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 (-0.903 kcal/mol/HA)
✓ Good fit quality (FQ -9.11)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (28.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-31.616
kcal/mol
LE
-0.903
kcal/mol/HA
Fit Quality
-9.11
FQ (Leeson)
HAC
35
heavy atoms
MW
480
Da
LogP
-0.01
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 28.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 4
Clashes 15
Severe clashes 1
| Final rank | 8.520788843301084 | Score | -31.6164 |
|---|---|---|---|
| Inter norm | -0.992785 | Intra norm | 0.0894588 |
| Top1000 | no | Excluded | yes |
| Contacts | 20 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 12 clashes; 1 protein clash; high strain Δ 31.1 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS178;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;A:TRP221;A:TYR174;A:TYR98;A:VAL206 | ||
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 | 18 | Native recall | 0.95 |
| Jaccard | 0.86 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 83 | 4.5873042972521745 | -1.18023 | -37.295 | 12 | 19 | 16 | 0.84 | 0.80 | - | no | Open |
| 84 | 4.716284470380016 | -1.09848 | -42.8105 | 8 | 20 | 18 | 0.95 | 0.80 | - | no | Open |
| 31 | 7.9812868098249865 | -0.824199 | -24.5192 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 82 | 6.8224046072338265 | -1.16339 | -37.9011 | 15 | 19 | 17 | 0.89 | 0.80 | - | yes | Open |
| 80 | 6.891582329858192 | -1.30717 | -37.5358 | 9 | 20 | 15 | 0.79 | 0.80 | - | yes | Open |
| 81 | 8.520788843301084 | -0.992785 | -31.6164 | 4 | 20 | 18 | 0.95 | 0.60 | - | yes | Current |
| 85 | 9.480117931138652 | -1.17124 | -38.3097 | 10 | 23 | 17 | 0.89 | 0.80 | - | yes | Open |
| 30 | 9.72018397125011 | -0.872739 | -24.9929 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 29 | 10.167993748513384 | -0.887012 | -25.4193 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 28 | 12.648802136135362 | -1.00556 | -32.4774 | 9 | 16 | 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
-31.616kcal/mol
Ligand efficiency (LE)
-0.9033kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.111
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
479.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.01
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
139.16kcal/mol
Minimised FF energy
110.98kcal/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.