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 (-0.530 kcal/mol/HA)
✓ Good fit quality (FQ -5.57)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (37.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-21.729
kcal/mol
LE
-0.530
kcal/mol/HA
Fit Quality
-5.57
FQ (Leeson)
HAC
41
heavy atoms
MW
559
Da
LogP
5.24
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 37.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 4
Clashes 12
Severe clashes 3
| Final rank | 11.834791345463259 | Score | -21.7294 |
|---|---|---|---|
| Inter norm | -0.701664 | Intra norm | 0.17168 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 17 clashes; 3 protein clashes; high strain Δ 44.2 | ||
| Residues | A:ALA212;A:ARG14;A:CYS168;A:GLU217;A:GLY214;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221 | ||
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 | 11 | Native recall | 0.58 |
| Jaccard | 0.48 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1216 | 6.740078592823252 | -0.325149 | -15.3861 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 659 | 6.848418995845831 | -0.54587 | -23.877 | 4 | 20 | 16 | 0.84 | 0.40 | - | no | Open |
| 1981 | 7.845023095666477 | -0.596057 | -24.1773 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1214 | 8.353105962035386 | -0.352087 | -11.2766 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1980 | 8.62717503630049 | -0.542338 | -10.0763 | 5 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 725 | 9.007211441369193 | -0.593522 | -18.8241 | 12 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1215 | 7.833416664295393 | -0.560892 | -25.23 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 657 | 8.075010895861169 | -0.738794 | -19.4295 | 4 | 18 | 15 | 0.79 | 0.40 | - | yes | Open |
| 656 | 8.728379444359497 | -0.654342 | -22.5585 | 7 | 15 | 12 | 0.63 | 0.40 | - | yes | Open |
| 655 | 11.433017028869171 | -0.718765 | -22.867 | 8 | 14 | 12 | 0.63 | 0.40 | - | yes | Open |
| 721 | 11.45130099675172 | -0.572249 | -14.229 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 654 | 11.834791345463259 | -0.701664 | -21.7294 | 9 | 15 | 11 | 0.58 | 0.40 | - | yes | Current |
| 724 | 12.698945712085667 | -0.503827 | -15.3486 | 12 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1982 | 12.854686527239082 | -0.516573 | -18.0504 | 2 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 720 | 14.67261542569625 | -0.606699 | -19.1125 | 14 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 723 | 15.52370107514838 | -0.592153 | -11.84 | 11 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 658 | 57.70738440415127 | -0.624437 | -23.3459 | 5 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1213 | 57.756968558170655 | -0.446925 | -17.3103 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1979 | 61.56503445513917 | -0.591115 | -19.0257 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 722 | 62.71962787254789 | -0.663494 | -18.6148 | 16 | 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
-21.729kcal/mol
Ligand efficiency (LE)
-0.5300kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.569
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
41HA
Physicochemical properties
Molecular weight
558.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.24
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
147.26kcal/mol
Minimised FF energy
109.31kcal/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.