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 (-1.508 kcal/mol/HA)
✓ Good fit quality (FQ -12.62)
✓ Good H-bonds (5 bonds)
✗ High strain energy (18.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.151
kcal/mol
LE
-1.508
kcal/mol/HA
Fit Quality
-12.62
FQ (Leeson)
HAC
20
heavy atoms
MW
331
Da
LogP
3.48
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 18.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 4
Clashes 3
Severe clashes 0
| Final rank | 2.2046035467081206 | Score | -30.1511 |
|---|---|---|---|
| Inter norm | -1.47574 | Intra norm | -0.0318148 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 5 |
| Artifact reason | geometry warning; 11 clashes; 3 protein contact clashes; moderate strain Δ 18.4 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;A:TYR174 | ||
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 | 12 | Native recall | 0.63 |
| Jaccard | 0.63 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1104 | 1.9209297477053677 | -1.48619 | -28.2833 | 8 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
| 1106 | 2.2046035467081206 | -1.47574 | -30.1511 | 5 | 12 | 12 | 0.63 | 0.40 | - | no | Current |
| 1008 | 2.674373615127031 | -1.06096 | -16.5435 | 0 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 1100 | 2.93502719037972 | -1.53811 | -29.1926 | 5 | 15 | 13 | 0.68 | 0.40 | - | no | Open |
| 1102 | 3.8256555715952345 | -1.31947 | -23.8277 | 6 | 12 | 12 | 0.63 | 0.40 | - | no | Open |
| 1006 | 4.093285467316733 | -1.13435 | -17.7219 | 1 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1007 | 5.311182866278844 | -0.847626 | -13.7104 | 0 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1103 | 6.368962566910486 | -1.58194 | -72.5661 | 7 | 15 | 11 | 0.58 | 0.60 | - | yes | Open |
| 1005 | 6.7741787659630965 | -1.02338 | -66.8108 | 1 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1101 | 9.16777172798654 | -1.17674 | -18.044 | 6 | 15 | 10 | 0.53 | 0.60 | - | yes | Open |
| 1099 | 9.607723910504175 | -1.25355 | -18.9327 | 6 | 15 | 10 | 0.53 | 0.60 | - | yes | Open |
| 1105 | 9.679980882366747 | -1.42721 | -18.6893 | 5 | 15 | 10 | 0.53 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-30.151kcal/mol
Ligand efficiency (LE)
-1.5076kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.616
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
331.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.48
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.31kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.09kcal/mol
Minimised FF energy
43.78kcal/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.