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 (-0.750 kcal/mol/HA)
✓ Good fit quality (FQ -7.44)
✓ Strong H-bond network (9 bonds)
✗ Very high strain energy (23.4 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-24.753
kcal/mol
LE
-0.750
kcal/mol/HA
Fit Quality
-7.44
FQ (Leeson)
HAC
33
heavy atoms
MW
447
Da
LogP
2.78
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 23.4 kcal/mol
Interaction summary
Collapsible panels
H-bonds 9
Hydrophobic 24
π–π 4
Clashes 12
Severe clashes 1
| Final rank | 8.53325070554073 | Score | -24.7526 |
|---|---|---|---|
| Inter norm | -0.919496 | Intra norm | 0.169416 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 9 |
| Artifact reason | excluded; geometry warning; 13 clashes; 1 protein clash; high strain Δ 39.6 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:MET163;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TYR174;A:VAL164 | ||
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | 12 | Native recall | 0.63 |
| Jaccard | 0.52 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 1 | Role recall | 0.20 |
| H-bond same residue | 2 | Residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1299 | 5.752180216571295 | -0.768978 | -16.8738 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 827 | 6.406292800265652 | -0.596367 | -11.4458 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1303 | 6.465793938784395 | -0.635253 | -15.7051 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1050 | 6.54588703754338 | -0.984045 | -28.9382 | 8 | 21 | 13 | 0.68 | 0.40 | - | no | Open |
| 1732 | 6.658729660090414 | -0.440653 | -6.02426 | 8 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 3130 | 7.382563025709787 | -0.550936 | -9.26817 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1049 | 7.568665222351072 | -0.964885 | -23.2533 | 12 | 18 | 12 | 0.63 | 0.40 | - | no | Open |
| 795 | 9.144947144102693 | -0.689423 | -14.8045 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 831 | 6.477716366125133 | -0.65885 | -13.2458 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1729 | 6.892186765656801 | -0.472582 | -10.4809 | 7 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 830 | 6.921351728111539 | -0.614096 | -10.0328 | 5 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3131 | 7.715012804359663 | -0.542545 | -14.4034 | 4 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1733 | 7.779429151432847 | -0.492017 | -9.69993 | 7 | 10 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1054 | 7.7850298411484715 | -0.884636 | -25.6916 | 8 | 19 | 14 | 0.74 | 0.40 | - | yes | Open |
| 1053 | 7.910783283220195 | -0.921235 | -24.2883 | 11 | 19 | 12 | 0.63 | 0.40 | - | yes | Open |
| 796 | 8.275569663309865 | -0.684241 | -18.6059 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1734 | 8.465194828859476 | -0.489927 | -11.5371 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1056 | 8.53325070554073 | -0.919496 | -24.7526 | 9 | 16 | 12 | 0.63 | 0.20 | - | yes | Current |
| 791 | 8.755780369521949 | -0.763071 | -14.473 | 15 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1730 | 8.918006274137584 | -0.583552 | -16.8151 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1055 | 9.346918705545136 | -0.879942 | -25.302 | 8 | 16 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1302 | 9.3534034729308 | -0.615452 | -10.8719 | 5 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 832 | 9.441916496247993 | -0.632948 | -16.0685 | 9 | 12 | 0 | 0.00 | 0.00 | - | yes | Open |
| 829 | 9.451566458846896 | -0.677978 | -6.62565 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3126 | 9.50785916439563 | -0.694616 | -16.7147 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1304 | 9.764372204867888 | -0.72286 | -19.2905 | 3 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1301 | 10.310890285662667 | -0.851027 | -14.1153 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3132 | 10.444857375642064 | -0.778666 | -16.8779 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3127 | 10.531440804148529 | -0.780129 | -20.4372 | 5 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3128 | 10.599414779357968 | -0.657745 | -16.0162 | 3 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3129 | 10.850975383060266 | -0.552587 | -12.4876 | 4 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 792 | 10.853850896897907 | -0.786848 | -20.8854 | 12 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 828 | 11.056936513202471 | -0.670967 | -15.8784 | 8 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1300 | 11.184958117667579 | -0.84987 | -23.53 | 5 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1731 | 12.034641062842804 | -0.434355 | -8.65102 | 7 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 793 | 12.18267700845879 | -0.785489 | -11.3927 | 16 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 794 | 12.285590442450683 | -0.930086 | -25.1977 | 9 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1052 | 13.376173420751345 | -1.28243 | -31.5208 | 10 | 17 | 11 | 0.58 | 0.60 | - | yes | Open |
| 1051 | 13.39531970759979 | -1.1525 | -28.5081 | 8 | 17 | 11 | 0.58 | 0.80 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.753kcal/mol
Ligand efficiency (LE)
-0.7501kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.442
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
447.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.78
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
23.44kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.16kcal/mol
Minimised FF energy
69.72kcal/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.