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 high
Native strong
SASA done
Strain ΔE
24.5 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.46, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
37% of hydrophobic surface appears solvent-exposed (10/27 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 (-0.526 kcal/mol/HA)
✓ Good fit quality (FQ -5.22)
✓ Strong H-bond network (9 bonds)
✓ Good burial (50% SASA buried)
✓ Lipophilic contacts well-matched (85%)
✗ High strain energy (24.5 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-17.371
kcal/mol
LE
-0.526
kcal/mol/HA
Fit Quality
-5.22
FQ (Leeson)
HAC
33
heavy atoms
MW
452
Da
LogP
5.61
cLogP
Interaction summary
HB 9
HY 11
PI 1
CLASH 2
⚠ Exposure 37%
Interaction summary
HB 9
HY 11
PI 1
CLASH 2
⚠ Exposure 37%
Partial hydrophobic solvent exposure
37% of hydrophobic surface appears solvent-exposed (10/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 27
Buried (contacted) 17
Exposed 10
LogP 5.61
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 2.768 | Score | -17.371 |
|---|---|---|---|
| Inter norm | -0.626 | Intra norm | 0.099 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 9 |
| Artifact reason | geometry warning; 12 clashes; 1 protein clash; moderate strain Δ 24.5 | ||
| Residues |
ASN402
GLU467
LYS407
LYS410
MET393
MET471
PHE396
SER394
SER395
SER470
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 | 6 | Native recall | 0.75 |
| Jaccard | 0.46 | RMSD | - |
| HB strict | 1 | Strict recall | 0.50 |
| HB same residue+role | 1 | HB role recall | 1.00 |
| HB same residue | 1 | HB residue recall | 1.00 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 323 | 0.9281368038146153 | -0.881859 | -27.4888 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 240 | 0.9326315971844619 | -0.794452 | -22.7292 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 255 | 1.6709017941564726 | -0.71887 | -19.1442 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 202 | 2.4158386797718454 | -0.908111 | -29.0361 | 6 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 333 | 2.5964806201553707 | -0.779283 | -26.5781 | 4 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 316 | 2.7681947305161128 | -0.62579 | -17.3714 | 9 | 11 | 6 | 0.75 | 1.00 | - | no | Current |
| 321 | 2.7847742168238394 | -0.855996 | -21.2829 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 208 | 3.2737333179935955 | -0.86353 | -26.0064 | 11 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 282 | 3.2908590644988394 | -0.643978 | -17.2385 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 266 | 3.6696914491795702 | -0.969686 | -27.9485 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 260 | 3.724512830525498 | -0.752336 | -20.2105 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 306 | 4.479899767376692 | -0.891979 | -23.8503 | 8 | 21 | 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
-17.371kcal/mol
Ligand efficiency (LE)
-0.5264kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.223
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
451.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.61
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.48kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
52.23kcal/mol
Minimised FF energy
27.74kcal/mol
SASA & burial
✓ computed
SASA (unbound)
756.6Ų
Total solvent-accessible surface area of free ligand
BSA total
376.9Ų
Buried surface area upon binding
BSA apolar
321.5Ų
Hydrophobic contacts buried
BSA polar
55.4Ų
Polar contacts buried
Fraction buried
49.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
85.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3216.3Ų
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
1503.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)