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 (-0.673 kcal/mol/HA)
✓ Good fit quality (FQ -6.84)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (37.8 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-24.227
kcal/mol
LE
-0.673
kcal/mol/HA
Fit Quality
-6.84
FQ (Leeson)
HAC
36
heavy atoms
MW
499
Da
LogP
1.32
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 37.8 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 1
Clashes 8
Severe clashes 0
| Final rank | 7.328521300895317 | Score | -24.2265 |
|---|---|---|---|
| Inter norm | -0.835982 | Intra norm | 0.163024 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | geometry warning; 14 clashes; 8 protein contact clashes; high strain Δ 57.8 | ||
| Residues | A:ARG14;A:ASN36;A:ASP161;A:CYS168;A:LEU208;A:LEU209;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:PRO99;A:TRP221;A:TYR174;A:TYR98;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.75 | 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: 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2011 | 5.706027826547977 | -0.743037 | -26.1446 | 5 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 2010 | 5.9821142219563175 | -0.743174 | -21.2134 | 5 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 2012 | 6.051728550566184 | -0.900154 | -28.1429 | 2 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 691 | 6.22419709568692 | -0.77832 | -29.295 | 4 | 17 | 15 | 0.79 | 0.40 | - | no | Open |
| 1157 | 6.367278112405428 | -0.574476 | -19.1031 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 689 | 7.328521300895317 | -0.835982 | -24.2265 | 5 | 16 | 15 | 0.79 | 0.40 | - | no | Current |
| 2905 | 7.425182853787874 | -0.547023 | -18.3027 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2903 | 7.478732233143111 | -0.489011 | -16.5786 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 2904 | 8.13758035989908 | -0.51539 | -14.5457 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 1156 | 8.144375397084657 | -0.604565 | -18.3073 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2902 | 7.706660613385158 | -0.610535 | -20.7255 | 8 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2013 | 7.72529690787295 | -0.860957 | -25.1423 | 5 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1159 | 8.146773064511025 | -0.65646 | -20.8734 | 10 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 690 | 9.409315266972218 | -1.05271 | -26.0105 | 4 | 17 | 15 | 0.79 | 0.20 | - | yes | Open |
| 1158 | 9.71105529201685 | -0.731116 | -19.4621 | 9 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 688 | 10.094372295044739 | -0.844333 | -21.5743 | 4 | 14 | 13 | 0.68 | 0.20 | - | yes | Open |
Molecular metrics
FreeSASA-based burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.227kcal/mol
Ligand efficiency (LE)
-0.6730kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.840
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
498.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.32
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.82kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.93kcal/mol
Minimised FF energy
19.11kcal/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.