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
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
13.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.69, Jaccard 0.58, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.250 kcal/mol/HA)
✓ Good fit quality (FQ -11.36)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ Moderate strain (13.0 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (6)
Score
-31.239
kcal/mol
LE
-1.250
kcal/mol/HA
Fit Quality
-11.36
FQ (Leeson)
HAC
25
heavy atoms
MW
354
Da
LogP
2.02
cLogP
Interaction summary
HB 12
HY 6
PI 3
CLASH 2
⚠ Exposure 52%
Interaction summary
HB 12
HY 6
PI 3
CLASH 2
⚠ Exposure 52%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 8
Exposed 9
LogP 2.02
H-bonds 12
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 2.697 | Score | -31.239 |
|---|---|---|---|
| Inter norm | -1.261 | Intra norm | 0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 12 |
| Artifact reason | geometry warning; 6 clashes; 2 protein clashes | ||
| Residues |
ARG140
ARG144
HIS105
HIS141
MET101
TYR97
ARG116
ARG46
ASP13
CYS72
GLY73
HIS14
ILE15
SER74
| ||
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
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 | 11 | Native recall | 0.69 |
| Jaccard | 0.58 | RMSD | - |
| HB strict | 6 | Strict recall | 0.50 |
| HB same residue+role | 4 | HB role recall | 0.40 |
| HB same residue | 6 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 37 | 0.004767659810388354 | -1.37861 | -30.4982 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 30 | 2.6969487096829448 | -1.26117 | -31.2387 | 12 | 14 | 11 | 0.69 | 0.40 | - | no | Current |
| 26 | 3.0481352297410775 | -0.910607 | -17.2426 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 3.230473428426704 | -0.987778 | -23.9638 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 32 | 3.8545254112429492 | -1.1403 | -20.7475 | 6 | 13 | 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
-31.239kcal/mol
Ligand efficiency (LE)
-1.2495kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.360
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
353.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.02
Lipinski: ≤ 5
Rotatable bonds
3
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-127.24kcal/mol
Minimised FF energy
-140.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
598.3Ų
Total solvent-accessible surface area of free ligand
BSA total
408.8Ų
Buried surface area upon binding
BSA apolar
323.9Ų
Hydrophobic contacts buried
BSA polar
84.8Ų
Polar contacts buried
Fraction buried
68.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2112.7Ų
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
847.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)