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
22.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.75, Jaccard 0.40, H-bond role recall 1.00
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.667 kcal/mol/HA)
✓ Good fit quality (FQ -6.56)
✓ Strong H-bond network (7 bonds)
✓ Good burial (55% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ High strain energy (22.0 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-21.354
kcal/mol
LE
-0.667
kcal/mol/HA
Fit Quality
-6.56
FQ (Leeson)
HAC
32
heavy atoms
MW
434
Da
LogP
3.50
cLogP
Interaction summary
HB 7
HY 16
PI 1
CLASH 2
Interaction summary
HB 7
HY 16
PI 1
CLASH 2
| Final rank | 6.043 | Score | -21.354 |
|---|---|---|---|
| Inter norm | -0.749 | Intra norm | 0.081 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 7 |
| Artifact reason | geometry warning; 16 clashes; 4 protein clashes; moderate strain Δ 22.0 | ||
| Residues |
ASN402
GLU466
GLU467
LEU399
LYS407
LYS410
MET400
PHE396
PRO398
SER395
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 461 | 2.5218174144170837 | -0.941146 | -34.7577 | 14 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 517 | 3.4967600637920304 | -0.859572 | -33.8612 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 442 | 3.539614290888217 | -0.942522 | -30.879 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 417 | 3.7628131150683823 | -1.03419 | -29.2761 | 14 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 434 | 4.039285790739431 | -1.04701 | -30.7908 | 11 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 501 | 4.482692559783027 | -1.00427 | -28.9224 | 7 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 491 | 5.352094304022408 | -0.947279 | -26.8801 | 11 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 464 | 6.042913748967145 | -0.748819 | -21.3543 | 7 | 13 | 6 | 0.75 | 1.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-21.354kcal/mol
Ligand efficiency (LE)
-0.6673kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.562
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
32HA
Physicochemical properties
Molecular weight
434.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.50
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.00kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
167.83kcal/mol
Minimised FF energy
145.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
736.0Ų
Total solvent-accessible surface area of free ligand
BSA total
401.2Ų
Buried surface area upon binding
BSA apolar
304.8Ų
Hydrophobic contacts buried
BSA polar
96.4Ų
Polar contacts buried
Fraction buried
54.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3131.9Ų
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
1520.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)