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 (-0.878 kcal/mol/HA)
✓ Good fit quality (FQ -8.19)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (14.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.711
kcal/mol
LE
-0.878
kcal/mol/HA
Fit Quality
-8.19
FQ (Leeson)
HAC
27
heavy atoms
MW
378
Da
LogP
2.27
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 14.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 12
π–π 2
Clashes 7
Severe clashes 1
⚠ Hydrophobic exposure 45%
Partial hydrophobic solvent exposure
45% of hydrophobic surface appears solvent-exposed (9/20 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 20
Buried (contacted) 11
Exposed 9
LogP 2.27
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 5.417837039329112 | Score | -23.7114 |
|---|---|---|---|
| Inter norm | -1.16631 | Intra norm | 0.287839 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash; high strain Δ 23.7 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS13;A:LYS178;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174;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 | 12 | Native recall | 0.63 |
| Jaccard | 0.55 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 358 | 4.004438895948854 | -1.12947 | -23.5798 | 3 | 14 | 10 | 0.53 | 0.40 | - | no | Open |
| 331 | 5.602887764862327 | -0.880775 | -19.0266 | 1 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 561 | 5.616389776825081 | -1.02465 | -23.7054 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 560 | 5.641678219640458 | -0.839733 | -17.9905 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 357 | 5.417837039329112 | -1.16631 | -23.7114 | 6 | 15 | 12 | 0.63 | 0.60 | - | yes | Current |
| 330 | 6.541513652330523 | -0.834209 | -16.5405 | 1 | 18 | 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
-23.711kcal/mol
Ligand efficiency (LE)
-0.8782kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.193
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
378.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.27
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
22.47kcal/mol
Minimised FF energy
7.74kcal/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.