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 (-1.613 kcal/mol/HA)
✓ Good fit quality (FQ -14.00)
✗ Very high strain energy (23.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-35.478
kcal/mol
LE
-1.613
kcal/mol/HA
Fit Quality
-14.00
FQ (Leeson)
HAC
22
heavy atoms
MW
291
Da
LogP
3.28
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 2
Hydrophobic 24
π–π 2
Clashes 13
Severe clashes 3
| Final rank | 10.139576705733996 | Score | -35.4778 |
|---|---|---|---|
| Inter norm | -1.22665 | Intra norm | -0.385976 |
| Top1000 | no | Excluded | yes |
| Contacts | 14 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 14 clashes; 3 protein clashes; high strain Δ 23.1 | ||
| 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 | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1325 | 2.25570982417766 | -1.39233 | -29.2087 | 4 | 13 | 13 | 0.68 | 0.40 | - | no | Open |
| 1327 | 2.4620140988579484 | -1.4255 | -33.0903 | 4 | 13 | 13 | 0.68 | 0.40 | - | no | Open |
| 1727 | 4.934121159327745 | -0.926483 | -21.4841 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1724 | 5.119099879970069 | -1.13244 | -22.5462 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1728 | 5.241121701334908 | -0.967304 | -20.3954 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1725 | 5.483450488463616 | -0.923711 | -18.3994 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1729 | 6.633007709077879 | -0.892696 | -19.0809 | 5 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1331 | 7.366131614032277 | -1.34499 | -32.3933 | 5 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1329 | 7.473737443928767 | -1.2943 | -27.6056 | 4 | 13 | 13 | 0.68 | 0.20 | - | yes | Open |
| 1730 | 9.000785013332667 | -0.98006 | -27.4666 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1726 | 9.04777474559883 | -1.17484 | -30.8377 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1324 | 9.134944882063524 | -1.56773 | -33.1942 | 6 | 15 | 11 | 0.58 | 0.60 | - | yes | Open |
| 1328 | 9.427982432108303 | -1.4591 | -33.0794 | 3 | 13 | 9 | 0.47 | 0.20 | - | yes | Open |
| 1330 | 9.858846981326668 | -1.23982 | -33.5707 | 2 | 14 | 10 | 0.53 | 0.00 | - | yes | Open |
| 1326 | 10.139576705733996 | -1.22665 | -35.4778 | 2 | 14 | 10 | 0.53 | 0.00 | - | yes | Current |
| 1731 | 13.545876231582596 | -0.954063 | -22.151 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-35.478kcal/mol
Ligand efficiency (LE)
-1.6126kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-14.001
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
291.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.28
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.01kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.55kcal/mol
Minimised FF energy
59.54kcal/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.