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 (-0.913 kcal/mol/HA)
✓ Good fit quality (FQ -8.90)
✓ Strong H-bond network (14 bonds)
✗ Very high strain energy (34.0 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.312
kcal/mol
LE
-0.913
kcal/mol/HA
Fit Quality
-8.90
FQ (Leeson)
HAC
31
heavy atoms
MW
430
Da
LogP
4.70
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 34.0 kcal/mol
Interaction summary
Collapsible panels
H-bonds 14
Hydrophobic 24
π–π 4
Clashes 20
Severe clashes 3
| Final rank | 13.950851576382302 | Score | -28.3118 |
|---|---|---|---|
| Inter norm | -0.993831 | Intra norm | 0.080547 |
| Top1000 | no | Excluded | yes |
| Contacts | 22 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 18 clashes; 3 protein clashes; high strain Δ 38.3 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLN166;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:LYS178;A:MET163;A:MET213;A:NAP301;A:PHE97;A:PRO167;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;A:VAL164;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: permissive.
| 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 | 1 | Strict recall | 0.17 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| H-bond same residue | 2 | Residue recall | 0.40 |
Hydrogen bonds
Mode: permissive. 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1259 | 3.6497453693948523 | -0.530826 | -13.5949 | 1 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1490 | 3.973675104281029 | -0.859579 | -25.7173 | 3 | 15 | 15 | 0.79 | 0.00 | - | no | Open |
| 1488 | 4.462251402768458 | -0.900121 | -25.5715 | 3 | 17 | 15 | 0.79 | 0.00 | - | no | Open |
| 2069 | 4.668869730821097 | -0.676537 | -19.0541 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1494 | 4.823751406916526 | -0.897173 | -26.6696 | 3 | 16 | 14 | 0.74 | 0.00 | - | no | Open |
| 1854 | 5.120348751279889 | -0.745874 | -19.4718 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1492 | 5.173410198340179 | -0.881342 | -30.6169 | 2 | 16 | 14 | 0.74 | 0.00 | - | no | Open |
| 2063 | 5.494046800330639 | -0.70665 | -17.9614 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 2064 | 5.5227021558999105 | -0.713014 | -21.158 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2067 | 5.856314367990815 | -0.664373 | -24.1905 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 2159 | 6.040718742398015 | -0.547162 | -15.6191 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2164 | 6.041572309855619 | -0.58151 | -23.3042 | 6 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1653 | 6.512835649078139 | -0.775606 | -19.9428 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1973 | 6.567957822646802 | -0.641823 | -16.2586 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2160 | 6.730081020555924 | -0.824135 | -23.5686 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 2165 | 7.164056298765203 | -0.529178 | -17.4568 | 3 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 2161 | 7.17223281675543 | -0.569434 | -16.9176 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 2065 | 5.335903990429511 | -0.640522 | -17.7041 | 1 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1855 | 6.361201257002141 | -0.802277 | -21.0517 | 6 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2070 | 6.421228727958864 | -0.646572 | -13.7186 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1651 | 6.513799869194488 | -0.783516 | -24.2517 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2068 | 6.549572074874895 | -0.685123 | -27.2944 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1489 | 6.595113784166348 | -1.02957 | -29.4148 | 4 | 17 | 15 | 0.79 | 0.60 | - | yes | Open |
| 2163 | 6.5997178669874135 | -0.527382 | -19.9552 | 2 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1859 | 6.690910192706849 | -0.919152 | -22.5547 | 4 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2162 | 6.970925186046526 | -0.711588 | -19.6991 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1658 | 7.431725546759866 | -0.875743 | -24.5588 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1857 | 7.458068134327386 | -0.877162 | -25.5239 | 4 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1980 | 7.479763324274574 | -0.649752 | -14.4098 | 7 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1975 | 7.577884274875608 | -0.654721 | -19.76 | 4 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1491 | 7.58307822139469 | -0.963186 | -25.1335 | 6 | 17 | 13 | 0.68 | 0.80 | - | yes | Open |
| 2166 | 7.784480397484815 | -0.757901 | -21.5771 | 6 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1261 | 7.8530312487336715 | -0.785418 | -25.9705 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1493 | 7.905627625297495 | -1.09943 | -35.0127 | 9 | 16 | 13 | 0.68 | 0.80 | - | yes | Open |
| 1264 | 8.37025550709463 | -0.728596 | -15.0404 | 6 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1258 | 8.38551577917271 | -0.635064 | -14.0828 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1977 | 8.658869952225302 | -0.586422 | -19.2173 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1652 | 8.863984281204237 | -0.997616 | -30.3793 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1979 | 9.030285144414126 | -0.746749 | -19.9469 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2066 | 9.073828626459404 | -0.707236 | -20.7389 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1657 | 9.163318181122168 | -0.72054 | -18.7699 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1656 | 9.183858304432263 | -0.848506 | -30.3857 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1655 | 9.474323180269442 | -0.769357 | -26.1833 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1262 | 9.77871278558418 | -0.701137 | -21.4153 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1856 | 10.085351776091334 | -0.847612 | -25.5523 | 7 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1858 | 10.37472393762559 | -0.705281 | -19.2238 | 6 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1654 | 10.469333040089493 | -0.932332 | -24.5506 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1976 | 10.702892102883332 | -0.605448 | -17.729 | 1 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1263 | 10.744889026048872 | -0.892234 | -23.397 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1260 | 11.051206583020377 | -0.600583 | -10.3961 | 9 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1974 | 11.784774006585344 | -0.767574 | -22.0757 | 6 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1978 | 12.799248303308774 | -0.711428 | -24.9211 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1495 | 13.950851576382302 | -0.993831 | -28.3118 | 5 | 22 | 16 | 0.84 | 0.40 | - | yes | Current |
| 1257 | 14.71164888246367 | -0.704693 | -14.531 | 10 | 16 | 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
-28.312kcal/mol
Ligand efficiency (LE)
-0.9133kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.897
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
429.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.70
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
33.95kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
136.24kcal/mol
Minimised FF energy
102.28kcal/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.