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 (-0.678 kcal/mol/HA)
✓ Good fit quality (FQ -6.79)
✗ High strain energy (19.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-23.068
kcal/mol
LE
-0.678
kcal/mol/HA
Fit Quality
-6.79
FQ (Leeson)
HAC
34
heavy atoms
MW
467
Da
LogP
4.87
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 19.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 1
Hydrophobic 24
π–π 5
Clashes 10
Severe clashes 1
| Final rank | 7.101209176856625 | Score | -23.0684 |
|---|---|---|---|
| Inter norm | -0.733236 | Intra norm | 0.0547545 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 1 |
| Artifact reason | excluded; geometry warning; 12 clashes; 1 protein clash; high strain Δ 24.1 | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER207;A:SER95;A:TRP221;A:TYR174;A:TYR98;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 | 0.80 | RMSD | - |
| H-bond strict | 1 | Strict recall | 0.17 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2035 | 4.694081126021725 | -0.855682 | -27.5085 | 6 | 11 | 8 | 0.42 | 0.40 | - | no | Open |
| 3016 | 4.801540287545092 | -0.956391 | -29.4261 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 3591 | 5.715464238322772 | -0.722138 | -23.6414 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 3595 | 6.000774929839941 | -0.738045 | -20.0611 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 3015 | 6.1143422407634285 | -0.81945 | -22.8118 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 3596 | 6.30265587682257 | -0.750662 | -23.3545 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3589 | 6.392303134329996 | -0.76255 | -22.5484 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1988 | 8.237308438236917 | -0.827627 | -26.681 | 2 | 18 | 13 | 0.68 | 0.00 | - | no | Open |
| 2033 | 6.01018580957263 | -0.796699 | -26.1676 | 3 | 17 | 13 | 0.68 | 0.40 | - | yes | Open |
| 3592 | 6.461756773303042 | -0.621306 | -21.9507 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1987 | 6.5407435082135645 | -0.871806 | -20.6974 | 0 | 15 | 12 | 0.63 | 0.00 | - | yes | Open |
| 2036 | 6.623910558534379 | -0.986887 | -31.8198 | 2 | 13 | 11 | 0.58 | 0.20 | - | yes | Open |
| 3019 | 6.695120878645682 | -0.786034 | -29.4525 | 0 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1993 | 6.852867089436183 | -0.798602 | -25.7871 | 3 | 13 | 12 | 0.63 | 0.00 | - | yes | Open |
| 3014 | 6.853072820427299 | -0.71665 | -21.161 | 0 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1990 | 6.907840345025812 | -0.802543 | -29.0538 | 4 | 19 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1986 | 7.101209176856625 | -0.733236 | -23.0684 | 1 | 17 | 16 | 0.84 | 0.20 | - | yes | Current |
| 3018 | 7.892649470627741 | -0.822823 | -23.7287 | 3 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3020 | 8.446452902340368 | -0.793438 | -21.1043 | 2 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3594 | 9.70957943150095 | -0.805989 | -29.2608 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1991 | 10.242089708916698 | -0.946124 | -29.5206 | 0 | 16 | 14 | 0.74 | 0.00 | - | yes | Open |
| 2034 | 55.992078554261276 | -0.840925 | -26.9181 | 3 | 18 | 14 | 0.74 | 0.00 | - | yes | Open |
| 1989 | 56.996523392442064 | -0.883629 | -31.2472 | 1 | 17 | 14 | 0.74 | 0.00 | - | yes | Open |
| 3021 | 57.456781196342696 | -0.798441 | -27.8792 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3593 | 58.56192729339746 | -0.741251 | -22.7497 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3017 | 59.19287817918776 | -0.810399 | -24.7281 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3590 | 59.504999651110296 | -0.699695 | -19.8092 | 5 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1992 | 60.7587420827621 | -0.869064 | -24.2589 | 3 | 20 | 14 | 0.74 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.068kcal/mol
Ligand efficiency (LE)
-0.6785kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.789
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
466.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.87
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.98kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.17kcal/mol
Minimised FF energy
79.19kcal/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.