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 (-1.161 kcal/mol/HA)
✓ Good fit quality (FQ -11.20)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (32.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-34.833
kcal/mol
LE
-1.161
kcal/mol/HA
Fit Quality
-11.20
FQ (Leeson)
HAC
30
heavy atoms
MW
459
Da
LogP
4.59
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 32.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 8
Clashes 12
Severe clashes 3
| Final rank | 9.483131774761153 | Score | -34.8331 |
|---|---|---|---|
| Inter norm | -1.19533 | Intra norm | 0.0342291 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 8 clashes; 3 protein clashes; high strain Δ 36.7 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;A:VAL206;D:HIS267 | ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.57 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2015 | 3.4682060112592965 | -0.545333 | -14.9021 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1120 | 3.643947498485026 | -0.839972 | -24.243 | 2 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1271 | 4.1939269832523465 | -0.927956 | -25.2362 | 2 | 15 | 12 | 0.63 | 0.00 | - | no | Open |
| 1983 | 4.78942812688077 | -0.886151 | -21.9132 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1985 | 6.003412359709169 | -0.76761 | -19.0395 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1272 | 4.855860591429698 | -0.931254 | -28.2839 | 3 | 15 | 15 | 0.79 | 0.20 | - | yes | Open |
| 2013 | 5.698126131080314 | -0.65996 | -17.4537 | 6 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1121 | 6.44328894203041 | -0.762319 | -19.2746 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2014 | 8.731483174774025 | -0.586029 | -12.7625 | 9 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1122 | 8.790750180079192 | -0.786824 | -21.257 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1270 | 9.483131774761153 | -1.19533 | -34.8331 | 9 | 17 | 13 | 0.68 | 0.40 | - | yes | Current |
| 1984 | 11.040485967616378 | -0.80145 | -22.2689 | 10 | 14 | 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
-34.833kcal/mol
Ligand efficiency (LE)
-1.1611kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.200
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
458.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.59
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.65kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
43.50kcal/mol
Minimised FF energy
10.85kcal/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.