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 (-0.901 kcal/mol/HA)
✓ Good fit quality (FQ -9.16)
✓ Good H-bonds (5 bonds)
✗ Very high strain energy (32.6 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-32.451
kcal/mol
LE
-0.901
kcal/mol/HA
Fit Quality
-9.16
FQ (Leeson)
HAC
36
heavy atoms
MW
482
Da
LogP
5.06
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 32.6 kcal/mol
Interaction summary
Collapsible panels
H-bonds 5
Hydrophobic 24
π–π 4
Clashes 12
Severe clashes 1
| Final rank | 8.632533309205227 | Score | -32.4514 |
|---|---|---|---|
| Inter norm | -0.784229 | Intra norm | -0.1172 |
| Top1000 | no | Excluded | yes |
| Contacts | 16 | H-bonds | 5 |
| Artifact reason | excluded; geometry warning; 15 clashes; 1 protein clash; high strain Δ 33.4 | ||
| Residues | A:ARG14;A:ASP161;A:GLU217;A:LEU208;A:LEU209;A:LYS220;A:MET169;A:MET213;A:NAP301;A:PHE171;A:PHE97;A:PRO210;A:SER95;A:TRP221;A:TYR174;D:HIS267 | ||
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 | 12 | Native recall | 0.63 |
| 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 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 2184 | 4.614540518243182 | -0.818501 | -26.2491 | 2 | 17 | 14 | 0.74 | 0.00 | - | no | Open |
| 2183 | 4.68727944917791 | -0.690042 | -22.7785 | 0 | 15 | 13 | 0.68 | 0.00 | - | no | Open |
| 3165 | 5.335877589857202 | -0.707983 | -27.7628 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 2186 | 5.879476557389142 | -0.795684 | -32.7539 | 1 | 13 | 13 | 0.68 | 0.00 | - | no | Open |
| 3160 | 7.490407099445143 | -0.580747 | -17.3863 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 3161 | 7.882129821552622 | -0.72906 | -17.4267 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 2187 | 6.585916680181024 | -0.695498 | -23.5563 | 0 | 14 | 13 | 0.68 | 0.00 | - | yes | Open |
| 2188 | 6.638558359145298 | -0.782849 | -29.2739 | 0 | 15 | 12 | 0.63 | 0.00 | - | yes | Open |
| 2185 | 8.632533309205227 | -0.784229 | -32.4514 | 5 | 16 | 12 | 0.63 | 0.20 | - | yes | Current |
| 3163 | 9.230738807532372 | -0.704018 | -30.3141 | 3 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3164 | 12.54575112579421 | -0.692076 | -22.3496 | 3 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 3162 | 13.238925520518073 | -0.678001 | -25.0814 | 6 | 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
-32.451kcal/mol
Ligand efficiency (LE)
-0.9014kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.162
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
481.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.06
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
134.38kcal/mol
Minimised FF energy
101.78kcal/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.