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 (-1.140 kcal/mol/HA)
✓ Good fit quality (FQ -10.77)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (24.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.930
kcal/mol
LE
-1.140
kcal/mol/HA
Fit Quality
-10.77
FQ (Leeson)
HAC
28
heavy atoms
MW
401
Da
LogP
3.56
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 24.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 3
Clashes 9
Severe clashes 3
| Final rank | 7.812210698198262 | Score | -31.9299 |
|---|---|---|---|
| Inter norm | -1.20333 | Intra norm | 0.062982 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 7 clashes; 3 protein clashes; high strain Δ 24.8 | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174;A:VAL206 | ||
Protein summary
275 residues
| Protein target | T07 | Atoms | 3932 |
|---|---|---|---|
| Residues | 275 | Chains | 3 |
| 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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1673 | 5.737475203427375 | -0.91101 | -23.2963 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1285 | 6.890745069608357 | -0.988051 | -16.9574 | 9 | 20 | 17 | 0.89 | 0.60 | - | no | Open |
| 1287 | 7.001942418776625 | -1.00296 | -18.7626 | 8 | 17 | 15 | 0.79 | 0.20 | - | no | Open |
| 1676 | 4.322828115982854 | -0.96178 | -24.5137 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1283 | 4.589975711251713 | -1.05034 | -19.359 | 7 | 15 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1678 | 5.084157200372924 | -0.874899 | -23.3987 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1677 | 5.282817208975257 | -0.813748 | -19.9481 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1284 | 5.679113106048209 | -1.24423 | -31.4622 | 7 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1674 | 7.560441904466741 | -0.857402 | -23.9223 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1288 | 7.812210698198262 | -1.20333 | -31.9299 | 7 | 16 | 13 | 0.68 | 0.40 | - | yes | Current |
| 1286 | 8.856921005756071 | -1.21668 | -30.0381 | 8 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1675 | 8.98639285873775 | -0.959127 | -20.0172 | 6 | 21 | 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
-31.930kcal/mol
Ligand efficiency (LE)
-1.1404kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.765
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
401.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.56
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
12.09kcal/mol
Minimised FF energy
-12.35kcal/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.