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 (-0.581 kcal/mol/HA)
✓ Good fit quality (FQ -5.54)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (23.7 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-16.841
kcal/mol
LE
-0.581
kcal/mol/HA
Fit Quality
-5.54
FQ (Leeson)
HAC
29
heavy atoms
MW
394
Da
LogP
2.53
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.7 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 24
π–π 3
Clashes 12
Severe clashes 3
| Final rank | 10.208847296040425 | Score | -16.8413 |
|---|---|---|---|
| Inter norm | -0.977842 | Intra norm | 0.397108 |
| Top1000 | no | Excluded | yes |
| Contacts | 13 | H-bonds | 4 |
| Artifact reason | excluded; geometry warning; 14 clashes; 3 protein clashes; high strain Δ 30.7 | ||
| Residues | A:ARG14;A:CYS168;A:GLU217;A:LEU208;A:LEU209;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:TRP221;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 | 11 | Native recall | 0.58 |
| Jaccard | 0.52 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1077 | 5.003438419027329 | -1.04612 | -27.0807 | 11 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 1604 | 5.1910895123134075 | -0.815377 | -21.9974 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1608 | 5.33148680171199 | -0.767169 | -27.1261 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1163 | 5.551448951917198 | -0.77159 | -16.3561 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1605 | 5.595679038556167 | -0.763376 | -19.0878 | 5 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 1698 | 5.762804483422982 | -0.580681 | -8.8695 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 1606 | 5.931587814186224 | -0.628975 | -14.4266 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1164 | 6.094346852211321 | -0.766971 | -10.1997 | 3 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1162 | 6.444413830024239 | -0.835369 | -9.13326 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1166 | 6.475041900743294 | -0.836178 | -14.6246 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 1695 | 6.640473401922036 | -0.750944 | -17.3946 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1194 | 7.497948552462457 | -0.989691 | -18.8202 | 7 | 14 | 13 | 0.68 | 0.40 | - | no | Open |
| 1607 | 6.386067244284125 | -0.781274 | -20.0784 | 3 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1693 | 6.862943417541378 | -0.607459 | -13.793 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1081 | 7.351840382609471 | -0.99993 | -24.2698 | 9 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1193 | 8.30331011879626 | -1.03911 | -20.7889 | 8 | 20 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1694 | 8.838393030440574 | -0.646642 | -17.0159 | 6 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1198 | 8.936511162310344 | -0.9705 | -20.3664 | 8 | 15 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1603 | 9.05979073358385 | -0.745663 | -19.6442 | 12 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1195 | 9.180771122448231 | -0.98797 | -20.7422 | 7 | 20 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1197 | 9.58358171648457 | -0.901259 | -8.96109 | 9 | 17 | 16 | 0.84 | 0.40 | - | yes | Open |
| 1076 | 9.681030475258796 | -0.933328 | -19.2815 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1697 | 9.696589521284785 | -0.583552 | -16.0209 | 7 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1696 | 10.07190966349914 | -0.726935 | -18.2131 | 9 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1196 | 10.208847296040425 | -0.977842 | -16.8413 | 4 | 13 | 11 | 0.58 | 0.20 | - | yes | Current |
| 1080 | 10.389098008978085 | -1.07129 | -19.5439 | 6 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1078 | 11.897146124212874 | -1.01195 | -18.6481 | 8 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1079 | 12.37917067131761 | -0.953674 | -14.2889 | 8 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1165 | 12.644067386113937 | -0.776387 | -2.86358 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1167 | 12.696086250357059 | -0.73911 | -10.8795 | 5 | 17 | 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
-16.841kcal/mol
Ligand efficiency (LE)
-0.5807kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.544
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
394.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.53
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.66kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
98.28kcal/mol
Minimised FF energy
74.62kcal/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.