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 medium
Native strong
SASA done
Strain ΔE
37.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.68, H-bond role recall 0.55
Reason: no major geometry red flags detected
1 protein-contact clashes
73% of hydrophobic surface is solvent-exposed (19/26 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.567 kcal/mol/HA)
✓ Good fit quality (FQ -5.72)
✓ Strong H-bond network (10 bonds)
✓ Good burial (57% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ Very high strain energy (37.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (16)
Score
-19.843
kcal/mol
LE
-0.567
kcal/mol/HA
Fit Quality
-5.72
FQ (Leeson)
HAC
35
heavy atoms
MW
492
Da
LogP
1.91
cLogP
Interaction summary
HB 10
HY 3
PI 1
CLASH 1
⚠ Exposure 73%
Interaction summary
HB 10
HY 3
PI 1
CLASH 1
⚠ Exposure 73%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
73% of hydrophobic surface is solvent-exposed (19/26 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 26
Buried (contacted) 7
Exposed 19
LogP 1.91
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 4.429 | Score | -19.843 |
|---|---|---|---|
| Inter norm | -0.795 | Intra norm | 0.228 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 10 |
| Artifact reason | geometry warning; 16 clashes; 2 protein clashes; high strain Δ 37.6 | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLU138
GLY73
HIS105
HIS14
HIS141
LEU136
THR74
TYR49
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 13 | Native recall | 0.76 |
| Jaccard | 0.68 | RMSD | - |
| HB strict | 8 | Strict recall | 0.62 |
| HB same residue+role | 6 | HB role recall | 0.55 |
| HB same residue | 7 | HB residue recall | 0.64 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 115 | 1.4028695381437135 | -0.944725 | -26.3156 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 90 | 2.704813851204706 | -0.711295 | -24.1711 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 94 | 3.1993237758746558 | -0.704553 | -22.829 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 102 | 3.3611055003370893 | -0.695238 | -25.8017 | 3 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 91 | 3.661011180748689 | -0.60391 | -21.9617 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 83 | 4.058036207553674 | -0.835089 | -25.7585 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 78 | 4.0591009172098715 | -0.773424 | -25.6746 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 45 | 4.428821280584197 | -0.795132 | -19.8429 | 10 | 15 | 13 | 0.76 | 0.55 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-19.843kcal/mol
Ligand efficiency (LE)
-0.5669kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.718
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
35HA
Physicochemical properties
Molecular weight
491.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.91
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.62kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
117.94kcal/mol
Minimised FF energy
80.32kcal/mol
SASA & burial
✓ computed
SASA (unbound)
788.1Ų
Total solvent-accessible surface area of free ligand
BSA total
446.2Ų
Buried surface area upon binding
BSA apolar
313.3Ų
Hydrophobic contacts buried
BSA polar
133.0Ų
Polar contacts buried
Fraction buried
56.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2317.6Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
711.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)