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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
82.9 kcal/mol
Protein clashes
0
Internal clashes
12
Native overlap
contact recall 0.62, Jaccard 0.50, H-bond role recall 0.00
Reason: 12 internal clashes, strain 82.9 kcal/mol
strain ΔE 82.9 kcal/mol
12 intramolecular clashes
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-0.603 kcal/mol/HA)
✓ Good fit quality (FQ -5.82)
✓ Strong H-bond network (7 bonds)
✗ Extreme strain energy (82.9 kcal/mol)
✗ Poor burial (40% SASA buried)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-18.083
kcal/mol
LE
-0.603
kcal/mol/HA
Fit Quality
-5.82
FQ (Leeson)
HAC
30
heavy atoms
MW
440
Da
LogP
-0.85
cLogP
Interaction summary
HB 7
HY 8
PI 1
CLASH 0
⚠ Exposure 41%
Interaction summary
HB 7
HY 8
PI 1
CLASH 0
⚠ Exposure 41%
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
No clash · clashes detected for this pose.
Partial hydrophobic solvent exposure
41% of hydrophobic surface appears solvent-exposed (7/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 10
Exposed 7
LogP -0.85
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.774 | Score | -18.083 |
|---|---|---|---|
| Inter norm | -0.734 | Intra norm | 0.132 |
| Top1000 | no | Excluded | no |
| Contacts | 7 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 2 protein clashes; high strain Δ 82.8 | ||
| Residues |
ASN402
GLU467
LYS410
PHE396
SER394
SER395
THR397
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 9IFH | Contacts | 8 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ASN402
GLU467
LEU399
PHE396
PRO398
SER394
SER470
THR397
| ||
| Current overlap | 5 | Native recall | 0.62 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
Protein summary
492 residues
| Protein target | T20 | Atoms | 7539 |
|---|---|---|---|
| Residues | 492 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:221 | ||
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:FAD501
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 596 | 2.3252128428059002 | -1.13727 | -26.7529 | 10 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 630 | 3.1472053235268254 | -1.23245 | -33.5359 | 14 | 23 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 3.7738766762258784 | -0.734441 | -18.0833 | 7 | 7 | 5 | 0.62 | 0.00 | - | no | Current |
| 621 | 4.08861341711193 | -0.995124 | -23.7831 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 609 | 4.296899294431502 | -1.03684 | -25.0444 | 11 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 4.996400449539082 | -0.832977 | -22.274 | 10 | 10 | 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
-18.083kcal/mol
Ligand efficiency (LE)
-0.6028kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.815
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
440.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.85
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
82.90kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
113.18kcal/mol
Minimised FF energy
30.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
611.7Ų
Total solvent-accessible surface area of free ligand
BSA total
242.4Ų
Buried surface area upon binding
BSA apolar
137.8Ų
Hydrophobic contacts buried
BSA polar
104.6Ų
Polar contacts buried
Fraction buried
39.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
56.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2918.7Ų
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
4069.8Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1521.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)