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 (-0.877 kcal/mol/HA)
✓ Good fit quality (FQ -7.86)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (23.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.055
kcal/mol
LE
-0.877
kcal/mol/HA
Fit Quality
-7.86
FQ (Leeson)
HAC
24
heavy atoms
MW
321
Da
LogP
2.50
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 5
Clashes 7
Severe clashes 1
| Final rank | 5.42833706964764 | Score | -21.0546 |
|---|---|---|---|
| Inter norm | -1.14442 | Intra norm | 0.267142 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 11 clashes; 1 protein clash; high strain Δ 23.9 | ||
| Residues | A:ARG14;A:CYS168;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174;D:HIS267 | ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1680 | 3.8684781010639266 | -1.06954 | -27.1497 | 5 | 16 | 13 | 0.68 | 0.40 | - | no | Open |
| 1681 | 4.261938943035762 | -1.34336 | -34.8563 | 7 | 14 | 12 | 0.63 | 0.20 | - | no | Open |
| 1683 | 5.807481972503691 | -1.11095 | -25.1371 | 5 | 12 | 11 | 0.58 | 0.20 | - | no | Open |
| 2107 | 6.275662249360153 | -0.987928 | -20.7902 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1682 | 5.42833706964764 | -1.14442 | -21.0546 | 4 | 13 | 11 | 0.58 | 0.20 | - | yes | Current |
| 2108 | 8.315913966414422 | -0.808528 | -15.7178 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2111 | 10.229640365059275 | -1.05379 | -19.0549 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2110 | 11.654708283551528 | -0.890852 | -17.2261 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2109 | 12.379593172827569 | -1.02033 | -24.4378 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2112 | 13.637826935666792 | -0.957642 | -15.1495 | 13 | 18 | 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
-21.055kcal/mol
Ligand efficiency (LE)
-0.8773kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.862
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
321.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.50
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
126.15kcal/mol
Minimised FF energy
103.09kcal/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.