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 (-1.133 kcal/mol/HA)
✓ Good fit quality (FQ -10.44)
✓ Strong H-bond network (7 bonds)
✗ High strain energy (17.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-29.470
kcal/mol
LE
-1.133
kcal/mol/HA
Fit Quality
-10.44
FQ (Leeson)
HAC
26
heavy atoms
MW
345
Da
LogP
1.93
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 17.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 24
π–π 4
Clashes 8
Severe clashes 1
| Final rank | 5.603465179791285 | Score | -29.4696 |
|---|---|---|---|
| Inter norm | -1.38948 | Intra norm | 0.256035 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 7 |
| Artifact reason | excluded; geometry warning; 12 clashes; 1 protein clash; high strain Δ 21.7 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLY205;A:LEU263;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TRP221;A:TYR174;A:VAL164;A:VAL206 | ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | 11 | Native recall | 0.58 |
| Jaccard | 0.46 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 193 | 2.341573079589889 | -0.795871 | -19.8565 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 187 | 2.600580136268462 | -1.00176 | -23.1171 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 192 | 2.612595909471465 | -0.814557 | -22.3807 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 186 | 3.181781192158638 | -1.01831 | -25.6436 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 188 | 3.1859197969722253 | -0.998321 | -23.6116 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 128 | 3.566475201443353 | -1.2388 | -31.1169 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 201 | 3.679863303157364 | -1.32526 | -34.0392 | 8 | 17 | 13 | 0.68 | 0.60 | - | no | Open |
| 194 | 3.742749019480482 | -0.789796 | -19.532 | 3 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 242 | 3.881589315785158 | -0.722011 | -20.936 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 202 | 5.603465179791285 | -1.38948 | -29.4696 | 7 | 16 | 11 | 0.58 | 0.60 | - | yes | Current |
| 200 | 7.192673937326427 | -1.22639 | -32.8511 | 9 | 19 | 15 | 0.79 | 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
-29.470kcal/mol
Ligand efficiency (LE)
-1.1334kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.443
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
345.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.93
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
76.02kcal/mol
Minimised FF energy
59.06kcal/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.