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 (-0.782 kcal/mol/HA)
✓ Good fit quality (FQ -7.76)
✓ Good H-bonds (4 bonds)
✗ High strain energy (16.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.814
kcal/mol
LE
-0.782
kcal/mol/HA
Fit Quality
-7.76
FQ (Leeson)
HAC
33
heavy atoms
MW
455
Da
LogP
2.76
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 16.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 1
Clashes 13
Severe clashes 2
| Final rank | 9.121379438290813 | Score | -25.8139 |
|---|---|---|---|
| Inter norm | -0.833537 | Intra norm | 0.0512973 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 13 clashes; 2 protein clashes; high strain Δ 27.0 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:GLY205;A:LEU208;A:LEU209;A:LYS220;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 602 | 3.4980537613957687 | -0.684213 | -23.5709 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 686 | 4.92437477206403 | -0.973172 | -27.5856 | 4 | 15 | 15 | 0.79 | 0.20 | - | no | Open |
| 2900 | 5.0201541838578745 | -0.573071 | -19.683 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1022 | 5.114437469287031 | -0.828931 | -26.0142 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 685 | 5.216394513217241 | -0.882698 | -28.1892 | 3 | 15 | 14 | 0.74 | 0.40 | - | no | Open |
| 1044 | 6.003031949778492 | -0.709141 | -16.628 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1047 | 6.610661532767928 | -0.588855 | -16.7661 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1024 | 6.510680163617971 | -0.749251 | -21.643 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2901 | 6.644118692637061 | -0.499245 | -16.8783 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 603 | 6.826511942276714 | -0.671396 | -21.3504 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1023 | 7.163305648661847 | -0.768911 | -16.4742 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2898 | 7.77401337863153 | -0.68783 | -19.4084 | 9 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1025 | 7.976348063144693 | -0.696183 | -19.5289 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1046 | 8.158597442904012 | -0.604681 | -15.966 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2899 | 9.02547777402997 | -0.737114 | -16.4763 | 7 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 687 | 9.121379438290813 | -0.833537 | -25.8139 | 4 | 17 | 15 | 0.79 | 0.20 | - | yes | Current |
| 684 | 10.101187914860692 | -1.02348 | -27.0051 | 6 | 16 | 13 | 0.68 | 0.20 | - | yes | Open |
| 1045 | 10.625349900521783 | -0.605207 | -15.0878 | 10 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 601 | 11.716117144152117 | -0.801922 | -28.1702 | 10 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 600 | 13.680140018305867 | -0.732487 | -22.034 | 11 | 22 | 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
-25.814kcal/mol
Ligand efficiency (LE)
-0.7822kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.761
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
454.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.76
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
62.12kcal/mol
Minimised FF energy
45.53kcal/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.