Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
25.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.94, Jaccard 0.80, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.026 kcal/mol/HA)
✓ Good fit quality (FQ -9.90)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (69% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ High strain energy (25.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-30.785
kcal/mol
LE
-1.026
kcal/mol/HA
Fit Quality
-9.90
FQ (Leeson)
HAC
30
heavy atoms
MW
407
Da
LogP
4.37
cLogP
Interaction summary
HB 9
HY 4
PI 3
CLASH 5
⚠ Exposure 39%
Interaction summary
HB 9
HY 4
PI 3
CLASH 5
⚠ Exposure 39%
Partial hydrophobic solvent exposure
39% of hydrophobic surface appears solvent-exposed (9/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 23
Buried (contacted) 14
Exposed 9
LogP 4.37
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 3.514 | Score | -30.785 |
|---|---|---|---|
| Inter norm | -0.826 | Intra norm | -0.200 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 9 |
| Artifact reason | geometry warning; 10 clashes; 2 protein clashes; moderate strain Δ 25.1 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
CYS72
GLU138
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
LEU136
SER46
THR74
TYR49
| ||
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 | ||
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 | 16 | Native recall | 0.94 |
| Jaccard | 0.80 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 6 | HB residue recall | 0.55 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 78 | 2.3495097114281864 | -0.904408 | -21.4609 | 8 | 19 | 5 | 0.29 | 0.09 | - | no | Open |
| 92 | 2.864091147420997 | -1.26016 | -37.4515 | 7 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 120 | 3.3139732099751726 | -0.931907 | -37.2136 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 98 | 3.4681785343771554 | -0.82925 | -33.093 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 53 | 3.5138179344876916 | -0.82574 | -30.7847 | 9 | 19 | 16 | 0.94 | 0.45 | - | no | Current |
| 131 | 4.482789258165662 | -0.708568 | -22.7724 | 7 | 12 | 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
-30.785kcal/mol
Ligand efficiency (LE)
-1.0262kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.899
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
406.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.37
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.14kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-80.06kcal/mol
Minimised FF energy
-105.20kcal/mol
SASA & burial
✓ computed
SASA (unbound)
751.1Ų
Total solvent-accessible surface area of free ligand
BSA total
515.4Ų
Buried surface area upon binding
BSA apolar
456.2Ų
Hydrophobic contacts buried
BSA polar
59.2Ų
Polar contacts buried
Fraction buried
68.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
88.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2413.1Ų
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
680.1Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)