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 (-0.854 kcal/mol/HA)
✓ Good fit quality (FQ -8.74)
✓ Good H-bonds (5 bonds)
✗ High strain energy (14.2 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-31.598
kcal/mol
LE
-0.854
kcal/mol/HA
Fit Quality
-8.74
FQ (Leeson)
HAC
37
heavy atoms
MW
552
Da
LogP
5.58
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 14.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 5
Clashes 13
Severe clashes 0
| Final rank | 6.307012846604738 | Score | -31.5976 |
|---|---|---|---|
| Inter norm | -0.901314 | Intra norm | 0.0473259 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 5 |
| Artifact reason | geometry warning; 14 clashes; 13 protein contact clashes; moderate strain Δ 17.5 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 158 | 5.587416605055933 | -0.517844 | -19.598 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 121 | 5.667270276886944 | -0.7865 | -24.1006 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 131 | 6.307012846604738 | -0.901314 | -31.5976 | 5 | 17 | 15 | 0.79 | 0.20 | - | no | Current |
| 142 | 6.382994348494224 | -0.773478 | -25.8026 | 2 | 14 | 11 | 0.58 | 0.20 | - | no | Open |
| 134 | 6.846316942572459 | -0.748384 | -26.9946 | 1 | 17 | 16 | 0.84 | 0.00 | - | no | Open |
| 122 | 6.956016934990709 | -0.800955 | -26.2534 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 58 | 7.119271038412155 | -0.551209 | -15.8152 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 59 | 7.257122895383278 | -0.648063 | -22.1081 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 132 | 9.96352026228432 | -0.636513 | -17.0854 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 156 | 5.937669063319742 | -0.565382 | -19.6431 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 130 | 7.131209958769979 | -0.541226 | -21.0962 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 123 | 7.7483350158359094 | -0.744352 | -27.9909 | 1 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 157 | 8.6076988519877 | -0.503016 | -18.1486 | 6 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 159 | 8.96580769477534 | -0.595766 | -21.543 | 5 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 133 | 9.24243102146462 | -0.893866 | -31.8275 | 3 | 17 | 15 | 0.79 | 0.20 | - | yes | Open |
| 60 | 9.406537947436496 | -0.602267 | -22.4837 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 143 | 9.643728377937702 | -0.780698 | -28.2201 | 0 | 14 | 13 | 0.68 | 0.00 | - | yes | Open |
| 124 | 9.840405290366467 | -0.710257 | -23.9882 | 2 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 145 | 10.059577142446992 | -0.961909 | -34.6797 | 6 | 19 | 15 | 0.79 | 0.40 | - | yes | Open |
| 132 | 10.151255150664152 | -0.938147 | -31.4622 | 5 | 17 | 15 | 0.79 | 0.40 | - | yes | Open |
| 61 | 11.120367863215355 | -0.674628 | -22.067 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 133 | 11.687455401746584 | -0.666768 | -25.3827 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 144 | 12.892570660312137 | -0.805227 | -26.3325 | 1 | 17 | 13 | 0.68 | 0.00 | - | yes | Open |
| 131 | 13.159373650829405 | -0.576407 | -16.4531 | 5 | 15 | 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
-31.598kcal/mol
Ligand efficiency (LE)
-0.8540kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.743
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
37HA
Physicochemical properties
Molecular weight
552.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.58
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.18kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.25kcal/mol
Minimised FF energy
37.07kcal/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.