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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.780 kcal/mol/HA)
✓ Good fit quality (FQ -7.74)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (26.7 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.729
kcal/mol
LE
-0.780
kcal/mol/HA
Fit Quality
-7.74
FQ (Leeson)
HAC
33
heavy atoms
MW
457
Da
LogP
3.92
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 26.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 3
Clashes 12
Severe clashes 0
| Final rank | 8.945918274633572 | Score | -25.7285 |
|---|---|---|---|
| Inter norm | -0.972896 | Intra norm | 0.193245 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 22 clashes; 12 protein contact clashes; high strain Δ 42.9 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:TRP221;A:TYR174;A:TYR98;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 | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 897 | 5.53811197605785 | -0.625265 | -15.9527 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1701 | 6.218606625679716 | -0.589 | -15.9327 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1302 | 6.470102764328849 | -0.729731 | -21.0126 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1154 | 6.558393565003106 | -0.954204 | -27.78 | 7 | 19 | 13 | 0.68 | 0.40 | - | no | Open |
| 1156 | 7.85978010280971 | -0.915875 | -27.2689 | 5 | 20 | 12 | 0.63 | 0.20 | - | no | Open |
| 1151 | 8.945918274633572 | -0.972896 | -25.7285 | 8 | 16 | 13 | 0.68 | 0.40 | - | no | Current |
| 1702 | 7.206234642980627 | -0.569592 | -10.953 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1705 | 7.405579087531156 | -0.590684 | -10.5833 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1300 | 7.659985865325133 | -0.783145 | -26.223 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1153 | 8.210054665774791 | -0.87117 | -26.2586 | 8 | 19 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1152 | 8.582389869685048 | -0.904738 | -25.3038 | 12 | 18 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1706 | 8.80232087381207 | -0.617411 | -17.6499 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1297 | 8.941772138479958 | -0.881279 | -26.9132 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1155 | 9.12540327366498 | -0.844638 | -21.035 | 4 | 18 | 12 | 0.63 | 0.20 | - | yes | Open |
| 901 | 9.52985094404211 | -0.602101 | -15.3011 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 899 | 10.416633230013058 | -0.558836 | -18.0835 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1299 | 10.423180365678041 | -0.725287 | -13.9931 | 12 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1301 | 10.637110262895824 | -0.891439 | -22.0875 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1704 | 11.068475813422337 | -0.619822 | -10.8087 | 5 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1298 | 11.280915198790206 | -0.753502 | -15.0852 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 900 | 11.404806029538733 | -0.651046 | -17.2327 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1703 | 11.964540230823818 | -0.522026 | -9.00449 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 898 | 12.179781502714734 | -0.557501 | -11.6164 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 896 | 12.773703348126334 | -0.682652 | -16.3925 | 8 | 14 | 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
-25.729kcal/mol
Ligand efficiency (LE)
-0.7797kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.736
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
457.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.92
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.73kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.73kcal/mol
Minimised FF energy
72.00kcal/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.