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
27.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.88, Jaccard 0.75, H-bond role recall 0.73
Reason: no major geometry red flags detected
1 protein-contact clashes
73% of hydrophobic surface is solvent-exposed (16/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Good LE (-0.355 kcal/mol/HA)
✓ Good fit quality (FQ -3.52)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ High strain energy (27.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-11.712
kcal/mol
LE
-0.355
kcal/mol/HA
Fit Quality
-3.52
FQ (Leeson)
HAC
33
heavy atoms
MW
489
Da
LogP
3.03
cLogP
Interaction summary
HB 16
HY 1
PI 1
CLASH 1
⚠ Exposure 72%
Interaction summary
HB 16
HY 1
PI 1
CLASH 1
⚠ Exposure 72%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
73% of hydrophobic surface is solvent-exposed (16/22 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 22
Buried (contacted) 6
Exposed 16
LogP 3.03
H-bonds 16
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 3.968 | Score | -11.712 |
|---|---|---|---|
| Inter norm | -0.753 | Intra norm | 0.370 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 16 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; moderate strain Δ 27.8 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
ASP44
CYS72
GLY73
GLY75
HIS105
HIS14
HIS141
LEU101
SER46
THR45
THR74
TYR49
| ||
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 | 0.75 | RMSD | - |
| HB strict | 10 | Strict recall | 0.77 |
| HB same residue+role | 8 | HB role recall | 0.73 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 502 | 3.075927174650944 | -0.804721 | -16.4608 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 471 | 3.967755251037284 | -0.752787 | -11.712 | 16 | 18 | 15 | 0.88 | 0.73 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-11.712kcal/mol
Ligand efficiency (LE)
-0.3549kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-3.521
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
488.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.03
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
27.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-45.13kcal/mol
Minimised FF energy
-72.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
776.1Ų
Total solvent-accessible surface area of free ligand
BSA total
509.1Ų
Buried surface area upon binding
BSA apolar
323.4Ų
Hydrophobic contacts buried
BSA polar
185.7Ų
Polar contacts buried
Fraction buried
65.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
63.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2282.8Ų
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
700.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)