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 (-1.140 kcal/mol/HA)
✓ Good fit quality (FQ -9.90)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (13.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.085
kcal/mol
LE
-1.140
kcal/mol/HA
Fit Quality
-9.90
FQ (Leeson)
HAC
22
heavy atoms
MW
309
Da
LogP
3.41
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 13.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 4
Clashes 10
Severe clashes 0
| Final rank | 4.189834154981539 | Score | -25.0846 |
|---|---|---|---|
| Inter norm | -1.30329 | Intra norm | 0.163079 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 10 protein contact clashes; moderate strain Δ 13.8 | ||
| Residues | A:ASN175;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TRP221;A:TYR174 | ||
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 | 0.50 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1981 | 3.532982449225196 | -1.09401 | -19.8894 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1640 | 3.53476968341585 | -1.49583 | -34.0754 | 2 | 15 | 12 | 0.63 | 0.00 | - | no | Open |
| 1980 | 3.8230085067019104 | -1.10862 | -24.4757 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1982 | 3.838404455144409 | -1.11419 | -26.8474 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1643 | 4.189834154981539 | -1.30329 | -25.0846 | 6 | 14 | 11 | 0.58 | 0.40 | - | no | Current |
| 1645 | 4.20474168417215 | -1.26906 | -22.508 | 4 | 14 | 14 | 0.74 | 0.40 | - | no | Open |
| 1984 | 4.585506428884255 | -1.03518 | -23.2856 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1983 | 4.668604187732116 | -1.11897 | -20.958 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1979 | 5.502597585409095 | -1.11148 | -25.178 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1642 | 6.478506684109223 | -1.29313 | -20.9291 | 5 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1641 | 7.225882595734374 | -1.23092 | -18.3957 | 5 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1644 | 7.377698751339138 | -1.37441 | -22.7088 | 5 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.085kcal/mol
Ligand efficiency (LE)
-1.1402kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.899
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
309.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.41
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
68.58kcal/mol
Minimised FF energy
54.81kcal/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.