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 (-1.354 kcal/mol/HA)
✓ Good fit quality (FQ -12.13)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (31.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-32.490
kcal/mol
LE
-1.354
kcal/mol/HA
Fit Quality
-12.13
FQ (Leeson)
HAC
24
heavy atoms
MW
326
Da
LogP
1.54
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 31.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 2
Clashes 10
Severe clashes 1
| Final rank | 6.976288637729562 | Score | -32.4902 |
|---|---|---|---|
| Inter norm | -1.37122 | Intra norm | 0.0174658 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 9 clashes; 1 protein clash; high strain Δ 43.6 | ||
| 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: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 | 12 | Native recall | 0.63 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2108 | 4.611660033386082 | -1.2811 | -35.4461 | 6 | 17 | 13 | 0.68 | 0.40 | - | no | Open |
| 2828 | 4.963501568761817 | -1.0687 | -29.4649 | 13 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2830 | 5.210627492933232 | -0.848085 | -25.6254 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2102 | 5.638385663781495 | -0.628008 | -19.8453 | 5 | 13 | 11 | 0.58 | 0.00 | - | yes | Open |
| 2104 | 6.55615323268211 | -1.33547 | -34.5059 | 7 | 19 | 15 | 0.79 | 0.40 | - | yes | Open |
| 2103 | 6.976288637729562 | -1.37122 | -32.4902 | 6 | 16 | 12 | 0.63 | 0.40 | - | yes | Current |
| 2106 | 7.515141940518402 | -0.700841 | -22.4901 | 2 | 14 | 11 | 0.58 | 0.00 | - | yes | Open |
| 2829 | 8.149959326718292 | -0.90048 | -24.4791 | 11 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2107 | 8.907793578370384 | -1.2676 | -37.8596 | 6 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 2827 | 57.27432270677918 | -0.693559 | -16.4165 | 10 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2109 | 59.06391079933566 | -1.22859 | -31.2828 | 8 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2105 | 59.098870444999214 | -1.26093 | -32.4916 | 8 | 14 | 14 | 0.74 | 0.40 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-32.490kcal/mol
Ligand efficiency (LE)
-1.3538kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.132
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
326.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.54
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
159.75kcal/mol
Minimised FF energy
128.13kcal/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.