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
123.4 kcal/mol
Protein clashes
12
Internal clashes
12
Native overlap
contact recall 0.88, Jaccard 0.83, H-bond role recall 0.82
Reason: 12 protein-contact clashes, 12 internal clashes, strain 123.4 kcal/mol
strain ΔE 123.4 kcal/mol
12 protein-contact clashes
12 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (6/16 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.426 kcal/mol/HA)
✓ Good fit quality (FQ -4.26)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (71% SASA buried)
✗ Extreme strain energy (123.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-14.476
kcal/mol
LE
-0.426
kcal/mol/HA
Fit Quality
-4.26
FQ (Leeson)
HAC
34
heavy atoms
MW
512
Da
LogP
0.84
cLogP
Final rank
5.6558
rank score
Inter norm
-0.696
normalised
Contacts
16
H-bonds 16
Interaction summary
HBD 2
HBA 8
PC 1
HY 3
PI 3
CLASH 12
Interaction summary
HBD 2
HBA 8
PC 1
HY 3
PI 3
CLASH 12
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 8.
PC · Polar contacts (possible, no H geometry)
HBD?/HBA? — heavy-atom distance only, H geometry unavailable. May be real H-bonds.
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 | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 15 | Native recall | 0.88 |
| Jaccard | 0.83 | RMSD | - |
| HB strict | 9 | Strict recall | 0.69 |
| HB same residue+role | 9 | HB role recall | 0.82 |
| HB same residue | 9 | HB residue recall | 0.82 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 352 | 2.6591088902554145 | -0.663334 | -20.9923 | 12 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 294 | 2.8169198974226206 | -0.763427 | -26.2094 | 9 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 279 | 2.9386173620887566 | -0.824993 | -29.3038 | 8 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 276 | 3.5602412451860346 | -0.921957 | -25.3809 | 11 | 22 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 4.2664490731645195 | -0.737645 | -24.1163 | 16 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 258 | 5.655842000188189 | -0.696138 | -14.4763 | 16 | 16 | 15 | 0.88 | 0.82 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-14.476kcal/mol
Ligand efficiency (LE)
-0.4258kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-4.260
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
34HA
Physicochemical properties
Molecular weight
512.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.84
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
123.42kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
18.74kcal/mol
Minimised FF energy
-104.68kcal/mol
SASA & burial
✓ computed
SASA (unbound)
675.6Ų
Total solvent-accessible surface area of free ligand
BSA total
479.8Ų
Buried surface area upon binding
BSA apolar
270.1Ų
Hydrophobic contacts buried
BSA polar
209.7Ų
Polar contacts buried
Fraction buried
71.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
56.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2135.8Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
658.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)