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 (-1.083 kcal/mol/HA)
✓ Good fit quality (FQ -10.10)
✓ Strong H-bond network (6 bonds)
✗ High strain energy (13.4 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-29.228
kcal/mol
LE
-1.083
kcal/mol/HA
Fit Quality
-10.10
FQ (Leeson)
HAC
27
heavy atoms
MW
356
Da
LogP
5.41
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 13.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 14
π–π 2
Clashes 9
Severe clashes 0
| Final rank | 4.368626651448511 | Score | -29.228 |
|---|---|---|---|
| Inter norm | -1.18488 | Intra norm | 0.102244 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 9 protein contact clashes; moderate strain Δ 17.3 | ||
| Residues | A:ARG14;A:ASP161;A:GLY205;A:LEU208;A:LEU209;A:LYS13;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:TRP221;A:VAL206;A:VAL211 | ||
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.45 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1002 | 3.399557892196137 | -1.26118 | -32.3744 | 6 | 13 | 9 | 0.47 | 0.40 | - | no | Open |
| 1478 | 4.014219343582825 | -0.68663 | -20.5123 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1001 | 4.368626651448511 | -1.18488 | -29.228 | 6 | 13 | 10 | 0.53 | 0.40 | - | no | Current |
| 1214 | 4.63661824605709 | -0.956451 | -23.6271 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1476 | 5.056035528523743 | -0.910424 | -13.4768 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1477 | 5.4363233801796245 | -0.619113 | -16.6402 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1000 | 5.851401134289665 | -1.32071 | -32.9059 | 6 | 14 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1215 | 7.7853297720256815 | -0.841018 | -21.2596 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1216 | 8.012703355022335 | -0.905398 | -20.8416 | 4 | 17 | 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
-29.228kcal/mol
Ligand efficiency (LE)
-1.0825kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.100
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.41
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.39kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
70.76kcal/mol
Minimised FF energy
57.37kcal/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.