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 (-1.376 kcal/mol/HA)
✓ Good fit quality (FQ -11.73)
✓ Strong H-bond network (8 bonds)
✗ High strain energy (10.5 kcal/mol)
✗ Geometry warnings
ℹ SASA not computed
Score
-28.891
kcal/mol
LE
-1.376
kcal/mol/HA
Fit Quality
-11.73
FQ (Leeson)
HAC
21
heavy atoms
MW
301
Da
LogP
3.21
cLogP
Overall: Promising but geometrically suspicious
Binding evidence: strong
Native-like contacts: strong
Ligand efficiency: excellent
Geometry reliability: low
Reason: geometry warning, clashes, strain 10.5 kcal/mol
Interaction summary
Collapsible panels
H-bonds 8
Hydrophobic 24
π–π 2
Clashes 16
Severe clashes 3
| Final rank | 9.230390786950247 | Score | -28.8908 |
|---|---|---|---|
| Inter norm | -1.46084 | Intra norm | 0.0850903 |
| Top1000 | no | Excluded | yes |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | excluded; geometry warning; 9 clashes; 3 protein clashes; moderate strain Δ 13.4 | ||
| Residues | A:ARG14;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:NAP301;A:PHE97;A:PRO210;A:SER207;A:SER95;A:TRP221;A:TYR174;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 | 13 | Native recall | 0.68 |
| Jaccard | 0.62 | RMSD | - |
| H-bond strict | 3 | Strict recall | 0.50 |
| H-bond same residue+role | 3 | Role recall | 0.60 |
| H-bond same residue | 3 | Residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1792 | 1.4918963490611599 | -1.50673 | -28.6964 | 8 | 13 | 13 | 0.68 | 0.40 | - | no | Open |
| 2253 | 1.6428988416419488 | -0.81451 | -16.028 | 3 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 1579 | 2.4535848355549774 | -1.17599 | -22.9774 | 3 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 2075 | 3.9923955234372066 | -1.08918 | -21.0466 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 1794 | 3.9844321309780257 | -1.371 | -26.0197 | 7 | 14 | 13 | 0.68 | 0.40 | - | yes | Open |
| 1578 | 4.065305819596276 | -1.29964 | -25.3355 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1580 | 4.212532780515022 | -1.29502 | -25.6162 | 2 | 13 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2076 | 5.473465590472017 | -1.26719 | -25.7151 | 7 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2251 | 5.685960752915353 | -0.972159 | -18.4492 | 2 | 14 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2074 | 6.105766032619169 | -1.40164 | -21.5647 | 7 | 21 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1793 | 9.230390786950247 | -1.46084 | -28.8908 | 8 | 15 | 13 | 0.68 | 0.60 | - | yes | Current |
| 2252 | 11.706424756399004 | -0.973628 | -19.2261 | 7 | 14 | 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
-28.891kcal/mol
Ligand efficiency (LE)
-1.3758kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.735
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
301.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.21
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
35.34kcal/mol
Minimised FF energy
24.87kcal/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.