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 (-1.501 kcal/mol/HA)
✓ Good fit quality (FQ -13.46)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (24.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-36.033
kcal/mol
LE
-1.501
kcal/mol/HA
Fit Quality
-13.46
FQ (Leeson)
HAC
24
heavy atoms
MW
325
Da
LogP
2.42
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 24.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 2
Clashes 3
Severe clashes 0
| Final rank | 3.078881408016236 | Score | -36.0333 |
|---|---|---|---|
| Inter norm | -1.43894 | Intra norm | -0.0624457 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 3 protein contact clashes; high strain Δ 29.1 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.59 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 208 | 2.8310249964429723 | -1.10127 | -26.7452 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 209 | 2.9036950248110562 | -1.07961 | -24.8487 | 10 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 248 | 3.044195362666372 | -1.51122 | -37.7581 | 8 | 16 | 13 | 0.68 | 0.60 | - | no | Open |
| 249 | 3.078881408016236 | -1.43894 | -36.0333 | 6 | 16 | 13 | 0.68 | 0.60 | - | no | Current |
| 250 | 3.4507517384190836 | -1.54266 | -37.9275 | 8 | 17 | 14 | 0.74 | 0.60 | - | no | Open |
| 210 | 3.6122169202787617 | -1.00823 | -24.9002 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 250 | 4.7961851719185855 | -0.986967 | -24.5766 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 252 | 4.879258263872926 | -0.992095 | -25.0548 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 251 | 5.286565630587863 | -0.979626 | -24.3637 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-36.033kcal/mol
Ligand efficiency (LE)
-1.5014kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.455
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
325.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.42
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.38kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
48.45kcal/mol
Minimised FF energy
24.07kcal/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.