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 (-1.281 kcal/mol/HA)
✓ Good fit quality (FQ -12.23)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (14.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-37.156
kcal/mol
LE
-1.281
kcal/mol/HA
Fit Quality
-12.23
FQ (Leeson)
HAC
29
heavy atoms
MW
385
Da
LogP
4.86
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 14.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 17
π–π 2
Clashes 7
Severe clashes 0
| Final rank | 3.9113654303296586 | Score | -37.1559 |
|---|---|---|---|
| Inter norm | -1.28064 | Intra norm | -0.00560265 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 7 protein contact clashes; moderate strain Δ 14.9 | ||
| Residues | A:ARG14;A:ASP161;A:GLY205;A:LEU208;A:LEU263;A:LYS13;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:SER37;A:TRP221;A:TYR174;A:VAL206;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 | 10 | Native recall | 0.53 |
| Jaccard | 0.42 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1474 | 3.4884034993745905 | -0.81077 | -22.6513 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 997 | 3.891091728023356 | -1.02158 | -26.92 | 4 | 15 | 11 | 0.58 | 0.20 | - | no | Open |
| 999 | 3.9113654303296586 | -1.28064 | -37.1559 | 6 | 15 | 10 | 0.53 | 0.40 | - | no | Current |
| 770 | 5.1079154112686185 | -0.949378 | -28.1075 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 998 | 6.888844267035802 | -1.1362 | -33.3091 | 6 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
| 768 | 7.171289953070955 | -1.08489 | -29.5785 | 6 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 769 | 7.3832580646510815 | -1.084 | -28.1728 | 2 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1473 | 7.518263910818152 | -1.01701 | -27.3469 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1475 | 8.942855900339884 | -0.776265 | -19.2401 | 6 | 14 | 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
-37.156kcal/mol
Ligand efficiency (LE)
-1.2812kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.230
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
385.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.86
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
75.97kcal/mol
Minimised FF energy
61.71kcal/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.