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 (-0.646 kcal/mol/HA)
✓ Good fit quality (FQ -6.67)
✓ Strong H-bond network (7 bonds)
✗ Very high strain energy (29.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.566
kcal/mol
LE
-0.646
kcal/mol/HA
Fit Quality
-6.67
FQ (Leeson)
HAC
38
heavy atoms
MW
515
Da
LogP
5.18
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 29.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 5
Clashes 13
Severe clashes 5
| Final rank | 13.90791226219642 | Score | -24.566 |
|---|---|---|---|
| Inter norm | -0.782514 | Intra norm | 0.135866 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 16 clashes; 5 protein clashes; high strain Δ 37.1 | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.67 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1224 | 4.655005214225548 | -0.484602 | -15.5856 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1014 | 5.105019058142142 | -0.605348 | -19.8969 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1221 | 6.370386724896184 | -0.41635 | -15.1312 | 5 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 6.400172688267178 | -0.762569 | -25.878 | 8 | 15 | 12 | 0.63 | 0.40 | - | no | Open |
| 1991 | 7.051437491616422 | -0.681096 | -25.1495 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1222 | 6.531760830123513 | -0.573627 | -18.5949 | 2 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1993 | 7.119321826583064 | -0.687894 | -19.7625 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1011 | 7.659122942096789 | -0.624349 | -21.4721 | 3 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1016 | 7.715255248601405 | -0.599842 | -24.1332 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1992 | 8.065732105702462 | -0.571842 | -23.1664 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 667 | 8.536720782848368 | -0.821892 | -27.8573 | 6 | 15 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1223 | 8.630879763671473 | -0.499288 | -19.2264 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1012 | 9.126618597058714 | -0.669323 | -26.5351 | 2 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 670 | 9.52214347548418 | -0.829467 | -25.5867 | 7 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 671 | 10.207353193760811 | -0.787479 | -27.9037 | 0 | 21 | 16 | 0.84 | 0.00 | - | yes | Open |
| 1015 | 10.554637340146453 | -0.765696 | -21.0966 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1225 | 10.660258035923938 | -0.601518 | -17.8603 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 666 | 13.90791226219642 | -0.782514 | -24.566 | 7 | 16 | 14 | 0.74 | 0.40 | - | yes | Current |
| 1994 | 57.51677514441389 | -0.583446 | -23.7228 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1226 | 58.23524297792672 | -0.569285 | -21.0713 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1013 | 59.332862727416845 | -0.566977 | -18.5546 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 668 | 63.28941991823524 | -0.744512 | -20.497 | 7 | 16 | 13 | 0.68 | 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
-24.566kcal/mol
Ligand efficiency (LE)
-0.6465kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.665
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
514.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.18
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.90kcal/mol
Minimised FF energy
105.58kcal/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.