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 (-0.752 kcal/mol/HA)
✓ Good fit quality (FQ -7.75)
✓ Strong H-bond network (6 bonds)
✗ Very high strain energy (24.3 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.587
kcal/mol
LE
-0.752
kcal/mol/HA
Fit Quality
-7.75
FQ (Leeson)
HAC
38
heavy atoms
MW
516
Da
LogP
3.89
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 24.3 kcal/mol
Interaction summary
Collapsible panels
H-bonds 6
Hydrophobic 24
π–π 4
Clashes 8
Severe clashes 1
| Final rank | 7.177700223651967 | Score | -28.5867 |
|---|---|---|---|
| Inter norm | -0.759922 | Intra norm | 0.00764054 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 6 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 22.8 | ||
| Residues | A:ALA212;A:ARG14;A:ASP161;A:GLU217;A:GLY214;A:LEU208;A:LEU209;A:LYS114;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98 | ||
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 | 13 | Native recall | 0.68 |
| Jaccard | 0.57 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 771 | 4.644117979520563 | -0.666517 | -24.3985 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 5.5960397256022825 | -0.826836 | -29.3945 | 8 | 14 | 11 | 0.58 | 0.60 | - | no | Open |
| 673 | 5.6720975554887 | -0.612799 | -20.4372 | 7 | 14 | 13 | 0.68 | 0.60 | - | no | Open |
| 2893 | 8.489736162627274 | -0.461701 | -17.6378 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 674 | 7.177700223651967 | -0.759922 | -28.5867 | 6 | 17 | 13 | 0.68 | 0.60 | - | yes | Current |
| 2895 | 7.1790071623859175 | -0.517594 | -21.0245 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 676 | 7.359967638348834 | -0.86137 | -32.3022 | 6 | 16 | 12 | 0.63 | 0.40 | - | yes | Open |
| 774 | 7.786125055693096 | -0.560383 | -21.0673 | 8 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 672 | 9.104944248209165 | -0.920315 | -32.7614 | 6 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 770 | 9.37291964270213 | -0.697132 | -26.8031 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2892 | 9.505919508226206 | -0.698653 | -25.0597 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 769 | 10.172569018575738 | -0.714249 | -25.0458 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 772 | 10.643832610050188 | -0.692123 | -21.3102 | 13 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 677 | 57.11685098221617 | -0.78235 | -26.6281 | 8 | 15 | 11 | 0.58 | 0.60 | - | yes | Open |
| 773 | 58.97483605307002 | -0.704735 | -22.6967 | 10 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2894 | 59.63775414616263 | -0.535682 | -21.3684 | 3 | 11 | 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
-28.587kcal/mol
Ligand efficiency (LE)
-0.7523kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.755
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
515.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.89
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
97.93kcal/mol
Minimised FF energy
73.62kcal/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.