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.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.217 kcal/mol/HA)
✓ Good fit quality (FQ -10.90)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (23.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-29.203
kcal/mol
LE
-1.217
kcal/mol/HA
Fit Quality
-10.90
FQ (Leeson)
HAC
24
heavy atoms
MW
320
Da
LogP
2.52
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 2
Clashes 15
Severe clashes 2
| Final rank | 8.729945437549336 | Score | -29.2029 |
|---|---|---|---|
| Inter norm | -1.28903 | Intra norm | 0.0722427 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 8 clashes; 2 protein clashes; high strain Δ 29.0 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TYR174;A:VAL164 | ||
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.43 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | Open |
| 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 | Current |
| 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.
Scoring & efficiency
Docking score
-29.203kcal/mol
Ligand efficiency (LE)
-1.2168kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.905
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)
23.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
151.01kcal/mol
Minimised FF energy
128.01kcal/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.