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 high
Native strong
SASA done
Strain ΔE
18.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.94, Jaccard 0.89, H-bond role recall 0.45
Reason: no major geometry red flags detected
2 protein-contact clashes
35% of hydrophobic surface appears solvent-exposed (6/17 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 (-0.843 kcal/mol/HA)
✓ Good fit quality (FQ -7.77)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (18.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (14)
Score
-21.929
kcal/mol
LE
-0.843
kcal/mol/HA
Fit Quality
-7.77
FQ (Leeson)
HAC
26
heavy atoms
MW
424
Da
LogP
2.94
cLogP
Interaction summary
HB 9
HY 4
PI 2
CLASH 2
⚠ Exposure 35%
Interaction summary
HB 9
HY 4
PI 2
CLASH 2
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP 2.94
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 4.619 | Score | -21.929 |
|---|---|---|---|
| Inter norm | -0.941 | Intra norm | 0.097 |
| Top1000 | no | Excluded | no |
| Contacts | 17 | H-bonds | 9 |
| Artifact reason | geometry warning; 14 clashes; 3 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU136
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 | 0.89 | RMSD | - |
| HB strict | 4 | Strict recall | 0.31 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 118 | 1.679070958897312 | -0.990653 | -16.9014 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 96 | 2.1404485338200856 | -0.907212 | -17.1648 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 96 | 2.224977979710623 | -0.981451 | -19.9899 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 100 | 3.3899381258696657 | -0.826209 | -21.5758 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 129 | 4.486299856448621 | -0.755038 | -13.3141 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 51 | 4.619208262629881 | -0.940757 | -21.9289 | 9 | 17 | 16 | 0.94 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.929kcal/mol
Ligand efficiency (LE)
-0.8434kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.771
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
424.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.94
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.37kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-63.22kcal/mol
Minimised FF energy
-81.59kcal/mol
SASA & burial
✓ computed
SASA (unbound)
623.6Ų
Total solvent-accessible surface area of free ligand
BSA total
418.9Ų
Buried surface area upon binding
BSA apolar
323.1Ų
Hydrophobic contacts buried
BSA polar
95.8Ų
Polar contacts buried
Fraction buried
67.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2175.2Ų
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
762.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)