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 (-0.734 kcal/mol/HA)
✓ Good fit quality (FQ -7.57)
✗ Very high strain energy (32.7 kcal/mol)
✗ No H-bonds detected
✗ Geometry warnings
ℹ SASA not computed
Score
-27.904
kcal/mol
LE
-0.734
kcal/mol/HA
Fit Quality
-7.57
FQ (Leeson)
HAC
38
heavy atoms
MW
516
Da
LogP
3.89
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 32.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 0
Hydrophobic 24
π–π 4
Clashes 11
Severe clashes 2
⚠ Hydrophobic exposure 36%
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (11/30 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 30
Buried (contacted) 19
Exposed 11
LogP 3.89
H-bonds 0
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 10.207353193760811 | Score | -27.9037 |
|---|---|---|---|
| Inter norm | -0.787479 | Intra norm | 0.0531705 |
| Top1000 | no | Excluded | yes |
| Contacts | 21 | H-bonds | 0 |
| Artifact reason | excluded; geometry warning; 15 clashes; 2 protein clashes; high strain Δ 47.4 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS224;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98;A:VAL206;D:ALA268;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 | 16 | Native recall | 0.84 |
| Jaccard | 0.67 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
Hydrogen bonds
No hydrogen bonds detected for this pose.
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 | Current |
| 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 | Open |
| 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
-27.904kcal/mol
Ligand efficiency (LE)
-0.7343kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.570
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
515.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
107.76kcal/mol
Minimised FF energy
75.08kcal/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.