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
28.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.38, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
36% of hydrophobic surface appears solvent-exposed (8/22 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 (-0.585 kcal/mol/HA)
✓ Good fit quality (FQ -5.65)
✓ Good H-bonds (5 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (28.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-17.562
kcal/mol
LE
-0.585
kcal/mol/HA
Fit Quality
-5.65
FQ (Leeson)
HAC
30
heavy atoms
MW
400
Da
LogP
2.26
cLogP
Interaction summary
HB 5
HY 17
PI 1
CLASH 1
⚠ Exposure 36%
Interaction summary
HB 5
HY 17
PI 1
CLASH 1
⚠ Exposure 36%
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (8/22 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 22
Buried (contacted) 14
Exposed 8
LogP 2.26
H-bonds 5
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 4.938 | Score | -17.562 |
|---|---|---|---|
| Inter norm | -0.642 | Intra norm | 0.056 |
| Top1000 | no | Excluded | no |
| Contacts | 14 | H-bonds | 5 |
| Artifact reason | geometry warning; 15 clashes; 3 protein clashes; moderate strain Δ 28.3 | ||
| Residues |
GLU466
GLU467
LEU399
MET393
MET400
MET471
PHE396
PRO398
PRO462
SER394
SER464
SER470
THR463
THR473
| ||
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 | 0.38 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 59 | 1.8077656603314811 | -1.33737 | -41.1817 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 21 | 1.8167442151259838 | -1.3248 | -40.6867 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 2.0383590711769224 | -1.31566 | -36.354 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 2.07494107366931 | -1.35194 | -41.1881 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 51 | 2.4756796252970026 | -0.987142 | -25.1715 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 17 | 2.659480533179131 | -0.988025 | -29.206 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 72 | 2.6888440031633536 | -0.750575 | -21.7979 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 17 | 3.58601093162473 | -0.977028 | -29.0743 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 44 | 3.8186271411229127 | -0.825732 | -21.4312 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 69 | 3.822991328266453 | -0.994304 | -25.3242 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 3.9945811977562276 | -1.07747 | -28.4735 | 11 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 6 | 4.1125363457515824 | -0.789709 | -22.5077 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 59 | 4.174917693331722 | -0.958177 | -28.341 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 51 | 4.210198956266459 | -1.07569 | -27.4595 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 18 | 4.247291649628563 | -0.861737 | -21.7221 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 77 | 4.253748462384305 | -0.861034 | -20.9423 | 10 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 15 | 4.305552679508108 | -0.796609 | -24.1605 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 14 | 4.938291489005273 | -0.642126 | -17.5617 | 5 | 14 | 6 | 0.75 | 1.00 | - | no | Current |
| 67 | 5.1022653534044835 | -0.644701 | -19.1146 | 6 | 14 | 6 | 0.75 | 1.00 | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-17.562kcal/mol
Ligand efficiency (LE)
-0.5854kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.647
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.26
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
10.19kcal/mol
Minimised FF energy
-18.09kcal/mol
SASA & burial
✓ computed
SASA (unbound)
683.9Ų
Total solvent-accessible surface area of free ligand
BSA total
426.4Ų
Buried surface area upon binding
BSA apolar
328.8Ų
Hydrophobic contacts buried
BSA polar
97.7Ų
Polar contacts buried
Fraction buried
62.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3113.2Ų
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
1519.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)