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
26.6 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.55, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
72% of hydrophobic surface is solvent-exposed (13/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.918 kcal/mol/HA)
✓ Good fit quality (FQ -8.67)
✓ Strong H-bond network (8 bonds)
✓ Good burial (50% SASA buried)
✓ Lipophilic contacts well-matched (86%)
✗ High strain energy (26.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-25.704
kcal/mol
LE
-0.918
kcal/mol/HA
Fit Quality
-8.67
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.31
cLogP
Interaction summary
HB 8
HY 5
PI 1
CLASH 2
⚠ Exposure 72%
Interaction summary
HB 8
HY 5
PI 1
CLASH 2
⚠ Exposure 72%
Solvent-exposed hydrophobic surface — desolvation penalty likely
72% of hydrophobic surface is solvent-exposed (13/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18
Buried (contacted) 5
Exposed 13
LogP 2.31
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 4.830 | Score | -25.704 |
|---|---|---|---|
| Inter norm | -0.682 | Intra norm | -0.236 |
| Top1000 | no | Excluded | no |
| Contacts | 9 | H-bonds | 8 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes; moderate strain Δ 26.6 | ||
| Residues |
ASN402
GLU466
GLU467
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 | 0.55 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 302 | 0.5239567590025211 | -1.18433 | -30.604 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 319 | 0.9940520654587742 | -0.944043 | -25.3008 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 1.0669444827431311 | -0.878088 | -31.4505 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 345 | 1.1134646347622539 | -0.877657 | -23.1229 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 369 | 1.570299553280359 | -0.935163 | -25.1037 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 285 | 1.846962516011115 | -1.10054 | -35.0271 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 333 | 2.430240854014312 | -0.961348 | -34.1213 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 2.7355217655896267 | -0.945999 | -28.0195 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 3.1357764599548372 | -1.01979 | -35.0482 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 3.33349022232488 | -1.04252 | -32.8619 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 3.427850034969361 | -1.24397 | -30.3675 | 11 | 26 | 0 | 0.00 | 0.00 | - | no | Open |
| 342 | 3.492057571577017 | -0.785111 | -22.7794 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 295 | 3.616137840018539 | -0.981468 | -32.0097 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 437 | 3.855523120955258 | -0.937716 | -27.4849 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 349 | 4.8296015227220686 | -0.681525 | -25.7042 | 8 | 9 | 6 | 0.75 | 1.00 | - | no | Current |
| 361 | 5.231781681702861 | -0.899682 | -33.3801 | 11 | 16 | 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
-25.704kcal/mol
Ligand efficiency (LE)
-0.9180kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.666
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.31
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
26.57kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-37.85kcal/mol
Minimised FF energy
-64.42kcal/mol
SASA & burial
✓ computed
SASA (unbound)
667.9Ų
Total solvent-accessible surface area of free ligand
BSA total
334.3Ų
Buried surface area upon binding
BSA apolar
287.9Ų
Hydrophobic contacts buried
BSA polar
46.4Ų
Polar contacts buried
Fraction buried
50.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3062.0Ų
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
1512.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)