Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
28.2 kcal/mol
Protein clashes
2
Internal clashes
12
Native overlap
contact recall 0.63, Jaccard 0.57, H-bond role recall 0.40
Reason: 12 internal clashes
2 protein-contact clashes
12 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.782 kcal/mol/HA)
✓ Good fit quality (FQ -7.76)
✓ Good H-bonds (3 bonds)
✓ Deep burial (76% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ High strain energy (28.2 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (12)
Score
-25.815
kcal/mol
LE
-0.782
kcal/mol/HA
Fit Quality
-7.76
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
4.67
cLogP
Final rank
0.6929
rank score
Inter norm
-0.935
normalised
Contacts
14
H-bonds 8
Interaction summary
HBD 3
HY 8
PI 3
CLASH 0
Interaction summary
HBD 3
HY 8
PI 3
CLASH 0
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 1.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
No clash · clashes detected for this pose.
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | TbPTR1_cW_6RX6_Ready | Contacts | 19 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG14
ASP161
CYS168
GLY205
LEU208
LEU209
LYS178
MET213
NAP301
PHE171
PHE97
PRO210
PRO99
SER207
SER95
TRP221
TYR174
TYR98
VAL206
| ||
| Current overlap | 12 | Native recall | 0.63 |
| Jaccard | 0.57 | RMSD | - |
| HB strict | 3 | Strict recall | 0.50 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | ||
Receptor context
1 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 1
Excluded HETATM 0
Kept cofactors / ions
A:NAP301
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 265 | 0.6928685697560298 | -0.935497 | -25.815 | 8 | 14 | 12 | 0.63 | 0.40 | - | no | Current |
| 259 | 0.9830793049011827 | -0.748171 | -20.7925 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 254 | 1.202887207889216 | -0.717884 | -18.2943 | 3 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 2.6034471676550193 | -0.91548 | -22.7969 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 3.7049459538704093 | -0.725884 | -19.9589 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.815kcal/mol
Ligand efficiency (LE)
-0.7823kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.762
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.67
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
56.31kcal/mol
Minimised FF energy
28.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
729.1Ų
Total solvent-accessible surface area of free ligand
BSA total
552.9Ų
Buried surface area upon binding
BSA apolar
441.1Ų
Hydrophobic contacts buried
BSA polar
111.8Ų
Polar contacts buried
Fraction buried
75.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1736.8Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA
2051.9Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
918.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)