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
24.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.75, Jaccard 0.50, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.764 kcal/mol/HA)
✓ Good fit quality (FQ -7.45)
✓ Good H-bonds (5 bonds)
✓ Good burial (44% SASA buried)
✓ Lipophilic contacts well-matched (90%)
✗ High strain energy (24.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-23.696
kcal/mol
LE
-0.764
kcal/mol/HA
Fit Quality
-7.45
FQ (Leeson)
HAC
31
heavy atoms
MW
500
Da
LogP
5.50
cLogP
Interaction summary
HB 5
HY 13
PI 0
CLASH 1
Interaction summary
HB 5
HY 13
PI 0
CLASH 1
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 3.744 | Score | -23.696 |
|---|---|---|---|
| Inter norm | -0.643 | Intra norm | -0.122 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 5 |
| Artifact reason | geometry warning; 13 clashes; 2 protein clashes; moderate strain Δ 24.2 | ||
| Residues |
ASN402
LEU399
LYS410
MET393
PHE396
PRO398
SER394
SER395
SER475
THR397
| ||
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 | 0.50 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 0 | HB residue recall | 0.00 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 572 | 0.5870117947832066 | -1.10765 | -37.5989 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 0.8823549273857154 | -0.910836 | -30.2227 | 2 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 592 | 1.310495564240597 | -0.754262 | -27.3292 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 611 | 1.7798849023795245 | -0.802683 | -26.2147 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 594 | 1.9412230667148331 | -0.877204 | -32.0703 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 584 | 2.0822003114507757 | -0.856641 | -25.7246 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 583 | 2.606119674997513 | -0.894636 | -26.6402 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 600 | 2.62217074979796 | -0.689693 | -24.6956 | 3 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 575 | 3.3580502961066707 | -0.8137 | -25.6478 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 595 | 3.5009994029016003 | -0.774293 | -24.4273 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 587 | 3.744243536944524 | -0.642671 | -23.6962 | 5 | 10 | 6 | 0.75 | 0.00 | - | no | Current |
| 600 | 3.987159201366124 | -1.08362 | -33.2245 | 13 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 591 | 6.027892840267617 | -0.912188 | -27.1412 | 8 | 19 | 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
-23.696kcal/mol
Ligand efficiency (LE)
-0.7644kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.447
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
500.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.50
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.25kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-31.13kcal/mol
Minimised FF energy
-55.38kcal/mol
SASA & burial
✓ computed
SASA (unbound)
766.5Ų
Total solvent-accessible surface area of free ligand
BSA total
340.5Ų
Buried surface area upon binding
BSA apolar
306.1Ų
Hydrophobic contacts buried
BSA polar
34.4Ų
Polar contacts buried
Fraction buried
44.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
89.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3125.7Ų
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
1569.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)