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 (-1.036 kcal/mol/HA)
✓ Good fit quality (FQ -9.99)
✓ Strong H-bond network (10 bonds)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.081
kcal/mol
LE
-1.036
kcal/mol/HA
Fit Quality
-9.99
FQ (Leeson)
HAC
30
heavy atoms
MW
446
Da
LogP
2.65
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 31.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 10
Hydrophobic 17
π–π 2
Clashes 6
Severe clashes 2
| Final rank | 6.936586780666548 | Score | -31.0807 |
|---|---|---|---|
| Inter norm | -1.04711 | Intra norm | 0.00912875 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 10 |
| Artifact reason | excluded; geometry warning; 10 clashes; 2 protein clashes; high strain Δ 34.7 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS13;A:NAP301;A:PHE97;A:PRO210;A:TRP221;A:TYR174;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 | 12 | Native recall | 0.63 |
| Jaccard | 0.60 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 669 | 3.8922765320298804 | -0.772346 | -23.2202 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1382 | 4.642601901256108 | -0.678033 | -19.9602 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 664 | 4.750332289710839 | -0.88385 | -25.3615 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1379 | 4.779271309829299 | -0.681149 | -21.0229 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 666 | 5.513766713286891 | -0.863036 | -19.3766 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1377 | 5.6643976693458775 | -0.650903 | -18.8759 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 868 | 5.674391699985516 | -0.946675 | -27.7469 | 9 | 17 | 16 | 0.84 | 0.80 | - | no | Open |
| 1381 | 5.886343167336648 | -0.736858 | -20.6793 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1239 | 5.908800315013041 | -0.696744 | -18.9376 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2128 | 5.914229069986902 | -0.818688 | -25.4767 | 1 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 6.169856997701089 | -0.84472 | -24.5236 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2129 | 6.2214407052564145 | -0.748765 | -20.9338 | 0 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1241 | 6.863308812971197 | -0.602247 | -17.3624 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1065 | 7.0324287513726365 | -0.663848 | -18.4035 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1380 | 7.288408200186212 | -0.754263 | -20.827 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 665 | 5.684297625290064 | -0.916521 | -26.3515 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2127 | 5.844616105203985 | -0.8037 | -24.7428 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1378 | 6.229523561042825 | -0.672605 | -20.5375 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 668 | 6.737119225520541 | -0.857366 | -24.9811 | 1 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 869 | 6.936586780666548 | -1.04711 | -31.0807 | 10 | 13 | 12 | 0.63 | 0.40 | - | yes | Current |
| 867 | 7.313702586179983 | -0.931335 | -24.7235 | 9 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1383 | 7.400611302871373 | -0.616353 | -17.0373 | 5 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1064 | 7.576988738420098 | -0.875363 | -25.7204 | 10 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 866 | 7.7744810733977285 | -1.14564 | -34.7998 | 11 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1063 | 8.31433797845171 | -0.888004 | -22.2524 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2130 | 8.347464761416191 | -0.85248 | -21.7854 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1243 | 8.82251081094913 | -0.636435 | -17.2373 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1242 | 10.418018329946815 | -0.780717 | -23.4612 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1240 | 11.210647318805645 | -0.757182 | -20.0427 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2131 | 11.293243709494899 | -0.825709 | -19.4923 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1238 | 11.399224789178154 | -0.5628 | -17.4864 | 5 | 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
-31.081kcal/mol
Ligand efficiency (LE)
-1.0360kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.994
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
445.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.65
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
20.69kcal/mol
Minimised FF energy
-10.64kcal/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.