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 (-1.601 kcal/mol/HA)
✓ Good fit quality (FQ -13.12)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (18.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-30.420
kcal/mol
LE
-1.601
kcal/mol/HA
Fit Quality
-13.12
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
-0.56
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 18.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 17
π–π 3
Clashes 7
Severe clashes 0
| Final rank | 3.0497083982874926 | Score | -30.4204 |
|---|---|---|---|
| Inter norm | -1.68268 | Intra norm | 0.0815996 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 7 protein contact clashes; high strain Δ 20.7 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:LYS178;A:MET213;A:NAP301;A:PHE171;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 | 16 | Native recall | 0.84 |
| Jaccard | 0.84 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 829 | 1.2807310471076065 | -1.62516 | -29.8488 | 8 | 16 | 14 | 0.74 | 0.60 | - | no | Open |
| 830 | 1.8739866326937267 | -1.58687 | -28.627 | 7 | 16 | 15 | 0.79 | 0.60 | - | no | Open |
| 1122 | 2.5099889893324385 | -1.35166 | -24.7621 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 2214 | 2.521084402156935 | -1.51737 | -27.3765 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2845 | 2.648125492870427 | -1.19415 | -20.2293 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 654 | 2.9467682920117726 | -1.4099 | -25.1999 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2978 | 3.043854102892444 | -1.26937 | -21.4516 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 831 | 3.0497083982874926 | -1.68268 | -30.4204 | 8 | 16 | 16 | 0.84 | 0.60 | - | no | Current |
| 653 | 3.3021318406056075 | -1.27364 | -22.7689 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2844 | 3.3519690484556217 | -1.25392 | -19.5039 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2215 | 3.356163655914087 | -1.13645 | -20.5341 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2979 | 4.640939591310978 | -0.985435 | -18.12 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1123 | 6.448465276160986 | -1.3296 | -21.2029 | 12 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2216 | 6.793531304660815 | -1.42105 | -26.0099 | 8 | 14 | 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
-30.420kcal/mol
Ligand efficiency (LE)
-1.6011kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-13.124
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
281.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.56
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.13kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-3.69kcal/mol
Minimised FF energy
-21.83kcal/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.