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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.570 kcal/mol/HA)
✓ Good fit quality (FQ -6.09)
✓ Strong H-bond network (8 bonds)
✗ Very high strain energy (60.9 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-25.088
kcal/mol
LE
-0.570
kcal/mol/HA
Fit Quality
-6.09
FQ (Leeson)
HAC
44
heavy atoms
MW
610
Da
LogP
0.40
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 60.9 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 0
Clashes 17
Severe clashes 1
| Final rank | 11.97617580348897 | Score | -25.0881 |
|---|---|---|---|
| Inter norm | -0.696189 | Intra norm | 0.126005 |
| Top1000 | no | Excluded | yes |
| Contacts | 22 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 16 clashes; 1 protein clash; high strain Δ 63.4 | ||
| Residues | A:ALA96;A:ARG14;A:ASN127;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:LYS178;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;A:TRP221;A:TYR174;A:TYR98;A:VAL206;D:HIS267 | ||
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 | 0.64 | 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
No π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 168 | 7.023665339492769 | -0.427398 | -17.79 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 153 | 7.330311277315124 | -0.557948 | -22.6725 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 265 | 7.350464938752037 | -0.624398 | -24.0475 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 164 | 7.674133302235749 | -0.459738 | -21.7239 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 263 | 7.786447145288811 | -0.601009 | -22.8534 | 4 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 185 | 7.888633566124654 | -0.541852 | -19.7561 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 155 | 7.922049680456461 | -0.507246 | -20.0911 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 163 | 7.956018962221468 | -0.419388 | -15.9905 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 262 | 8.956853229979028 | -0.63853 | -22.0415 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 166 | 9.030198863594844 | -0.464352 | -19.1092 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 171 | 9.18959634695467 | -0.649389 | -27.0531 | 9 | 20 | 15 | 0.79 | 0.60 | - | no | Open |
| 264 | 9.389217612215772 | -0.508652 | -14.0927 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 260 | 9.430921070530088 | -0.583211 | -19.2894 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 184 | 8.320188869547547 | -0.495622 | -26.1935 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 167 | 9.755807243465343 | -0.506314 | -20.4667 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 152 | 10.509612507824277 | -0.384727 | -16.1175 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 172 | 11.97617580348897 | -0.696189 | -25.0881 | 8 | 22 | 16 | 0.84 | 0.60 | - | yes | Current |
| 154 | 13.278137543188803 | -0.516905 | -20.8765 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 261 | 56.64284635921081 | -0.580188 | -24.5406 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 165 | 58.754962801835134 | -0.660802 | -27.1569 | 4 | 21 | 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
-25.088kcal/mol
Ligand efficiency (LE)
-0.5702kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.092
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
44HA
Physicochemical properties
Molecular weight
609.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.40
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
60.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
94.11kcal/mol
Minimised FF energy
33.17kcal/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.