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 (-0.949 kcal/mol/HA)
✓ Good fit quality (FQ -9.24)
✗ High strain energy (17.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-29.403
kcal/mol
LE
-0.949
kcal/mol/HA
Fit Quality
-9.24
FQ (Leeson)
HAC
31
heavy atoms
MW
426
Da
LogP
3.08
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 17.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 24
π–π 3
Clashes 10
Severe clashes 2
| Final rank | 7.964486530158161 | Score | -29.4028 |
|---|---|---|---|
| Inter norm | -0.953833 | Intra norm | 0.0053567 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 13 clashes; 2 protein clashes; high strain Δ 24.5 | ||
| Residues | A:ARG14;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;A:TRP221;A:TYR174;A:TYR98;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.79 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2037 | 4.468051330952002 | -0.971195 | -29.3656 | 3 | 15 | 13 | 0.68 | 0.00 | - | no | Open |
| 2760 | 6.165290630432863 | -0.697596 | -21.1452 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2035 | 6.45680009336731 | -0.827871 | -26.405 | 6 | 14 | 14 | 0.74 | 0.20 | - | no | Open |
| 2764 | 6.320464494635614 | -1.00267 | -28.7297 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2034 | 6.691547129394948 | -0.989687 | -28.8904 | 3 | 16 | 16 | 0.84 | 0.40 | - | yes | Open |
| 2038 | 7.964486530158161 | -0.953833 | -29.4028 | 2 | 15 | 15 | 0.79 | 0.20 | - | yes | Current |
| 2759 | 8.264937391821597 | -0.919279 | -29.2487 | 10 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2039 | 8.474901022873706 | -0.91028 | -25.5532 | 2 | 13 | 10 | 0.53 | 0.40 | - | yes | Open |
| 2763 | 8.990405596505154 | -0.937698 | -28.9838 | 12 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2761 | 12.937488263772991 | -0.735309 | -20.4817 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2036 | 57.398455514050504 | -1.03629 | -32.732 | 8 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
| 2762 | 62.39301824279694 | -0.71015 | -21.5696 | 9 | 17 | 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
-29.403kcal/mol
Ligand efficiency (LE)
-0.9485kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.240
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
426.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.08
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
11.98kcal/mol
Minimised FF energy
-5.58kcal/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.