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
13.1 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 0.00
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.755 kcal/mol/HA)
✓ Good fit quality (FQ -7.21)
✓ Strong H-bond network (7 bonds)
✓ Good burial (55% SASA buried)
✓ Lipophilic contacts well-matched (83%)
✗ Moderate strain (13.1 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (7)
✗ Many internal clashes (12)
Score
-21.900
kcal/mol
LE
-0.755
kcal/mol/HA
Fit Quality
-7.21
FQ (Leeson)
HAC
29
heavy atoms
MW
443
Da
LogP
5.77
cLogP
Interaction summary
HB 7
HY 18
PI 1
CLASH 3
⚠ Exposure 38%
Interaction summary
HB 7
HY 18
PI 1
CLASH 3
⚠ Exposure 38%
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
Partial hydrophobic solvent exposure
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 13
Exposed 8
LogP 5.77
H-bonds 7
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.823 | Score | -21.900 |
|---|---|---|---|
| Inter norm | -0.704 | Intra norm | -0.052 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 7 |
| Artifact reason | geometry warning; 12 clashes; 7 protein contact clashes | ||
| Residues |
ASN402
GLU466
GLU467
LEU399
LYS407
LYS410
PHE396
PRO398
SER395
THR397
THR463
| ||
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 | 6 | Native recall | 0.75 |
| Jaccard | 0.46 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 405 | 0.2853552136087226 | -0.907637 | -24.6214 | 1 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 1.8230804083906484 | -0.703539 | -21.9002 | 7 | 11 | 6 | 0.75 | 0.00 | - | no | Current |
| 417 | 2.6132480506910896 | -0.942434 | -23.9627 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 368 | 2.9426670215919564 | -1.14768 | -32.7619 | 7 | 23 | 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
-21.900kcal/mol
Ligand efficiency (LE)
-0.7552kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.209
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
29HA
Physicochemical properties
Molecular weight
443.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.77
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.12kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
55.66kcal/mol
Minimised FF energy
42.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
688.4Ų
Total solvent-accessible surface area of free ligand
BSA total
379.4Ų
Buried surface area upon binding
BSA apolar
315.1Ų
Hydrophobic contacts buried
BSA polar
64.2Ų
Polar contacts buried
Fraction buried
55.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3095.4Ų
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
1586.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)