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
22.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.40, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
47% of hydrophobic surface appears solvent-exposed (8/17 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 (-0.933 kcal/mol/HA)
✓ Good fit quality (FQ -8.48)
✓ Strong H-bond network (11 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (22.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-23.319
kcal/mol
LE
-0.933
kcal/mol/HA
Fit Quality
-8.48
FQ (Leeson)
HAC
25
heavy atoms
MW
356
Da
LogP
2.23
cLogP
Interaction summary
HB 11
HY 9
PI 1
CLASH 1
⚠ Exposure 47%
Interaction summary
HB 11
HY 9
PI 1
CLASH 1
⚠ Exposure 47%
Partial hydrophobic solvent exposure
47% of hydrophobic surface appears solvent-exposed (8/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 9
Exposed 8
LogP 2.23
H-bonds 11
Exposed fragments:
phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.337 | Score | -23.319 |
|---|---|---|---|
| Inter norm | -0.960 | Intra norm | 0.027 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 11 |
| Artifact reason | geometry warning; 7 clashes; 2 protein clashes; moderate strain Δ 22.7 | ||
| Residues |
ASN402
GLU466
GLU467
HIS461
LEU399
LYS407
LYS410
PHE396
PRO398
PRO462
SER464
THR397
THR463
| ||
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 | 0.40 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 613 | 0.3306519453204769 | -1.08162 | -26.4832 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 0.36934626421649913 | -1.02585 | -20.7811 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 0.3731963767257122 | -0.923569 | -24.115 | 1 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 623 | 1.6316030669638548 | -1.1021 | -24.3015 | 6 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 619 | 1.8963284840180428 | -0.922081 | -17.5343 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 603 | 2.445716149633084 | -1.02364 | -24.9584 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 625 | 2.904649738910798 | -1.08342 | -24.739 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 628 | 2.926952741865505 | -1.0052 | -20.509 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 615 | 3.336867848722131 | -0.959593 | -23.3189 | 11 | 13 | 6 | 0.75 | 1.00 | - | no | Current |
| 607 | 3.6933906595283736 | -1.0718 | -26.3483 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 601 | 3.8658657511488674 | -1.1213 | -27.725 | 10 | 12 | 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
-23.319kcal/mol
Ligand efficiency (LE)
-0.9328kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.480
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.23
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
74.86kcal/mol
Minimised FF energy
52.12kcal/mol
SASA & burial
✓ computed
SASA (unbound)
632.5Ų
Total solvent-accessible surface area of free ligand
BSA total
389.9Ų
Buried surface area upon binding
BSA apolar
288.4Ų
Hydrophobic contacts buried
BSA polar
101.5Ų
Polar contacts buried
Fraction buried
61.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3023.7Ų
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
1528.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)