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
17.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.76, Jaccard 0.65, H-bond role recall 0.45
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
42% of hydrophobic surface appears solvent-exposed (8/19 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 (-0.909 kcal/mol/HA)
✓ Good fit quality (FQ -8.48)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (17.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-24.534
kcal/mol
LE
-0.909
kcal/mol/HA
Fit Quality
-8.48
FQ (Leeson)
HAC
27
heavy atoms
MW
363
Da
LogP
2.73
cLogP
Interaction summary
HB 16
HY 5
PI 3
CLASH 5
⚠ Exposure 42%
Interaction summary
HB 16
HY 5
PI 3
CLASH 5
⚠ Exposure 42%
Partial hydrophobic solvent exposure
42% of hydrophobic surface appears solvent-exposed (8/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 11
Exposed 8
LogP 2.73
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 3.998 | Score | -24.534 |
|---|---|---|---|
| Inter norm | -0.912 | Intra norm | 0.004 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 16 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes | ||
| Residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP44
CYS72
GLY73
GLY77
HIS105
HIS14
HIS141
SER46
THR45
THR74
TYR49
| ||
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 | ||
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 | 0.65 | RMSD | - |
| HB strict | 7 | Strict recall | 0.54 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 92 | 1.0569874525188159 | -1.10517 | -24.005 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 104 | 1.46016853012659 | -0.985948 | -23.9799 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 95 | 1.6104257095050154 | -0.899281 | -27.1083 | 7 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 118 | 1.9879243078262165 | -0.764076 | -22.6199 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 150 | 2.5978360506406286 | -0.935679 | -26.7983 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 149 | 2.6998886413891503 | -1.08536 | -29.2372 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 130 | 3.061999676869863 | -0.986049 | -19.8883 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 88 | 3.162065719758737 | -1.14272 | -35.6793 | 10 | 15 | 5 | 0.29 | 0.27 | - | no | Open |
| 63 | 3.99786131386113 | -0.912238 | -24.5335 | 16 | 16 | 13 | 0.76 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-24.534kcal/mol
Ligand efficiency (LE)
-0.9086kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.477
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
363.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.73
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
17.70kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
139.40kcal/mol
Minimised FF energy
121.70kcal/mol
SASA & burial
✓ computed
SASA (unbound)
637.9Ų
Total solvent-accessible surface area of free ligand
BSA total
504.5Ų
Buried surface area upon binding
BSA apolar
406.3Ų
Hydrophobic contacts buried
BSA polar
98.2Ų
Polar contacts buried
Fraction buried
79.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2261.1Ų
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
675.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)