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 (-0.968 kcal/mol/HA)
✓ Good fit quality (FQ -9.69)
✓ Strong H-bond network (16 bonds)
✗ Very high strain energy (20.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-32.920
kcal/mol
LE
-0.968
kcal/mol/HA
Fit Quality
-9.69
FQ (Leeson)
HAC
34
heavy atoms
MW
465
Da
LogP
1.64
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 20.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 16
Hydrophobic 24
π–π 3
Clashes 7
Severe clashes 1
| Final rank | 6.6365893953289605 | Score | -32.9196 |
|---|---|---|---|
| Inter norm | -1.01865 | Intra norm | 0.050425 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 18 clashes; 1 protein clash; moderate strain Δ 19.9 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;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: permissive.
| 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 | 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: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 77 | 5.497893660577265 | -1.07542 | -35.462 | 10 | 16 | 16 | 0.84 | 0.80 | - | no | Open |
| 16 | 5.507049233836736 | -0.883124 | -28.9788 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 80 | 6.170447394229309 | -0.888501 | -26.7226 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 6.1576544954245245 | -1.04369 | -36.6137 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 76 | 6.6365893953289605 | -1.01865 | -32.9196 | 8 | 18 | 16 | 0.84 | 0.80 | - | yes | Current |
| 79 | 6.675765004733855 | -0.748393 | -24.6119 | 11 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 78 | 6.812252767364694 | -1.03725 | -30.7735 | 8 | 19 | 16 | 0.84 | 0.80 | - | yes | Open |
| 17 | 8.747999594432303 | -0.764781 | -23.2494 | 4 | 15 | 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
-32.920kcal/mol
Ligand efficiency (LE)
-0.9682kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.688
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
464.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.64
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.08kcal/mol
Minimised FF energy
60.70kcal/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.