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 (-0.871 kcal/mol/HA)
✓ Good fit quality (FQ -8.98)
✓ Strong H-bond network (12 bonds)
✗ Very high strain energy (21.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-33.107
kcal/mol
LE
-0.871
kcal/mol/HA
Fit Quality
-8.98
FQ (Leeson)
HAC
38
heavy atoms
MW
508
Da
LogP
2.47
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 21.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 12
Hydrophobic 24
π–π 3
Clashes 11
Severe clashes 1
| Final rank | 7.816993661109642 | Score | -33.107 |
|---|---|---|---|
| Inter norm | -0.946794 | Intra norm | 0.0755572 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 12 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash; high strain Δ 23.9 | ||
| Residues | A:ALA212;A:ALA96;A:ARG14;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.65 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 158 | 5.354508440677042 | -0.655116 | -23.32 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 230 | 5.560534728314991 | -0.740588 | -27.4889 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 168 | 5.917092291574864 | -0.851611 | -31.7023 | 4 | 14 | 11 | 0.58 | 0.00 | - | no | Open |
| 170 | 9.272759406378022 | -0.810912 | -29.3265 | 2 | 17 | 13 | 0.68 | 0.00 | - | no | Open |
| 187 | 10.382193694125345 | -0.866971 | -24.8948 | 6 | 20 | 14 | 0.74 | 0.60 | - | no | Open |
| 231 | 7.644149737780507 | -0.724795 | -25.3534 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 188 | 7.816993661109642 | -0.946794 | -33.107 | 12 | 19 | 15 | 0.79 | 0.60 | - | yes | Current |
| 159 | 8.145814525409154 | -0.607126 | -22.0738 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 189 | 10.02774065723656 | -0.839379 | -29.3354 | 3 | 14 | 12 | 0.63 | 0.00 | - | yes | Open |
| 160 | 10.311097537481704 | -0.51022 | -21.2969 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 169 | 10.553100865605575 | -0.85533 | -28.6024 | 3 | 15 | 11 | 0.58 | 0.00 | - | yes | Open |
| 232 | 10.808934482346375 | -0.740547 | -26.5086 | 2 | 19 | 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
-33.107kcal/mol
Ligand efficiency (LE)
-0.8712kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.982
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
507.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.47
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
104.99kcal/mol
Minimised FF energy
83.63kcal/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.