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
21.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.35, H-bond role recall 1.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.589 kcal/mol/HA)
✓ Good fit quality (FQ -5.99)
✓ Good H-bonds (3 bonds)
✓ Good burial (62% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ High strain energy (21.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-21.211
kcal/mol
LE
-0.589
kcal/mol/HA
Fit Quality
-5.99
FQ (Leeson)
HAC
36
heavy atoms
MW
519
Da
LogP
4.37
cLogP
Interaction summary
HB 3
HY 20
PI 2
CLASH 1
Interaction summary
HB 3
HY 20
PI 2
CLASH 1
| Final rank | 2.976 | Score | -21.211 |
|---|---|---|---|
| Inter norm | -0.540 | Intra norm | -0.050 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 3 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash; moderate strain Δ 21.6 | ||
| Residues |
GLU466
GLU467
HIS461
LEU399
MET393
MET400
MET471
PHE396
PRO398
PRO462
SER394
SER395
SER464
SER470
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 | 0.35 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 669 | 2.242959162236587 | -0.630998 | -24.4217 | 2 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 658 | 2.348686823393062 | -1.02818 | -37.7301 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 666 | 2.6812968608128886 | -0.619624 | -21.6677 | 4 | 24 | 0 | 0.00 | 0.00 | - | no | Open |
| 647 | 2.681307657453689 | -0.654945 | -24.3869 | 1 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 2.976194309743088 | -0.539639 | -21.2114 | 3 | 15 | 6 | 0.75 | 1.00 | - | no | Current |
| 677 | 3.703549043285708 | -0.923151 | -32.1561 | 6 | 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
-21.211kcal/mol
Ligand efficiency (LE)
-0.5892kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.989
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
518.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.37
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.58kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
31.61kcal/mol
Minimised FF energy
10.03kcal/mol
SASA & burial
✓ computed
SASA (unbound)
790.2Ų
Total solvent-accessible surface area of free ligand
BSA total
489.8Ų
Buried surface area upon binding
BSA apolar
362.2Ų
Hydrophobic contacts buried
BSA polar
127.7Ų
Polar contacts buried
Fraction buried
62.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
73.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3193.3Ų
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
1517.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)