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 (-0.769 kcal/mol/HA)
✓ Good fit quality (FQ -7.63)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (40.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.386
kcal/mol
LE
-0.769
kcal/mol/HA
Fit Quality
-7.63
FQ (Leeson)
HAC
33
heavy atoms
MW
467
Da
LogP
2.20
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 40.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 2
Clashes 5
Severe clashes 0
| Final rank | 6.227235650424467 | Score | -25.3855 |
|---|---|---|---|
| Inter norm | -0.869908 | Intra norm | 0.100651 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 5 protein contact clashes; high strain Δ 61.1 | ||
| Residues | A:ALA212;A:ARG14;A:LEU208;A:LEU209;A:LYS13;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;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 | 0.45 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 457 | 6.227235650424467 | -0.869908 | -25.3855 | 6 | 13 | 10 | 0.53 | 0.20 | - | no | Current |
| 499 | 7.924145885427372 | -0.811154 | -25.1852 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 500 | 8.047603473549973 | -0.650302 | -17.0635 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 502 | 7.886561522190485 | -0.671567 | -20.5051 | 0 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 458 | 9.071259306486594 | -0.892016 | -21.1864 | 6 | 20 | 16 | 0.84 | 0.40 | - | yes | Open |
| 498 | 10.948540452705352 | -0.672343 | -13.0016 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 501 | 11.089205202628005 | -0.806644 | -22.0054 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 497 | 11.339105867695721 | -0.802805 | -23.1126 | 3 | 18 | 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
-25.386kcal/mol
Ligand efficiency (LE)
-0.7693kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.632
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
466.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.20
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
40.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
42.90kcal/mol
Minimised FF energy
2.22kcal/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.