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 (-1.115 kcal/mol/HA)
✓ Good fit quality (FQ -10.86)
✓ Strong H-bond network (9 bonds)
✗ High strain energy (18.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-34.559
kcal/mol
LE
-1.115
kcal/mol/HA
Fit Quality
-10.86
FQ (Leeson)
HAC
31
heavy atoms
MW
417
Da
LogP
3.02
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 18.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 6
Clashes 8
Severe clashes 2
| Final rank | 7.357415661344403 | Score | -34.5592 |
|---|---|---|---|
| Inter norm | -1.25747 | Intra norm | 0.12969 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 16 clashes; 2 protein clashes; moderate strain Δ 17.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206;D:HIS267 | ||
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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.83 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 206 | 3.62518003355243 | -1.15957 | -31.5435 | 7 | 18 | 15 | 0.79 | 0.80 | - | no | Open |
| 199 | 4.202675710840571 | -0.904928 | -26.0653 | 11 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 177 | 4.7825035427253315 | -0.724736 | -21.6806 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 208 | 5.56163375977375 | -1.27976 | -33.3386 | 10 | 17 | 15 | 0.79 | 0.80 | - | no | Open |
| 238 | 6.5021490482611854 | -1.01128 | -28.6914 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 240 | 8.048534187557069 | -0.937664 | -16.8084 | 3 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 207 | 5.72548440102922 | -1.22278 | -33.4571 | 7 | 16 | 15 | 0.79 | 0.80 | - | yes | Open |
| 200 | 6.232864882160108 | -0.830738 | -24.814 | 10 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 201 | 6.4696044670287485 | -0.845079 | -19.2167 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 237 | 6.518007267026661 | -0.936931 | -25.8277 | 10 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 205 | 7.357415661344403 | -1.25747 | -34.5592 | 9 | 16 | 14 | 0.74 | 0.80 | - | yes | Current |
| 198 | 7.813567380863088 | -0.770268 | -21.9739 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 178 | 7.960284270164372 | -0.912308 | -27.3911 | 12 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 239 | 9.61435439629328 | -0.873592 | -20.8094 | 4 | 19 | 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
-34.559kcal/mol
Ligand efficiency (LE)
-1.1148kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.861
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.02
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.50kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
116.57kcal/mol
Minimised FF energy
98.08kcal/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.