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 (-0.876 kcal/mol/HA)
✓ Good fit quality (FQ -8.70)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (34.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.925
kcal/mol
LE
-0.876
kcal/mol/HA
Fit Quality
-8.70
FQ (Leeson)
HAC
33
heavy atoms
MW
471
Da
LogP
1.54
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 34.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 2
Clashes 8
Severe clashes 0
| Final rank | 5.278968410304379 | Score | -28.9249 |
|---|---|---|---|
| Inter norm | -0.985977 | Intra norm | 0.109464 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 8 protein contact clashes; high strain Δ 34.1 | ||
| Residues | A:ALA96;A:ARG14;A:CYS168;A:GLU217;A:GLY205;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 434 | 4.456996322894289 | -0.531388 | -18.8379 | 2 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 424 | 4.528322462088256 | -0.688843 | -18.1325 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 437 | 4.849139461292341 | -0.593807 | -19.1876 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 438 | 4.948638766001479 | -0.955453 | -32.2024 | 4 | 16 | 14 | 0.74 | 0.20 | - | no | Open |
| 422 | 5.030200640419314 | -0.638629 | -18.2511 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 439 | 5.278968410304379 | -0.985977 | -28.9249 | 8 | 15 | 13 | 0.68 | 0.40 | - | no | Current |
| 391 | 5.450553624473277 | -0.616694 | -18.6622 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 425 | 5.584263536951543 | -0.627099 | -19.2035 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 393 | 5.710246405518468 | -0.777083 | -23.5659 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 440 | 6.511761445613525 | -0.486658 | -14.0877 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 541 | 6.598142479138917 | -0.700926 | -21.073 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 392 | 6.7715681865957835 | -0.662095 | -16.4205 | 1 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 387 | 7.093652330376924 | -0.724201 | -23.4788 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 8.052655510670427 | -0.585368 | -17.3389 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 438 | 5.723765445293511 | -0.533092 | -14.5972 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 549 | 6.252241887285235 | -0.613646 | -17.5768 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 543 | 6.377444244024381 | -0.638333 | -18.965 | 2 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 436 | 6.72045132913513 | -0.594331 | -11.3563 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 440 | 6.750753314471163 | -0.967531 | -26.4897 | 6 | 19 | 13 | 0.68 | 0.40 | - | yes | Open |
| 545 | 7.234184722469295 | -0.637684 | -21.1199 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 548 | 7.403316755903007 | -0.632707 | -20.8002 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 428 | 7.446528870819005 | -0.836962 | -22.2953 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 394 | 7.55184594641649 | -0.691504 | -21.9629 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 392 | 7.997241099158538 | -0.826412 | -24.3048 | 11 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 426 | 8.164069743370593 | -0.51977 | -15.9675 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 442 | 8.175013983476727 | -0.961746 | -29.356 | 4 | 16 | 13 | 0.68 | 0.20 | - | yes | Open |
| 390 | 8.251485434079314 | -0.857986 | -25.9459 | 13 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 433 | 8.267285131072356 | -0.565958 | -17.4953 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 540 | 8.30385201927366 | -0.723672 | -21.3961 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 423 | 8.569785298996283 | -0.789865 | -21.947 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 544 | 8.64709174434811 | -0.704658 | -21.6805 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 391 | 8.807668029147248 | -0.748717 | -22.5146 | 10 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 444 | 8.819832162858637 | -0.958514 | -27.0437 | 6 | 19 | 14 | 0.74 | 0.40 | - | yes | Open |
| 396 | 9.061670445186238 | -0.686082 | -18.1156 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 546 | 9.71834974962832 | -0.76395 | -23.605 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 385 | 10.08798920369021 | -0.616846 | -15.9771 | 7 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 389 | 10.117559782958857 | -0.655812 | -18.8498 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 443 | 10.208072263639407 | -0.955781 | -29.9015 | 6 | 17 | 11 | 0.58 | 0.60 | - | yes | Open |
| 388 | 10.964522120209883 | -0.775684 | -23.2208 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 384 | 12.478635709588078 | -0.812216 | -22.8974 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 435 | 57.424626779536865 | -0.586668 | -14.174 | 5 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 439 | 57.50717372986112 | -0.590213 | -15.6451 | 4 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 421 | 57.88112885252023 | -0.542499 | -16.9639 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 542 | 57.947241220805616 | -0.687206 | -20.3362 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 427 | 58.036760833819315 | -0.676412 | -13.4779 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 397 | 58.48498350222056 | -0.634866 | -20.3938 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 547 | 59.43702208647829 | -0.601044 | -16.832 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 390 | 59.59261102622274 | -0.74573 | -23.1418 | 4 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 437 | 59.90977727864694 | -0.809152 | -24.5361 | 7 | 18 | 12 | 0.63 | 0.40 | - | yes | Open |
| 393 | 60.33579344457996 | -0.792917 | -20.1177 | 11 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 386 | 60.3976517509893 | -0.702436 | -12.5469 | 10 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 441 | 61.23092989594881 | -0.968924 | -29.5507 | 6 | 20 | 12 | 0.63 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.925kcal/mol
Ligand efficiency (LE)
-0.8765kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.697
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
470.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.54
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
34.61kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.28kcal/mol
Minimised FF energy
17.68kcal/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.