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 (-0.867 kcal/mol/HA)
✓ Good fit quality (FQ -7.65)
✓ Good H-bonds (3 bonds)
✗ High strain energy (19.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-19.940
kcal/mol
LE
-0.867
kcal/mol/HA
Fit Quality
-7.65
FQ (Leeson)
HAC
23
heavy atoms
MW
352
Da
LogP
3.58
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 19.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 14
π–π 1
Clashes 6
Severe clashes 0
| Final rank | 3.8503173755325215 | Score | -19.9403 |
|---|---|---|---|
| Inter norm | -1.11654 | Intra norm | 0.249572 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 3 |
| Artifact reason | geometry warning; 11 clashes; 6 protein contact clashes; high strain Δ 20.7 | ||
| Residues | A:ALA96;A:ARG14;A:LEU208;A:LEU209;A:LYS13;A:NAP301;A:PHE97;A:PRO210;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 | 8 | Native recall | 0.42 |
| Jaccard | 0.38 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 232 | 2.834794242434497 | -1.02933 | -17.7647 | 0 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 235 | 3.1016599288773388 | -0.942173 | -17.8202 | 0 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 3.3728629943587816 | -1.36419 | -26.244 | 2 | 15 | 14 | 0.74 | 0.20 | - | no | Open |
| 572 | 3.8503173755325215 | -1.11654 | -19.9403 | 3 | 10 | 8 | 0.42 | 0.40 | - | no | Current |
| 233 | 3.9172101203965464 | -1.02313 | -17.9656 | 0 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 230 | 4.521749855716406 | -0.912026 | -16.9128 | 0 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 4.557625005324844 | -0.962951 | -16.7474 | 0 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 573 | 4.96742283390219 | -1.0902 | -18.1066 | 1 | 16 | 14 | 0.74 | 0.00 | - | yes | Open |
| 231 | 55.328014273835905 | -0.934761 | -16.9919 | 0 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 575 | 56.143906454773145 | -1.22344 | -24.7009 | 2 | 15 | 13 | 0.68 | 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
-19.940kcal/mol
Ligand efficiency (LE)
-0.8670kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.652
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
352.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.58
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.77kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.53kcal/mol
Minimised FF energy
36.76kcal/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.