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 (-1.087 kcal/mol/HA)
✓ Good fit quality (FQ -10.49)
✓ Good H-bonds (5 bonds)
✗ High strain energy (13.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-32.618
kcal/mol
LE
-1.087
kcal/mol/HA
Fit Quality
-10.49
FQ (Leeson)
HAC
30
heavy atoms
MW
404
Da
LogP
2.84
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 13.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 5
Clashes 15
Severe clashes 3
| Final rank | 9.47761859361748 | Score | -32.6184 |
|---|---|---|---|
| Inter norm | -1.08508 | Intra norm | -0.00220033 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 11 clashes; 3 protein clashes; moderate strain Δ 15.1 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS178;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;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 | 16 | Native recall | 0.84 |
| Jaccard | 0.76 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 540 | 5.6360014678149986 | -1.15574 | -29.0726 | 6 | 19 | 15 | 0.79 | 0.60 | - | no | Open |
| 541 | 9.47761859361748 | -1.08508 | -32.6184 | 5 | 18 | 16 | 0.84 | 0.60 | - | yes | Current |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.618kcal/mol
Ligand efficiency (LE)
-1.0873kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.488
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
403.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-62.20kcal/mol
Minimised FF energy
-76.11kcal/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.