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 (-0.767 kcal/mol/HA)
✓ Good fit quality (FQ -7.80)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (89.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-27.630
kcal/mol
LE
-0.767
kcal/mol/HA
Fit Quality
-7.80
FQ (Leeson)
HAC
36
heavy atoms
MW
505
Da
LogP
-1.64
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 89.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 3
Clashes 7
Severe clashes 1
| Final rank | 7.123379913345838 | Score | -27.6303 |
|---|---|---|---|
| Inter norm | -0.814469 | Intra norm | 0.0469616 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 6 clashes; 1 protein clash; high strain Δ 61.7 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:LYS178;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;A:TRP221;A:TYR174;A:TYR98 | ||
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 | 16 | Native recall | 0.84 |
| Jaccard | 0.80 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2247 | 3.7946447387886195 | -0.537129 | -17.9266 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1569 | 4.3560499969789905 | -0.783677 | -27.735 | 0 | 17 | 15 | 0.79 | 0.00 | - | no | Open |
| 2791 | 4.718392721164976 | -0.746661 | -23.6458 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3414 | 4.792925367259253 | -0.702076 | -24.8734 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2862 | 5.5336761737609566 | -0.763306 | -24.8595 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1704 | 6.239251212045458 | -0.853476 | -27.9229 | 4 | 16 | 14 | 0.74 | 0.40 | - | no | Open |
| 1705 | 5.3234168554522086 | -0.860086 | -28.9056 | 6 | 17 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1567 | 5.3642442253055655 | -0.848022 | -28.6428 | 3 | 16 | 14 | 0.74 | 0.40 | - | yes | Open |
| 2790 | 6.024767363233897 | -0.725953 | -22.5538 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1568 | 6.293675845619628 | -0.897491 | -30.3221 | 7 | 17 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1570 | 7.123379913345838 | -0.814469 | -27.6303 | 3 | 17 | 16 | 0.84 | 0.60 | - | yes | Current |
| 1706 | 7.38344745843832 | -0.820296 | -28.5862 | 4 | 17 | 16 | 0.84 | 0.60 | - | yes | Open |
| 2789 | 7.805520615979624 | -0.750888 | -22.9192 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2863 | 10.436316152341254 | -0.748481 | -24.1855 | 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
-27.630kcal/mol
Ligand efficiency (LE)
-0.7675kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.801
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
504.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-1.64
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
89.43kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
141.82kcal/mol
Minimised FF energy
52.39kcal/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.