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 (-0.983 kcal/mol/HA)
✓ Good fit quality (FQ -9.49)
✓ Good H-bonds (5 bonds)
✗ High strain energy (11.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-29.503
kcal/mol
LE
-0.983
kcal/mol/HA
Fit Quality
-9.49
FQ (Leeson)
HAC
30
heavy atoms
MW
410
Da
LogP
4.14
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 11.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 17
π–π 3
Clashes 8
Severe clashes 0
| Final rank | 4.200770998451506 | Score | -29.5032 |
|---|---|---|---|
| Inter norm | -0.971176 | Intra norm | -0.0122653 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 5 |
| Artifact reason | geometry warning; 12 clashes; 8 protein contact clashes; moderate strain Δ 15.1 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:LEU208;A:LEU209;A:LYS114;A:LYS178;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174;A:TYR98 | ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2795 | 3.4618565814228215 | -0.757096 | -23.032 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 815 | 4.200770998451506 | -0.971176 | -29.5032 | 5 | 13 | 11 | 0.58 | 0.80 | - | no | Current |
| 1266 | 4.244775686920395 | -0.971128 | -26.73 | 9 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 996 | 4.585725607781447 | -0.815055 | -21.9899 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1267 | 7.130787680913325 | -0.910334 | -24.6161 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 997 | 7.420151372082239 | -0.78482 | -22.1937 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 816 | 7.499924799333206 | -1.08652 | -30.5394 | 8 | 13 | 10 | 0.53 | 0.60 | - | yes | Open |
| 2796 | 11.317281758909388 | -0.723787 | -20.0219 | 11 | 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
-29.503kcal/mol
Ligand efficiency (LE)
-0.9834kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.487
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
410.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.14
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
11.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.09kcal/mol
Minimised FF energy
52.09kcal/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.