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 (-0.943 kcal/mol/HA)
✓ Good fit quality (FQ -8.05)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (15.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-19.811
kcal/mol
LE
-0.943
kcal/mol/HA
Fit Quality
-8.05
FQ (Leeson)
HAC
21
heavy atoms
MW
343
Da
LogP
3.27
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 15.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 10
π–π 1
Clashes 8
Severe clashes 1
⚠ Hydrophobic exposure 50%
Partial hydrophobic solvent exposure
50% of hydrophobic surface appears solvent-exposed (7/14 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 14
Buried (contacted) 7
Exposed 7
LogP 3.27
H-bonds 6
Exposed fragments:
phenyl (3/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 5.31128705726271 | Score | -19.811 |
|---|---|---|---|
| Inter norm | -1.13647 | Intra norm | 0.193095 |
| Top1000 | no | Excluded | yes |
| Contacts | 7 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 7 clashes; 1 protein clash; high strain Δ 22.1 | ||
| Residues | A:ALA212;A:ARG14;A:LEU209;A:NAP301;A:PHE97;A:PRO210;A:VAL211 | ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | 5 | Native recall | 0.26 |
| Jaccard | 0.24 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 847 | 4.284101654517455 | -1.35012 | -27.4121 | 4 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 846 | 4.794038761736944 | -1.24222 | -25.5132 | 2 | 15 | 13 | 0.68 | 0.00 | - | yes | Open |
| 845 | 4.942948917130457 | -1.52191 | -31.5849 | 2 | 13 | 13 | 0.68 | 0.20 | - | yes | Open |
| 844 | 5.31128705726271 | -1.13647 | -19.811 | 6 | 7 | 5 | 0.26 | 0.40 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.811kcal/mol
Ligand efficiency (LE)
-0.9434kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.047
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
343.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.27
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-33.15kcal/mol
Minimised FF energy
-48.48kcal/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.