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
38.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.56, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
63% of hydrophobic surface is solvent-exposed (17/27 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.
✓ Excellent LE (-0.690 kcal/mol/HA)
✓ Good fit quality (FQ -7.11)
✓ Strong H-bond network (12 bonds)
✓ Good burial (60% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (38.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (17)
Score
-26.223
kcal/mol
LE
-0.690
kcal/mol/HA
Fit Quality
-7.11
FQ (Leeson)
HAC
38
heavy atoms
MW
541
Da
LogP
3.23
cLogP
Interaction summary
HB 12
HY 5
PI 2
CLASH 2
⚠ Exposure 63%
Interaction summary
HB 12
HY 5
PI 2
CLASH 2
⚠ Exposure 63%
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
63% of hydrophobic surface is solvent-exposed (17/27 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 27
Buried (contacted) 10
Exposed 17
LogP 3.23
H-bonds 12
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 5.238 | Score | -26.223 |
|---|---|---|---|
| Inter norm | -0.724 | Intra norm | 0.030 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 12 |
| Artifact reason | geometry warning; 17 clashes; 3 protein clashes; high strain Δ 38.4 | ||
| Residues |
ARG140
ARG144
ASP139
HIS105
HIS141
ARG116
ARG46
CYS72
GLY73
HIS14
ILE15
SER74
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXS | Contacts | 16 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG140
ARG144
ASN106
HIS105
HIS141
ARG46
ASP13
CYS72
GLY73
GLY75
GLY77
HIS14
ILE15
ILE76
SER74
TYR49
| ||
| Current overlap | 10 | Native recall | 0.62 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 4 | HB residue recall | 0.40 |
Protein summary
302 residues
| Protein target | T12 | Atoms | 4598 |
|---|---|---|---|
| Residues | 302 | Chains | 2 |
| Residue summary | ARG:576; ILE:456; VAL:448; GLU:360; ALA:340; LEU:304; TYR:252; HIS:204; PRO:196; THR:196; GLY:182; LYS:176; ASP:168; PHE:160; MET:153; SER:121 | ||
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:CSD72
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 531 | 3.242744825916433 | -0.725186 | -24.7121 | 3 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 506 | 5.237531043117076 | -0.723606 | -26.2233 | 12 | 12 | 10 | 0.62 | 0.40 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-26.223kcal/mol
Ligand efficiency (LE)
-0.6901kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.114
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
38HA
Physicochemical properties
Molecular weight
540.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.23
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.41kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
88.49kcal/mol
Minimised FF energy
50.08kcal/mol
SASA & burial
✓ computed
SASA (unbound)
838.0Ų
Total solvent-accessible surface area of free ligand
BSA total
504.8Ų
Buried surface area upon binding
BSA apolar
394.4Ų
Hydrophobic contacts buried
BSA polar
110.3Ų
Polar contacts buried
Fraction buried
60.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2362.1Ų
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
2454.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
781.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)