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 (-0.651 kcal/mol/HA)
✓ Good fit quality (FQ -5.84)
✗ Very high strain energy (22.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-15.632
kcal/mol
LE
-0.651
kcal/mol/HA
Fit Quality
-5.84
FQ (Leeson)
HAC
24
heavy atoms
MW
347
Da
LogP
3.09
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 22.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 2
Hydrophobic 17
π–π 1
Clashes 9
Severe clashes 1
| Final rank | 5.716597349995585 | Score | -15.6321 |
|---|---|---|---|
| Inter norm | -0.690234 | Intra norm | 0.0388957 |
| Top1000 | no | Excluded | yes |
| Contacts | 8 | H-bonds | 2 |
| Artifact reason | excluded; geometry warning; 7 clashes; 1 protein clash; high strain Δ 25.0 | ||
| Residues | A:ALA96;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:SER95;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 | 7 | Native recall | 0.37 |
| Jaccard | 0.35 | RMSD | - |
| H-bond strict | 0 | Strict recall | 0.00 |
| H-bond same residue+role | 0 | Role recall | 0.00 |
| H-bond same residue | 0 | Residue recall | 0.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2056 | 2.965964730211452 | -1.31817 | -26.5799 | 9 | 15 | 12 | 0.63 | 0.80 | - | no | Open |
| 2052 | 3.5782485906837955 | -1.31007 | -24.406 | 9 | 14 | 12 | 0.63 | 0.80 | - | no | Open |
| 3292 | 3.8182101734069924 | -0.808396 | -22.0925 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2062 | 4.557219606276952 | -1.02728 | -25.8457 | 10 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
| 2049 | 5.025862431370976 | -1.20141 | -27.8983 | 9 | 14 | 14 | 0.74 | 0.60 | - | no | Open |
| 2053 | 5.116704790720837 | -1.20577 | -25.7688 | 9 | 15 | 11 | 0.58 | 0.60 | - | no | Open |
| 2048 | 4.726770964583309 | -1.51808 | -30.7727 | 10 | 14 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2060 | 5.716597349995585 | -0.690234 | -15.6321 | 2 | 8 | 7 | 0.37 | 0.00 | - | yes | Current |
| 2040 | 5.767455337585181 | -1.52157 | -28.402 | 11 | 14 | 13 | 0.68 | 0.60 | - | yes | Open |
| 2050 | 6.007021862417375 | -1.25666 | -32.4733 | 6 | 15 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2065 | 6.04002873234573 | -1.23192 | -28.9399 | 12 | 17 | 12 | 0.63 | 0.60 | - | yes | Open |
| 3287 | 6.254498242708624 | -0.740209 | -17.4357 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2063 | 6.983018233790668 | -1.3033 | -25.6195 | 11 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2057 | 7.205123519814007 | -1.09166 | -24.5805 | 8 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2045 | 7.2574095998955235 | -0.869393 | -19.1765 | 2 | 13 | 13 | 0.68 | 0.00 | - | yes | Open |
| 2046 | 7.5824980676335985 | -1.47048 | -34.1979 | 11 | 18 | 18 | 0.95 | 0.60 | - | yes | Open |
| 2066 | 7.710338781820241 | -1.2533 | -30.6513 | 10 | 18 | 18 | 0.95 | 0.60 | - | yes | Open |
| 2069 | 7.73726377924259 | -1.18253 | -26.9817 | 12 | 16 | 11 | 0.58 | 0.60 | - | yes | Open |
| 2054 | 7.847428786718228 | -1.25644 | -30.198 | 11 | 14 | 14 | 0.74 | 0.60 | - | yes | Open |
| 2041 | 7.906399196376276 | -0.972299 | -19.3743 | 8 | 15 | 14 | 0.74 | 0.20 | - | yes | Open |
| 2058 | 7.915030197617651 | -1.17946 | -32.0591 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2071 | 8.149102801482055 | -1.40584 | -27.4408 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2042 | 8.349276579910809 | -1.42232 | -35.1625 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2070 | 9.060333640076191 | -1.23131 | -28.9467 | 12 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2067 | 9.611974141654335 | -1.30291 | -27.0611 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2047 | 9.668956863680648 | -1.47679 | -29.4583 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 3286 | 20.393621010513513 | -0.763429 | -14.5481 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2051 | 55.417218450436 | -1.32116 | -29.3422 | 11 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 3280 | 56.12657470814826 | -0.960319 | -23.3028 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2055 | 56.276739608945434 | -1.46078 | -32.6022 | 10 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2061 | 57.22281760189239 | -1.33207 | -29.6162 | 12 | 17 | 12 | 0.63 | 0.60 | - | yes | Open |
| 2059 | 57.9745233602124 | -1.34927 | -32.1484 | 10 | 16 | 16 | 0.84 | 0.60 | - | yes | Open |
| 2043 | 58.12647388510335 | -1.54524 | -34.4 | 10 | 17 | 17 | 0.89 | 0.60 | - | yes | Open |
| 2064 | 59.63626584761522 | -0.934916 | -14.6905 | 8 | 17 | 16 | 0.84 | 0.60 | - | yes | Open |
| 2068 | 59.912556799045646 | -0.808957 | -11.5731 | 7 | 15 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2044 | 60.20617532892632 | -1.09501 | -17.9522 | 12 | 16 | 14 | 0.74 | 0.60 | - | yes | Open |
| 3284 | 63.415332441772826 | -0.853633 | -19.9607 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3282 | 77.01288841238684 | -0.853023 | -19.2209 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3283 | 79.9566432942168 | -0.824964 | -19.0476 | 11 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3294 | 84.83325127156529 | -0.7665 | -21.4373 | 8 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3288 | 93.66567738057711 | -0.816869 | -17.1156 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3295 | 99.2093667151486 | -0.707034 | -16.2352 | 8 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3291 | 100.05823578326022 | -0.883098 | -17.2007 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3289 | 100.78465263969053 | -0.833208 | -18.7539 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3290 | 151.61404216905783 | -0.729519 | -15.9586 | 11 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3281 | 167.334941416719 | -0.964714 | -22.767 | 12 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3293 | 167.3708325252304 | -0.737765 | -17.6234 | 10 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3285 | 198.5752277994019 | -0.743395 | -12.1456 | 13 | 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
-15.632kcal/mol
Ligand efficiency (LE)
-0.6513kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.837
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
347.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.09
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.53kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
79.69kcal/mol
Minimised FF energy
57.16kcal/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.