74	0.60	-	no	Current
251	4.604457747254389	-1.32222	-32.4251	9	14	13	0.68	0.60	-	yes	Open
247	4.663386289268596	-1.4479	-35.08	9	16	15	0.79	0.60	-	yes	Open
255	5.098194977650718	-1.23081	-30.222	9	15	13	0.68	0.60	-	yes	Open
257	6.332033946357751	-0.695458	-15.1174	2	17	13	0.68	0.20	-	yes	Open
250	6.865034736574391	-0.642758	-15.6596	4	16	14	0.74	0.40	-	yes	Open
248	8.67822563607149	-1.20593	-29.3986	7	17	16	0.84	0.60	-	yes	Open
254	9.009653382181178	-0.695281	-15.8435	3	17	14	0.74	0.20	-	yes	Open
249	9.132964637938462	-0.729481	-17.8293	5	13	13	0.68	0.40	-	yes	Open
252	58.319481585561334	-1.12908	-28.0199	7	15	14	0.74	0.60	-	yes	Open
246	59.14568617759906	-0.744521	-17.8929	5	14	13	0.68	0.40	-	yes	Open
256	60.069848521623314	-0.946767	-23.6052	6	16	15	0.79	0.60	-	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 -14.117kcal/mol

Ligand efficiency (LE) -0.5647kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -5.133

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

Heavy atom count 25HA

Physicochemical properties

Molecular weight 344.3Da

Lipinski: ≤ 500 Da

LogP (cLogP) 2.08

Lipinski: ≤ 5

Rotatable bonds 1

Conformational strain (MMFF94s)

Strain energy (ΔE) 17.20kcal/mol

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

Docked FF energy 57.38kcal/mol

Minimised FF energy 40.18kcal/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.

OHD_TbNat_133