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 (-0.756 kcal/mol/HA)
✓ Good fit quality (FQ -7.50)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (38.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.948
kcal/mol
LE
-0.756
kcal/mol/HA
Fit Quality
-7.50
FQ (Leeson)
HAC
33
heavy atoms
MW
490
Da
LogP
0.45
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 38.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 14
π–π 2
Clashes 4
Severe clashes 0
| Final rank | 5.200928899941576 | Score | -24.9476 |
|---|---|---|---|
| Inter norm | -0.840416 | Intra norm | 0.0844276 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 4 |
| Artifact reason | geometry warning; 13 clashes; 4 protein contact clashes; high strain Δ 44.4 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:LYS114;A:LYS13;A:NAP301;A:PHE97;A:PRO210;A:SER95;A:TYR174;A:TYR98;A:VAL211 | ||
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 | 8 | Native recall | 0.42 |
| Jaccard | 0.35 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 386 | 5.085288510691997 | -0.710606 | -20.7985 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 428 | 5.200928899941576 | -0.840416 | -24.9476 | 4 | 12 | 8 | 0.42 | 0.20 | - | no | Current |
| 426 | 6.409115044551615 | -0.832693 | -24.7562 | 8 | 13 | 11 | 0.58 | 0.40 | - | no | Open |
| 352 | 6.784018793191597 | -0.722913 | -20.125 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 519 | 7.200618088230804 | -0.646882 | -16.4173 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 351 | 7.382749137583236 | -0.652739 | -17.9865 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 520 | 7.811156201947812 | -0.615289 | -18.7174 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 425 | 8.084470919690176 | -0.837646 | -22.8532 | 8 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 429 | 8.514623065145567 | -0.904015 | -23.3915 | 3 | 15 | 12 | 0.63 | 0.20 | - | yes | Open |
| 388 | 8.604300193071667 | -0.791234 | -23.8674 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 385 | 9.841987897063017 | -0.688551 | -17.7444 | 9 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 387 | 58.864497368582974 | -0.643644 | -17.7356 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 427 | 59.950991929186905 | -0.863919 | -25.9306 | 3 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 518 | 60.30165008406329 | -0.709683 | -21.4521 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 384 | 62.42327380424096 | -0.724805 | -21.5218 | 3 | 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
-24.948kcal/mol
Ligand efficiency (LE)
-0.7560kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.501
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
490.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.45
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.10kcal/mol
Minimised FF energy
96.11kcal/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.