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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.328 kcal/mol/HA)
✓ Good fit quality (FQ -12.81)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (16.3 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-39.833
kcal/mol
LE
-1.328
kcal/mol/HA
Fit Quality
-12.81
FQ (Leeson)
HAC
30
heavy atoms
MW
399
Da
LogP
2.84
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 16.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 4
Clashes 4
Severe clashes 0
| Final rank | 3.421159330711923 | Score | -39.8328 |
|---|---|---|---|
| Inter norm | -1.30787 | Intra norm | -0.0198866 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 6 |
| Artifact reason | geometry warning; 15 clashes; 4 protein contact clashes; moderate strain Δ 16.0 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;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 | 16 | Native recall | 0.84 |
| Jaccard | 0.80 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 223 | 3.1858172775679083 | -1.23148 | -37.5009 | 7 | 17 | 16 | 0.84 | 0.80 | - | no | Open |
| 89 | 3.421159330711923 | -1.30787 | -39.8328 | 6 | 17 | 16 | 0.84 | 0.80 | - | no | Current |
| 99 | 3.4721198023924362 | -1.23393 | -38.4263 | 4 | 18 | 16 | 0.84 | 0.60 | - | no | Open |
| 90 | 3.555956026672406 | -1.35194 | -41.1881 | 8 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
| 268 | 3.6445191534565207 | -0.802406 | -19.5407 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 3.7167456352456476 | -1.32763 | -40.8812 | 7 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
| 101 | 4.058612320414625 | -1.27331 | -37.5337 | 5 | 18 | 16 | 0.84 | 0.60 | - | no | Open |
| 96 | 4.095656485850893 | -0.795921 | -22.6999 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 225 | 4.328742379177729 | -1.25317 | -37.4868 | 6 | 17 | 16 | 0.84 | 0.80 | - | no | Open |
| 299 | 4.415693416521252 | -0.929381 | -28.5256 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 100 | 4.534880202538158 | -1.3248 | -40.6867 | 9 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
| 195 | 4.893796472953285 | -0.83355 | -23.7941 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 224 | 5.332544073186912 | -1.31566 | -36.354 | 9 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
| 300 | 5.523605867480585 | -0.974715 | -29.3448 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 6.888145404060353 | -1.07747 | -28.4735 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 196 | 7.120607776593641 | -1.07569 | -27.4595 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 301 | 8.645619895076276 | -0.994304 | -25.3242 | 10 | 18 | 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
-39.833kcal/mol
Ligand efficiency (LE)
-1.3278kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.808
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
399.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.84
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
128.30kcal/mol
Minimised FF energy
111.98kcal/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.