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 (-1.600 kcal/mol/HA)
✓ Good fit quality (FQ -13.12)
✓ Strong H-bond network (11 bonds)
✗ High strain energy (17.0 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.402
kcal/mol
LE
-1.600
kcal/mol/HA
Fit Quality
-13.12
FQ (Leeson)
HAC
19
heavy atoms
MW
280
Da
LogP
0.02
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 17.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 11
Hydrophobic 17
π–π 1
Clashes 12
Severe clashes 0
| Final rank | 3.9134046702727576 | Score | -30.4019 |
|---|---|---|---|
| Inter norm | -1.74874 | Intra norm | 0.148639 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 12 protein contact clashes; moderate strain Δ 18.3 | ||
| Residues | A:ALA96;A:ARG14;A:ASP161;A:GLY205;A:LEU208;A:LEU209;A:LYS178;A:NAP301;A:PHE97;A:PRO210;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 | 14 | Native recall | 0.74 |
| Jaccard | 0.70 | RMSD | - |
| H-bond strict | 4 | Strict recall | 0.67 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 928 | 2.6662103575983664 | -1.85511 | -29.1252 | 9 | 15 | 14 | 0.74 | 0.80 | - | no | Open |
| 927 | 2.817027839794606 | -1.72753 | -30.0181 | 12 | 13 | 12 | 0.63 | 0.80 | - | no | Open |
| 848 | 2.944523796123663 | -1.87039 | -29.4322 | 9 | 15 | 14 | 0.74 | 0.80 | - | no | Open |
| 2268 | 3.1170949224775 | -1.30574 | -24.3182 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 910 | 3.39635074445896 | -1.07503 | -17.9023 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 847 | 3.9134046702727576 | -1.74874 | -30.4019 | 11 | 15 | 14 | 0.74 | 0.80 | - | no | Current |
| 2266 | 4.1761537048642605 | -1.48177 | -26.4623 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 911 | 5.211462340964783 | -1.17556 | -21.6784 | 5 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2267 | 5.442531889953567 | -1.66307 | -31.0938 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 912 | 6.8469444483002535 | -1.25726 | -17.7812 | 10 | 20 | 0 | 0.00 | 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
-30.402kcal/mol
Ligand efficiency (LE)
-1.6001kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.116
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
280.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.02
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-79.80kcal/mol
Minimised FF energy
-96.76kcal/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.