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 (-0.640 kcal/mol/HA)
✓ Good fit quality (FQ -6.64)
✓ Good H-bonds (3 bonds)
✗ Very high strain energy (20.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.952
kcal/mol
LE
-0.640
kcal/mol/HA
Fit Quality
-6.64
FQ (Leeson)
HAC
39
heavy atoms
MW
563
Da
LogP
5.00
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 20.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 3
Hydrophobic 24
π–π 5
Clashes 12
Severe clashes 1
| Final rank | 8.391633141213417 | Score | -24.952 |
|---|---|---|---|
| Inter norm | -0.740138 | Intra norm | 0.100343 |
| Top1000 | no | Excluded | yes |
| Contacts | 19 | H-bonds | 3 |
| Artifact reason | excluded; geometry warning; 14 clashes; 1 protein clash; high strain Δ 32.0 | ||
| Residues | A:ALA170;A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:SER95;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 | 16 | Native recall | 0.84 |
| Jaccard | 0.73 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 1 | Residue recall | 0.20 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1517 | 5.638791330156456 | -0.667795 | -27.1168 | 4 | 16 | 15 | 0.79 | 0.20 | - | no | Open |
| 1522 | 5.714183409418502 | -0.685914 | -32.1574 | 1 | 17 | 13 | 0.68 | 0.00 | - | no | Open |
| 1520 | 6.0613735494179375 | -0.836047 | -34.6794 | 4 | 19 | 15 | 0.79 | 0.00 | - | no | Open |
| 1521 | 7.392456645551796 | -0.700733 | -31.0763 | 4 | 14 | 14 | 0.74 | 0.20 | - | no | Open |
| 1515 | 6.714685739867728 | -0.745681 | -28.668 | 3 | 15 | 13 | 0.68 | 0.00 | - | yes | Open |
| 1516 | 8.391633141213417 | -0.740138 | -24.952 | 3 | 19 | 16 | 0.84 | 0.00 | - | yes | Current |
| 1519 | 10.263658085221024 | -0.677176 | -30.7957 | 5 | 16 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1518 | 13.675639011320333 | -0.49049 | -14.0247 | 0 | 18 | 14 | 0.74 | 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
-24.952kcal/mol
Ligand efficiency (LE)
-0.6398kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.640
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
39HA
Physicochemical properties
Molecular weight
563.1Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.00
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
20.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
152.04kcal/mol
Minimised FF energy
131.60kcal/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.