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 (-0.681 kcal/mol/HA)
✓ Good fit quality (FQ -6.81)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (28.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-23.145
kcal/mol
LE
-0.681
kcal/mol/HA
Fit Quality
-6.81
FQ (Leeson)
HAC
34
heavy atoms
MW
476
Da
LogP
2.21
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 28.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 4
Clashes 11
Severe clashes 0
| Final rank | 7.22100360803336 | Score | -23.1455 |
|---|---|---|---|
| Inter norm | -0.859112 | Intra norm | 0.178362 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | geometry warning; 18 clashes; 11 protein contact clashes; high strain Δ 27.4 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98;A:VAL206 | ||
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 | 16 | Native recall | 0.84 |
| Jaccard | 0.80 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 595 | 3.9341581049443373 | -0.710666 | -24.4966 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 581 | 4.282745008505717 | -0.68514 | -21.7812 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 483 | 5.2731107880362655 | -0.456027 | -14.805 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 525 | 5.673400274663612 | -0.620281 | -16.6317 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 355 | 6.008002756593954 | -0.848434 | -24.5052 | 6 | 15 | 12 | 0.63 | 0.20 | - | no | Open |
| 458 | 6.353833965137834 | -0.573579 | -16.4356 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 6.553898090852462 | -0.595387 | -20.1733 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 356 | 7.22100360803336 | -0.859112 | -23.1455 | 3 | 17 | 16 | 0.84 | 0.20 | - | no | Current |
| 587 | 7.5607842448802085 | -0.654499 | -19.1132 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 484 | 7.60209807389249 | -0.432026 | -14.2696 | 3 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 585 | 7.9277803557794595 | -0.751934 | -23.4535 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 582 | 8.265578791653883 | -0.737044 | -24.0613 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 298 | 8.293629467447701 | -0.723532 | -22.4786 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 457 | 8.38952515541677 | -0.64544 | -22.9491 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 597 | 8.41994214849559 | -0.925503 | -28.3157 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 586 | 10.136144917381559 | -0.651522 | -21.4293 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 583 | 10.500702289716479 | -0.733825 | -22.7596 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 523 | 10.835684701034554 | -0.615721 | -19.452 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 299 | 11.567318324474874 | -0.690034 | -22.0973 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 524 | 11.690269149733975 | -0.711682 | -23.8607 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 596 | 12.488535517146342 | -0.848985 | -25.4123 | 4 | 15 | 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
-23.145kcal/mol
Ligand efficiency (LE)
-0.6807kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.812
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
475.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.21
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.30kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
87.24kcal/mol
Minimised FF energy
58.94kcal/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.