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 (-1.013 kcal/mol/HA)
✓ Good fit quality (FQ -9.56)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (17.2 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.366
kcal/mol
LE
-1.013
kcal/mol/HA
Fit Quality
-9.56
FQ (Leeson)
HAC
28
heavy atoms
MW
374
Da
LogP
2.42
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: mixed
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 17.2 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 3
Clashes 16
Severe clashes 1
| Final rank | 8.23663025844888 | Score | -28.3664 |
|---|---|---|---|
| Inter norm | -1.21123 | Intra norm | 0.198139 |
| Top1000 | no | Excluded | yes |
| Contacts | 17 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 12 clashes; 1 protein clash; high strain Δ 21.6 | ||
| Residues | A:ALA212;A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLN166;A:LEU208;A:LEU209;A:MET163;A:NAP301;A:PHE171;A:PHE97;A:PRO167;A:PRO210;A:TYR174;A:VAL164;A:VAL211 | ||
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 | 10 | Native recall | 0.53 |
| Jaccard | 0.38 | RMSD | - |
| H-bond strict | 2 | Strict recall | 0.33 |
| H-bond same residue+role | 2 | Role recall | 0.40 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 878 | 5.151764811412993 | -0.797513 | -18.2199 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1123 | 5.694220904721237 | -1.17846 | -30.5307 | 7 | 15 | 12 | 0.63 | 0.40 | - | no | Open |
| 880 | 5.983531140926949 | -0.705043 | -13.9413 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 1581 | 7.267477622857065 | -0.887244 | -16.1619 | 10 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1176 | 7.414903963062568 | -0.908052 | -20.0444 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 1586 | 7.589349558442824 | -0.992616 | -25.644 | 15 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 1584 | 7.21115482623696 | -0.835791 | -19.8884 | 11 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1582 | 7.228672952198619 | -1.011 | -20.7076 | 15 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1122 | 7.831646225438104 | -1.26081 | -32.3451 | 11 | 16 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1124 | 8.124710367781676 | -1.34752 | -35.2625 | 10 | 15 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1120 | 8.23663025844888 | -1.21123 | -28.3664 | 8 | 17 | 10 | 0.53 | 0.40 | - | yes | Current |
| 881 | 8.260508591184918 | -0.715247 | -18.3194 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1177 | 8.275512512475922 | -1.12345 | -29.739 | 14 | 23 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1125 | 8.377764478916168 | -1.07186 | -27.4605 | 10 | 18 | 14 | 0.74 | 0.40 | - | yes | Open |
| 882 | 8.837321834503404 | -0.854772 | -15.2388 | 7 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1585 | 8.838518981129381 | -0.834553 | -18.4089 | 13 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1121 | 9.062731677201793 | -1.1159 | -28.415 | 6 | 15 | 11 | 0.58 | 0.40 | - | yes | Open |
| 1173 | 9.501258788101971 | -1.08173 | -29.0657 | 16 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1172 | 9.585146496999934 | -0.935562 | -18.0715 | 14 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 879 | 9.917960979683405 | -0.859654 | -22.7368 | 8 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1174 | 10.803856422427396 | -0.915727 | -18.8171 | 11 | 22 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1583 | 10.855453592613786 | -0.766744 | -18.3666 | 14 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 883 | 11.094780032477365 | -0.801976 | -15.4882 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1175 | 16.158590208868393 | -0.879257 | -18.5992 | 16 | 20 | 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
-28.366kcal/mol
Ligand efficiency (LE)
-1.0131kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.564
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
374.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.42
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.24kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
76.76kcal/mol
Minimised FF energy
59.52kcal/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.