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
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.185 kcal/mol/HA)
✓ Good fit quality (FQ -10.62)
✓ Good H-bonds (5 bonds)
✗ Moderate strain (8.1 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.442
kcal/mol
LE
-1.185
kcal/mol/HA
Fit Quality
-10.62
FQ (Leeson)
HAC
24
heavy atoms
MW
319
Da
LogP
2.43
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 6
Clashes 6
Severe clashes 1
| Final rank | 4.75548282926137 | Score | -28.4424 |
|---|---|---|---|
| Inter norm | -1.25695 | Intra norm | 0.0718491 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 12 clashes; 1 protein clash | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS178;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.75 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 126 | 3.346261047892889 | -1.14178 | -26.341 | 2 | 13 | 11 | 0.58 | 0.20 | - | no | Open |
| 168 | 3.8750009500436993 | -0.966408 | -22.5545 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 170 | 4.259848891787768 | -0.976324 | -20.4038 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 125 | 4.75548282926137 | -1.25695 | -28.4424 | 5 | 16 | 15 | 0.79 | 0.40 | - | yes | Current |
| 127 | 4.762114870323443 | -0.960783 | -20.5827 | 2 | 16 | 12 | 0.63 | 0.00 | - | yes | Open |
| 172 | 4.885622712999086 | -0.953284 | -18.7002 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 169 | 6.281793352458804 | -0.894601 | -20.7243 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 171 | 6.921382619854965 | -0.896362 | -20.1594 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 128 | 56.58294796157425 | -1.12966 | -26.4617 | 1 | 14 | 14 | 0.74 | 0.20 | - | yes | Open |
| 167 | 57.36914056148628 | -0.931533 | -20.3103 | 3 | 20 | 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
-28.442kcal/mol
Ligand efficiency (LE)
-1.1851kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.621
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
319.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.43
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
8.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.64kcal/mol
Minimised FF energy
35.58kcal/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.