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 (-1.228 kcal/mol/HA)
✓ Good fit quality (FQ -10.47)
✓ Strong H-bond network (7 bonds)
✗ High strain energy (16.1 kcal/mol)
✗ Geometry warnings
✗ Protein contact clashes
ℹ SASA not computed
Score
-25.779
kcal/mol
LE
-1.228
kcal/mol/HA
Fit Quality
-10.47
FQ (Leeson)
HAC
21
heavy atoms
MW
307
Da
LogP
1.71
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 16.1 kcal/mol
Interaction summary
Collapsible panels
H-bonds 7
Hydrophobic 18
π–π 2
Clashes 3
Severe clashes 0
| Final rank | 2.7870416321352645 | Score | -25.7789 |
|---|---|---|---|
| Inter norm | -1.52737 | Intra norm | 0.299802 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 3 protein contact clashes; high strain Δ 26.8 | ||
| Residues | A:ARG14;A:ASP161;A:CYS168;A:GLY205;A:LEU208;A:LEU209;A:LEU263;A:MET163;A:MET213;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 | 15 | Native recall | 0.79 |
| Jaccard | 0.71 | RMSD | - |
| H-bond strict | 5 | Strict recall | 0.83 |
| H-bond same residue+role | 4 | Role recall | 0.80 |
| H-bond same residue | 4 | Residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1154 | 1.994071832540214 | -1.48556 | -25.3543 | 7 | 17 | 15 | 0.79 | 0.80 | - | no | Open |
| 1152 | 2.432058040367128 | -1.46558 | -25.8481 | 7 | 17 | 15 | 0.79 | 0.80 | - | no | Open |
| 2565 | 2.6903141750786395 | -1.17616 | -22.9912 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 1148 | 2.7870416321352645 | -1.52737 | -25.7789 | 7 | 17 | 15 | 0.79 | 0.80 | - | no | Current |
| 1150 | 3.1342219026699247 | -1.41158 | -25.2853 | 7 | 17 | 15 | 0.79 | 0.60 | - | no | Open |
| 2563 | 5.053100332607366 | -1.05388 | -22.081 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2564 | 5.378442657506171 | -1.11044 | -23.005 | 3 | 18 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2562 | 5.433527013535248 | -1.09184 | -21.6078 | 2 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2559 | 6.42490854696753 | -1.27478 | -21.6805 | 3 | 16 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2561 | 7.732318744832049 | -1.13251 | -19.9453 | 4 | 17 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2566 | 8.330865954274609 | -1.10945 | -20.0265 | 9 | 19 | 0 | 0.00 | 0.00 | - | yes | Open |
| 2560 | 8.34233097022693 | -1.1334 | -20.7664 | 6 | 20 | 0 | 0.00 | 0.00 | - | yes | Open |
| 1153 | 8.89312562391331 | -1.14068 | -24.0029 | 5 | 16 | 13 | 0.68 | 0.60 | - | yes | Open |
| 1155 | 9.328601816548494 | -1.29952 | -26.6414 | 4 | 17 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1151 | 9.735707183582283 | -1.12798 | -23.2641 | 4 | 17 | 14 | 0.74 | 0.60 | - | yes | Open |
| 1149 | 10.361254172244239 | -1.2739 | -25.8909 | 4 | 17 | 14 | 0.74 | 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
-25.779kcal/mol
Ligand efficiency (LE)
-1.2276kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.471
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
306.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.71
Lipinski: ≤ 5
Rotatable bonds
1
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.06kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
68.72kcal/mol
Minimised FF energy
52.66kcal/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.