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 (-1.000 kcal/mol/HA)
✓ Good fit quality (FQ -10.38)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (38.9 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-38.996
kcal/mol
LE
-1.000
kcal/mol/HA
Fit Quality
-10.38
FQ (Leeson)
HAC
39
heavy atoms
MW
527
Da
LogP
2.82
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 38.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 3
Clashes 2
Severe clashes 0
| Final rank | 5.316952564828583 | Score | -38.9963 |
|---|---|---|---|
| Inter norm | -0.923397 | Intra norm | -0.0765079 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 7 |
| Artifact reason | geometry warning; 21 clashes; 2 protein contact clashes; high strain Δ 38.0 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:SER95;A:TRP221;A:TYR174;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 | 0.73 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.83 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 57 | 4.558706331096513 | -0.969977 | -38.7032 | 9 | 19 | 16 | 0.84 | 0.80 | - | no | Open |
| 56 | 5.316952564828583 | -0.923397 | -38.9963 | 7 | 19 | 16 | 0.84 | 0.80 | - | no | Current |
| 58 | 6.075260472483174 | -0.962437 | -40.2519 | 7 | 19 | 16 | 0.84 | 0.80 | - | no | Open |
| 72 | 8.918246884165283 | -0.598542 | -20.7155 | 12 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 98 | 9.117215121004701 | -0.69453 | -22.5704 | 11 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 8 | 9.31166288367184 | -0.661104 | -16.044 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 6 | 11.706246338544839 | -0.846386 | -25.6976 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 73 | 14.994885260763583 | -0.631646 | -24.6039 | 3 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 7 | 15.024825254720277 | -0.649781 | -20.0045 | 7 | 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
-38.996kcal/mol
Ligand efficiency (LE)
-0.9999kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.377
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
526.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.82
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.28kcal/mol
Minimised FF energy
67.40kcal/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.