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 (-0.910 kcal/mol/HA)
✓ Good fit quality (FQ -8.87)
✓ Good H-bonds (4 bonds)
✗ Very high strain energy (26.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-28.220
kcal/mol
LE
-0.910
kcal/mol/HA
Fit Quality
-8.87
FQ (Leeson)
HAC
31
heavy atoms
MW
421
Da
LogP
-0.34
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, protein contact clashes, strain 26.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 4
Hydrophobic 21
π–π 3
Clashes 6
Severe clashes 0
| Final rank | 5.466725979332567 | Score | -28.2197 |
|---|---|---|---|
| Inter norm | -1.06122 | Intra norm | 0.150721 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 4 |
| Artifact reason | geometry warning; 17 clashes; 6 protein contact clashes; high strain Δ 30.7 | ||
| Residues | A:ARG14;A:ASN175;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LYS13;A:MET163;A:NAP301;A:PHE97;A:PRO167;A:PRO210;A:SER207;A:TYR174;A:VAL164;A:VAL206;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 | 12 | Native recall | 0.63 |
| Jaccard | 0.48 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1194 | 5.466725979332567 | -1.06122 | -28.2197 | 4 | 18 | 12 | 0.63 | 0.40 | - | no | Current |
| 1198 | 6.221328890971486 | -1.14839 | -30.5185 | 10 | 15 | 12 | 0.63 | 0.80 | - | no | Open |
| 1488 | 7.285544461068796 | -0.766167 | -21.2539 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 1193 | 7.554299538595485 | -1.05048 | -27.9446 | 12 | 15 | 9 | 0.47 | 0.40 | - | no | Open |
| 1196 | 7.318867442376427 | -0.935129 | -23.6139 | 12 | 16 | 10 | 0.53 | 0.40 | - | yes | Open |
| 1192 | 8.052524400964316 | -1.10805 | -33.7137 | 5 | 16 | 11 | 0.58 | 0.20 | - | yes | Open |
| 1489 | 8.411024238175122 | -0.788953 | -14.3344 | 6 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1197 | 8.891419257546488 | -1.0263 | -29.5759 | 12 | 15 | 9 | 0.47 | 0.40 | - | yes | Open |
| 1485 | 9.280173969850093 | -0.70491 | -11.2643 | 9 | 9 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1490 | 9.411386545350116 | -0.698673 | -13.0662 | 9 | 11 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1487 | 9.927926558126137 | -0.71471 | -18.3399 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1191 | 10.614700195417168 | -0.997848 | -16.6423 | 7 | 16 | 11 | 0.58 | 0.60 | - | yes | Open |
| 1486 | 10.999130185955533 | -0.639955 | -16.4797 | 9 | 15 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1492 | 11.044445367730235 | -0.710975 | -20.5088 | 9 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1491 | 13.382989889053693 | -0.735607 | -21.7688 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1195 | 13.482300131113973 | -1.11646 | -27.1816 | 12 | 20 | 12 | 0.63 | 0.60 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-28.220kcal/mol
Ligand efficiency (LE)
-0.9103kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.869
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
421.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.34
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
106.57kcal/mol
Minimised FF energy
79.75kcal/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.