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 (-0.706 kcal/mol/HA)
✓ Good fit quality (FQ -6.73)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (38.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-20.459
kcal/mol
LE
-0.706
kcal/mol/HA
Fit Quality
-6.73
FQ (Leeson)
HAC
29
heavy atoms
MW
428
Da
LogP
4.13
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 38.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 3
Clashes 13
Severe clashes 2
| Final rank | 57.473277396142976 | Score | -20.459 |
|---|---|---|---|
| Inter norm | -1.07679 | Intra norm | 0.371308 |
| Top1000 | no | Excluded | yes |
| Contacts | 18 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 9 clashes; 2 protein clashes; high strain Δ 38.7 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL164;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 | 0.61 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 370 | 2.3383136773503708 | -0.872658 | -23.5022 | 2 | 15 | 15 | 0.79 | 0.00 | - | no | Open |
| 1454 | 3.196696243841163 | -0.754096 | -20.3144 | 1 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1453 | 3.6035711837592688 | -0.692876 | -14.8813 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 513 | 3.9819855414167846 | -0.770045 | -22.0967 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 5.290306243752046 | -0.779382 | -19.7942 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1847 | 5.4312798056880816 | -0.874831 | -22.5239 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 512 | 9.10946685161051 | -0.785602 | -19.0233 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 396 | 55.739825177777384 | -0.776563 | -17.428 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 369 | 57.473277396142976 | -1.07679 | -20.459 | 3 | 18 | 14 | 0.74 | 0.00 | - | yes | Current |
| 1846 | 58.78976647395454 | -0.768065 | -20.3155 | 3 | 15 | 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
-20.459kcal/mol
Ligand efficiency (LE)
-0.7055kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.734
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
427.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
84.29kcal/mol
Minimised FF energy
45.61kcal/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.