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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.540 kcal/mol/HA)
✓ Good fit quality (FQ -5.44)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (54.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-18.892
kcal/mol
LE
-0.540
kcal/mol/HA
Fit Quality
-5.44
FQ (Leeson)
HAC
35
heavy atoms
MW
525
Da
LogP
2.91
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 54.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 1
Clashes 6
Severe clashes 0
| Final rank | 5.750339237800145 | Score | -18.8923 |
|---|---|---|---|
| Inter norm | -0.667951 | Intra norm | 0.128171 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 6 protein contact clashes; high strain Δ 46.0 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS114;A:LYS178;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98;A:VAL206 | ||
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 | 16 | Native recall | 0.84 |
| Jaccard | 0.76 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 706 | 5.079669888762837 | -0.702406 | -20.4925 | 4 | 19 | 16 | 0.84 | 0.40 | - | no | Open |
| 704 | 5.750339237800145 | -0.667951 | -18.8923 | 6 | 18 | 16 | 0.84 | 0.40 | - | no | Current |
| 973 | 5.776981978429328 | -0.711398 | -22.6349 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 972 | 6.281881188565866 | -0.57114 | -19.4326 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 703 | 6.7628958944344255 | -0.844589 | -29.0251 | 4 | 19 | 17 | 0.89 | 0.40 | - | no | Open |
| 971 | 7.337413345837669 | -0.750742 | -20.2062 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 705 | 54.35133594720192 | -0.752311 | -22.6814 | 3 | 17 | 13 | 0.68 | 0.20 | - | yes | Open |
| 970 | 56.35512560165496 | -0.621185 | -20.23 | 4 | 17 | 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
-18.892kcal/mol
Ligand efficiency (LE)
-0.5398kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.444
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
524.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.91
Lipinski: ≤ 5
Rotatable bonds
12
Conformational strain (MMFF94s)
Strain energy (ΔE)
54.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.35kcal/mol
Minimised FF energy
-12.38kcal/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.