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 (-0.722 kcal/mol/HA)
✓ Good fit quality (FQ -7.03)
✓ Strong H-bond network (7 bonds)
✗ High strain energy (19.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-22.384
kcal/mol
LE
-0.722
kcal/mol/HA
Fit Quality
-7.03
FQ (Leeson)
HAC
31
heavy atoms
MW
579
Da
LogP
6.35
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 19.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 2
Clashes 13
Severe clashes 0
| Final rank | 5.42708209221541 | Score | -22.3835 |
|---|---|---|---|
| Inter norm | -0.860859 | Intra norm | 0.13881 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 7 |
| Artifact reason | geometry warning; 8 clashes; 13 protein contact clashes; high strain Δ 20.7 | ||
| Residues | A:ALA212;A:ARG14;A:LEU209;A:LYS13;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TYR98;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 | 9 | Native recall | 0.47 |
| Jaccard | 0.41 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2887 | 3.414963134473647 | -0.551203 | -14.229 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 3956 | 3.7660552795564186 | -0.766214 | -19.3411 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3268 | 3.7672505163013295 | -0.885791 | -23.5325 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2335 | 5.42708209221541 | -0.860859 | -22.3835 | 7 | 12 | 9 | 0.47 | 0.40 | - | no | Current |
| 3267 | 5.16073252267854 | -0.826746 | -21.5372 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3955 | 6.163318175457395 | -0.76589 | -20.2546 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2888 | 6.433157960684139 | -0.577658 | -13.742 | 3 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2336 | 7.073888021885322 | -1.1178 | -29.0905 | 3 | 18 | 15 | 0.79 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.384kcal/mol
Ligand efficiency (LE)
-0.7220kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.034
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
579.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.35
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
38.94kcal/mol
Minimised FF energy
19.24kcal/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.