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 (-1.068 kcal/mol/HA)
✓ Good fit quality (FQ -10.19)
✓ Good H-bonds (5 bonds)
✗ High strain energy (16.8 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-30.966
kcal/mol
LE
-1.068
kcal/mol/HA
Fit Quality
-10.19
FQ (Leeson)
HAC
29
heavy atoms
MW
406
Da
LogP
4.77
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 16.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 5
Clashes 15
Severe clashes 3
| Final rank | 9.337208204140472 | Score | -30.9663 |
|---|---|---|---|
| Inter norm | -1.13725 | Intra norm | 0.0694432 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 9 clashes; 3 protein clashes; high strain Δ 20.2 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;A:NAP301;A:PHE97;A:SER95;A:TRP221;A:TYR174;A:VAL206;D:HIS267 | ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.59 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 3152 | 2.7579956849187175 | -0.878597 | -26.6463 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2674 | 4.4516764824536175 | -0.798642 | -22.469 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2214 | 5.139814124543248 | -0.922463 | -27.9165 | 3 | 17 | 14 | 0.74 | 0.40 | - | no | Open |
| 3153 | 5.624806773008751 | -0.904941 | -28.8219 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2672 | 5.874045561805357 | -0.659252 | -20.3391 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3154 | 6.257420675520935 | -0.766625 | -23.3372 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2213 | 6.641947121768947 | -0.98327 | -28.2933 | 6 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2215 | 6.688919328324171 | -0.958953 | -27.2615 | 6 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2676 | 7.649519352897946 | -0.607324 | -18.9177 | 5 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3155 | 8.143062988875135 | -0.795634 | -24.7112 | 2 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2675 | 8.582234440119034 | -0.655823 | -23.0224 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2673 | 8.733873976281536 | -0.819674 | -22.8534 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2212 | 9.337208204140472 | -1.13725 | -30.9663 | 5 | 16 | 13 | 0.68 | 0.60 | - | yes | Current |
| 2677 | 10.237349671390962 | -0.685877 | -20.7905 | 6 | 13 | 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
-30.966kcal/mol
Ligand efficiency (LE)
-1.0678kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.193
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
405.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.77
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
66.36kcal/mol
Minimised FF energy
49.55kcal/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.