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
Likely artefact or unreliable pose
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
39.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.62, Jaccard 0.42, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
44% of hydrophobic surface appears solvent-exposed (17/39 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 (-0.475 kcal/mol/HA)
✓ Good fit quality (FQ -5.10)
✓ Strong H-bond network (9 bonds)
✓ Good burial (42% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Very high strain energy (39.0 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (8)
✗ Many internal clashes (16)
Score
-21.381
kcal/mol
LE
-0.475
kcal/mol/HA
Fit Quality
-5.10
FQ (Leeson)
HAC
45
heavy atoms
MW
619
Da
LogP
8.03
cLogP
Interaction summary
HB 9
HY 9
PI 1
CLASH 1
⚠ Exposure 43%
Interaction summary
HB 9
HY 9
PI 1
CLASH 1
⚠ Exposure 43%
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (17/39 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 39
Buried (contacted) 22
Exposed 17
LogP 8.03
H-bonds 9
Exposed fragments:
phenyl (5/5 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (10 atoms exposed)
| Final rank | 2.706 | Score | -21.381 |
|---|---|---|---|
| Inter norm | -0.415 | Intra norm | -0.061 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 9 |
| Artifact reason | geometry warning; 16 clashes; 8 protein contact clashes; high strain Δ 39.0 | ||
| Residues |
ASN402
GLU466
HIS461
LEU399
LYS407
LYS410
PHE396
PRO398
THR397
| ||
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
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 | 0.42 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 80 | 2.7055510612303437 | -0.414504 | -21.3815 | 9 | 9 | 5 | 0.62 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.381kcal/mol
Ligand efficiency (LE)
-0.4751kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.103
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
45HA
Physicochemical properties
Molecular weight
618.9Da
Lipinski: ≤ 500 Da
LogP (cLogP)
8.03
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
38.96kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
131.60kcal/mol
Minimised FF energy
92.64kcal/mol
SASA & burial
✓ computed
SASA (unbound)
883.4Ų
Total solvent-accessible surface area of free ligand
BSA total
367.5Ų
Buried surface area upon binding
BSA apolar
286.7Ų
Hydrophobic contacts buried
BSA polar
80.8Ų
Polar contacts buried
Fraction buried
41.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3309.5Ų
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
1526.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)