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 (-1.299 kcal/mol/HA)
✓ Good fit quality (FQ -12.40)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (32.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-37.664
kcal/mol
LE
-1.299
kcal/mol/HA
Fit Quality
-12.40
FQ (Leeson)
HAC
29
heavy atoms
MW
392
Da
LogP
1.85
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 32.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 3
Clashes 1
Severe clashes 0
| Final rank | 2.845547249397635 | Score | -37.6645 |
|---|---|---|---|
| Inter norm | -1.23023 | Intra norm | -0.0685471 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 1 protein contact clash; high strain Δ 32.2 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.83 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 82 | 2.845547249397635 | -1.23023 | -37.6645 | 7 | 17 | 15 | 0.79 | 0.80 | - | no | Current |
| 84 | 2.8921848619815904 | -1.25496 | -37.7142 | 6 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
| 83 | 3.04027547708536 | -1.31011 | -40.3971 | 8 | 18 | 16 | 0.84 | 0.80 | - | no | Open |
| 56 | 3.3633971384109724 | -0.889546 | -23.6866 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 84 | 4.24799337945639 | -0.791827 | -22.7525 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 86 | 5.231282017838392 | -1.00775 | -31.4427 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 85 | 5.525046159799851 | -0.835961 | -25.9689 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 58 | 6.850903484624114 | -0.951751 | -29.1576 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 57 | 9.740356828460516 | -0.927401 | -27.0133 | 9 | 17 | 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
-37.664kcal/mol
Ligand efficiency (LE)
-1.2988kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.398
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
392.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.85
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.22kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
114.30kcal/mol
Minimised FF energy
82.08kcal/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.