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 (-1.084 kcal/mol/HA) ✓ Good fit quality (FQ -10.12) ✓ Strong H-bond network (13 bonds) ✗ Very high strain energy (32.3 kcal/mol) ✗ Geometry warnings ℹ SASA not computed

Score

-29.271

kcal/mol

-1.084

kcal/mol/HA

Fit Quality

-10.12

FQ (Leeson)

HAC

heavy atoms

360

LogP

3.51

cLogP

Strain ΔE

32.3 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 32.3 kcal/mol

Interaction summary

Collapsible panels

H-bonds 13 Hydrophobic 24 π–π 4 Clashes 17 Severe clashes 2

Final rank	11.099150418037073	Score	-29.2714
Inter norm	-1.23486	Intra norm	0.150729
Top1000	no	Excluded	yes
Contacts	17	H-bonds	13
Artifact reason	excluded; geometry warning; 13 clashes; 2 protein clashes; high strain Δ 41.6
Residues	A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLN166;A:GLY205;A:LEU209;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:SER95;A:TRP221;A:TYR174;A:VAL164;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	12	Native recall	0.63
Jaccard	0.50	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
1350	6.368429692861138	-1.14051	-32.2538	10	15	14	0.74	0.80	-	no	Open
1342	6.37464339184996	-1.2076	-33.6607	9	16	14	0.74	0.80	-	no	Open
1243	7.682395223398659	-1.01711	-31.2954	5	16	0	0.00	0.00	-	no	Open
1241	6.2050469711850536	-1.06201	-33.6266	6	18	0	0.00	0.00	-	yes	Open
1351	6.868541609444626	-1.36088	-39.2253	10	16	13	0.68	0.40	-	yes	Open
1238	7.865627785166034	-1.03442	-33.5541	2	20	0	0.00	0.00	-	yes	Open
1239	8.243476814029648	-1.15289	-27.3125	6	17	0	0.00	0.00	-	yes	Open
1346	8.422554756715886	-1.16049	-29.8111	9	17	15	0.79	0.80	-	yes	Open
1340	9.129780181242895	-1.20545	-31.4084	8	17	13	0.68	0.40	-	yes	Open
1237	9.626482630642181	-1.18181	-33.9235	8	18	0	0.00	0.00	-	yes	Open
1353	9.795331183638245	-1.04355	-28.2372	10	17	12	0.63	0.60	-	yes	Open
1354	9.93173632573481	-1.21887	-31.2593	8	17	15	0.79	0.60	-	yes	Open
1230	10.072067892203235	-1.15156	-30.1296	5	19	0	0.00	0.00	-	yes	Open
1355	10.077327041637302	-1.37189	-41.258	11	16	14	0.74	0.60	-	yes	Open
1345	10.437623286391318	-1.23532	-33.0789	12	19	15	0.79	0.60	-	yes	Open
1232	10.470276764827098	-1.177	-34.9719	7	21	0	0.00	0.00	-	yes	Open
1229	10.602310011648374	-1.10454	-29.8669	7	18	0	0.00	0.00	-	yes	Open
1343	10.81940935606428	-1.40602	-42.0237	11	15	14	0.74	0.60	-	yes	Open
1242	10.853026622214346	-1.12393	-27.2198	5	18	0	0.00	0.00	-	yes	Open
1349	11.099150418037073	-1.23486	-29.2714	13	17	12	0.63	0.60	-	yes	Current
1235	11.354116909170855	-1.10896	-32.0991	8	22	0	0.00	0.00	-	yes	Open
1347	11.787185805666386	-1.15474	-35.8338	10	16	16	0.84	0.60	-	yes	Open
1234	12.409298722333222	-1.1196	-33.1721	13	17	0	0.00	0.00	-	yes	Open
1236	14.185381666724265	-1.22874	-39.0889	6	20	0	0.00	0.00	-	yes	Open
1240	58.41397290988954	-1.20729	-32.1969	10	19	0	0.00	0.00	-	yes	Open
1348	59.61112319919978	-1.15288	-32.6853	8	17	13	0.68	0.40	-	yes	Open
1231	60.04677310843543	-1.05497	-30.7014	9	24	0	0.00	0.00	-	yes	Open
1341	60.164811830584526	-1.17742	-33.8833	10	17	12	0.63	0.80	-	yes	Open
1244	60.35387765645741	-1.11168	-36.8206	8	18	0	0.00	0.00	-	yes	Open
1352	62.663945433853726	-1.13045	-23.9483	5	17	13	0.68	0.00	-	yes	Open
1233	74.3506118216329	-0.782983	-136.922	4	13	0	0.00	0.00	-	yes	Open
1344	80.16353719934	-0.9167	-133.266	13	16	15	0.79	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 -29.271kcal/mol

Ligand efficiency (LE) -1.0841kcal/mol/HA

Score / heavy atom count

Fit quality (FQ) -10.115

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

Heavy atom count 27HA

Physicochemical properties

Molecular weight 360.4Da

Lipinski: ≤ 500 Da

LogP (cLogP) 3.51

Lipinski: ≤ 5

Rotatable bonds 5

Conformational strain (MMFF94s)

Strain energy (ΔE) 32.31kcal/mol

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

Docked FF energy 122.89kcal/mol

Minimised FF energy 90.58kcal/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.

Z49620451