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 (-0.626 kcal/mol/HA)
✓ Good fit quality (FQ -5.69)
✓ Good H-bonds (4 bonds)
✗ High strain energy (15.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-15.660
kcal/mol
LE
-0.626
kcal/mol/HA
Fit Quality
-5.69
FQ (Leeson)
HAC
25
heavy atoms
MW
344
Da
LogP
2.08
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 15.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 2
Clashes 12
Severe clashes 1
| Final rank | 6.865034736574391 | Score | -15.6596 |
|---|---|---|---|
| Inter norm | -0.642758 | Intra norm | 0.0163732 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash; moderate strain Δ 15.6 | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:TRP221;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 253 | 6.940391670352547 | -0.617226 | -14.1169 | 10 | 15 | 14 | 0.74 | 0.60 | - | no | Open |
| 251 | 4.604457747254389 | -1.32222 | -32.4251 | 9 | 14 | 13 | 0.68 | 0.60 | - | yes | Open |
| 247 | 4.663386289268596 | -1.4479 | -35.08 | 9 | 16 | 15 | 0.79 | 0.60 | - | yes | Open |
| 255 | 5.098194977650718 | -1.23081 | -30.222 | 9 | 15 | 13 | 0.68 | 0.60 | - | yes | Open |
| 257 | 6.332033946357751 | -0.695458 | -15.1174 | 2 | 17 | 13 | 0.68 | 0.20 | - | yes | Open |
| 250 | 6.865034736574391 | -0.642758 | -15.6596 | 4 | 16 | 14 | 0.74 | 0.40 | - | yes | Current |
| 248 | 8.67822563607149 | -1.20593 | -29.3986 | 7 | 17 | 16 | 0.84 | 0.60 | - | yes | Open |
| 254 | 9.009653382181178 | -0.695281 | -15.8435 | 3 | 17 | 14 | 0.74 | 0.20 | - | yes | Open |
| 249 | 9.132964637938462 | -0.729481 | -17.8293 | 5 | 13 | 13 | 0.68 | 0.40 | - | yes | Open |
| 252 | 58.319481585561334 | -1.12908 | -28.0199 | 7 | 15 | 14 | 0.74 | 0.60 | - | yes | Open |
| 246 | 59.14568617759906 | -0.744521 | -17.8929 | 5 | 14 | 13 | 0.68 | 0.40 | - | yes | Open |
| 256 | 60.069848521623314 | -0.946767 | -23.6052 | 6 | 16 | 15 | 0.79 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-15.660kcal/mol
Ligand efficiency (LE)
-0.6264kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.694
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
344.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.08
Lipinski: ≤ 5
Rotatable bonds
1
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.55kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.05kcal/mol
Minimised FF energy
40.50kcal/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.