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 (-1.004 kcal/mol/HA)
✓ Good fit quality (FQ -9.96)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (31.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-33.135
kcal/mol
LE
-1.004
kcal/mol/HA
Fit Quality
-9.96
FQ (Leeson)
HAC
33
heavy atoms
MW
489
Da
LogP
1.87
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 4
Hydrophobic 24
π–π 3
Clashes 11
Severe clashes 1
| Final rank | 8.340255251751657 | Score | -33.1349 |
|---|---|---|---|
| Inter norm | -0.963491 | Intra norm | -0.040596 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 14 clashes; 1 protein clash; high strain Δ 39.6 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:TRP221;A:TYR174;A:VAL206;D:HIS267 | ||
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 | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 560 | 5.361935577660347 | -0.442118 | -13.4612 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 329 | 5.4476484884868235 | -0.670264 | -19.0797 | 0 | 18 | 15 | 0.79 | 0.00 | - | no | Open |
| 328 | 6.469701678479211 | -0.887545 | -27.5912 | 2 | 19 | 15 | 0.79 | 0.00 | - | no | Open |
| 559 | 6.762194051194756 | -0.667356 | -15.746 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 534 | 7.237307039609728 | -0.628827 | -18.9505 | 2 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 532 | 8.346075822945409 | -0.624845 | -19.1316 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 561 | 7.841296062863094 | -0.504614 | -14.0323 | 3 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 330 | 8.340255251751657 | -0.963491 | -33.1349 | 4 | 15 | 11 | 0.58 | 0.00 | - | yes | Current |
| 533 | 9.5346180834116 | -0.653776 | -20.9196 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 562 | 55.7265951811803 | -0.52394 | -13.4643 | 3 | 12 | 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
-33.135kcal/mol
Ligand efficiency (LE)
-1.0041kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.962
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
489.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.43kcal/mol
Minimised FF energy
62.16kcal/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.