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 (-0.957 kcal/mol/HA)
✓ Good fit quality (FQ -9.32)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (25.6 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-29.673
kcal/mol
LE
-0.957
kcal/mol/HA
Fit Quality
-9.32
FQ (Leeson)
HAC
31
heavy atoms
MW
418
Da
LogP
3.00
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 25.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 5
Clashes 7
Severe clashes 0
| Final rank | 5.400652215111898 | Score | -29.6732 |
|---|---|---|---|
| Inter norm | -1.00289 | Intra norm | 0.0456875 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 6 |
| Artifact reason | geometry warning; 17 clashes; 7 protein contact clashes; high strain Δ 25.3 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL206 | ||
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 | 17 | Native recall | 0.89 |
| Jaccard | 0.81 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 338 | 4.30344868335865 | -0.982321 | -30.4433 | 7 | 17 | 15 | 0.79 | 0.40 | - | no | Open |
| 273 | 4.686171315488087 | -0.63408 | -18.8224 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 481 | 4.890836947739789 | -1.01821 | -31.341 | 6 | 19 | 17 | 0.89 | 0.60 | - | no | Open |
| 337 | 5.142744230564611 | -0.984747 | -28.4413 | 7 | 16 | 16 | 0.84 | 0.40 | - | no | Open |
| 480 | 5.165106327420536 | -1.02849 | -31.2916 | 6 | 17 | 16 | 0.84 | 0.60 | - | no | Open |
| 335 | 5.235768030452294 | -0.959781 | -26.4174 | 4 | 16 | 15 | 0.79 | 0.40 | - | no | Open |
| 336 | 5.373058815181301 | -0.994641 | -28.9981 | 7 | 17 | 15 | 0.79 | 0.40 | - | no | Open |
| 478 | 5.400652215111898 | -1.00289 | -29.6732 | 6 | 19 | 17 | 0.89 | 0.60 | - | no | Current |
| 466 | 7.211126743405219 | -0.662419 | -17.4669 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 7.307481733132459 | -0.708796 | -15.6296 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 479 | 55.01644585145063 | -1.03446 | -29.5939 | 6 | 19 | 16 | 0.84 | 0.60 | - | no | Open |
| 465 | 9.377851986553342 | -0.841964 | -17.4762 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 272 | 56.082892562415005 | -0.739871 | -16.5868 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 463 | 60.61271507046932 | -0.798729 | -22.2983 | 5 | 14 | 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
-29.673kcal/mol
Ligand efficiency (LE)
-0.9572kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.325
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
418.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.00
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-86.94kcal/mol
Minimised FF energy
-112.58kcal/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.