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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
75.4 kcal/mol
Protein clashes
6
Internal clashes
9
Native overlap
contact recall 0.84, Jaccard 0.70, H-bond role recall 0.40
Reason: 9 internal clashes, strain 75.4 kcal/mol
strain ΔE 75.4 kcal/mol
6 protein-contact clashes
9 intramolecular clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.881 kcal/mol/HA)
✓ Good fit quality (FQ -8.96)
✓ Good H-bonds (3 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Extreme strain energy (75.4 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (10)
✗ Many internal clashes (18)
Score
-31.735
kcal/mol
LE
-0.881
kcal/mol/HA
Fit Quality
-8.96
FQ (Leeson)
HAC
36
heavy atoms
MW
525
Da
LogP
4.53
cLogP
Final rank
2.7720
rank score
Inter norm
-0.974
normalised
Contacts
20
H-bonds 8
Interaction summary
HBD 2
HBA 1
HY 8
PI 3
CLASH 9
Interaction summary
HBD 2
HBA 1
HY 8
PI 3
CLASH 9
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 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 | 16 | Native recall | 0.84 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 2 | Strict recall | 0.33 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 3 | HB residue recall | 0.60 |
Protein summary
258 residues
| Protein target | T08 | Atoms | 3881 |
|---|---|---|---|
| Residues | 258 | Chains | 2 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 296 | 2.7719581256481582 | -0.973682 | -31.7345 | 8 | 20 | 16 | 0.84 | 0.40 | - | no | Current |
| 278 | 4.873498478943113 | -0.844723 | -30.8097 | 11 | 16 | 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
-31.735kcal/mol
Ligand efficiency (LE)
-0.8815kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.959
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
524.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.53
Lipinski: ≤ 5
Rotatable bonds
11
Conformational strain (MMFF94s)
Strain energy (ΔE)
75.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-5.42kcal/mol
Minimised FF energy
-80.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
793.8Ų
Total solvent-accessible surface area of free ligand
BSA total
709.9Ų
Buried surface area upon binding
BSA apolar
566.9Ų
Hydrophobic contacts buried
BSA polar
143.0Ų
Polar contacts buried
Fraction buried
89.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1736.6Ų
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
924.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)