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
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.269 kcal/mol/HA)
✓ Good fit quality (FQ -10.17)
✓ Strong H-bond network (9 bonds)
✗ High strain energy (19.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-22.837
kcal/mol
LE
-1.269
kcal/mol/HA
Fit Quality
-10.17
FQ (Leeson)
HAC
18
heavy atoms
MW
263
Da
LogP
1.68
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 19.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 18
π–π 2
Clashes 5
Severe clashes 1
| Final rank | 3.616345015909825 | Score | -22.8371 |
|---|---|---|---|
| Inter norm | -1.32724 | Intra norm | 0.0585093 |
| Top1000 | no | Excluded | yes |
| Contacts | 12 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 4 clashes; 1 protein clash; high strain Δ 21.9 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU263;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:TRP221;A:TYR174;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 | 10 | Native recall | 0.53 |
| Jaccard | 0.48 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1031 | 2.0381618079367367 | -1.37578 | -17.6259 | 7 | 12 | 12 | 0.63 | 0.60 | - | no | Open |
| 1018 | 2.3742118689288376 | -1.49579 | -25.5864 | 9 | 12 | 10 | 0.53 | 0.60 | - | no | Open |
| 1026 | 2.6493486540728846 | -1.31469 | -22.5056 | 8 | 13 | 11 | 0.58 | 0.40 | - | no | Open |
| 1027 | 3.5668431861625054 | -1.48064 | -21.5159 | 6 | 14 | 13 | 0.68 | 0.60 | - | no | Open |
| 1022 | 2.5750952863735455 | -1.59586 | -25.7934 | 9 | 11 | 9 | 0.47 | 0.60 | - | yes | Open |
| 1034 | 2.706098857918717 | -1.48004 | -25.998 | 9 | 11 | 9 | 0.47 | 0.60 | - | yes | Open |
| 1021 | 3.513961746830127 | -1.54411 | -31.1086 | 7 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1030 | 3.616345015909825 | -1.32724 | -22.8371 | 9 | 12 | 10 | 0.53 | 0.60 | - | yes | Current |
| 1025 | 3.9042123423454065 | -1.57498 | -30.6893 | 7 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1033 | 3.910932654842785 | -1.43857 | -28.3706 | 7 | 12 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1029 | 4.103473943845535 | -1.4077 | -28.6588 | 7 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1037 | 4.644329122510198 | -1.33291 | -25.1575 | 5 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1036 | 5.214243660927361 | -1.63339 | -29.0172 | 9 | 12 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1023 | 5.794981951346065 | -1.54572 | -22.736 | 8 | 14 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1019 | 6.593021792389351 | -1.63229 | -25.7022 | 6 | 13 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1032 | 53.54441937639131 | -1.54153 | -27.3891 | 7 | 12 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1028 | 53.90769279043912 | -1.47037 | -27.3693 | 8 | 12 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1035 | 54.894914709641625 | -1.29518 | -18.0521 | 8 | 13 | 12 | 0.63 | 0.60 | - | yes | Open |
| 1024 | 55.394594478149486 | -1.72273 | -31.3242 | 9 | 13 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1020 | 55.56912060956212 | -1.66864 | -31.2896 | 6 | 12 | 12 | 0.63 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-22.837kcal/mol
Ligand efficiency (LE)
-1.2687kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.168
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
18HA
Physicochemical properties
Molecular weight
263.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.68
Lipinski: ≤ 5
Rotatable bonds
2
Conformational strain (MMFF94s)
Strain energy (ΔE)
19.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
63.17kcal/mol
Minimised FF energy
43.70kcal/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.