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
28.3 kcal/mol
Protein clashes
1
Internal clashes
4
Native overlap
contact recall 0.47, Jaccard 0.40, H-bond role recall 0.50
Reason: no major geometry red flags detected
1 protein-contact clashes
4 intramolecular clashes
35% of hydrophobic surface appears solvent-exposed (6/17 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 (-1.060 kcal/mol/HA)
✓ Good fit quality (FQ -9.50)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ High strain energy (28.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.434
kcal/mol
LE
-1.060
kcal/mol/HA
Fit Quality
-9.50
FQ (Leeson)
HAC
24
heavy atoms
MW
338
Da
LogP
3.36
cLogP
Interaction summary
HB 9
HY 11
PI 3
CLASH 4
⚠ Exposure 35%
Interaction summary
HB 9
HY 11
PI 3
CLASH 4
⚠ Exposure 35%
Partial hydrophobic solvent exposure
35% of hydrophobic surface appears solvent-exposed (6/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 11
Exposed 6
LogP 3.36
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 1.851 | Score | -25.434 |
|---|---|---|---|
| Inter norm | -1.169 | Intra norm | 0.110 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 1 protein clash; 4 cofactor-context clashes; moderate strain Δ 28.3 | ||
| Residues |
ARG17
ASP181
LEU188
LEU226
MET183
NDP302
PHE113
SER112
TYR194
VAL230
ARG287
| ||
Protein summary
274 residues
| Protein target | T05 | Atoms | 4108 |
|---|---|---|---|
| Residues | 274 | Chains | 2 |
| Residue summary | LEU:494; ALA:421; ARG:384; VAL:368; THR:295; TYR:231; SER:198; PRO:196; ILE:190; LYS:176; ASN:154; GLU:150; GLY:126; PHE:120; HIS:119; ASP:108 | ||
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:NDP302
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | ligand | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS198
MET233
NDP302
PHE113
PRO115
SER111
SER227
TYR191
TYR194
VAL230
ARG287
| ||
| Current overlap | 8 | Native recall | 0.47 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 4 | Strict recall | 0.57 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 114 | 1.5860172937477603 | -1.21455 | -24.4039 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 1.8505603394551924 | -1.16929 | -25.4341 | 9 | 11 | 8 | 0.47 | 0.50 | - | no | Current |
| 93 | 2.19739498584036 | -1.11561 | -31.8453 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 70 | 2.7036207493563826 | -1.08888 | -29.501 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 157 | 3.4093172975048245 | -0.908923 | -21.6596 | 4 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 118 | 3.6102345461159344 | -1.03637 | -23.389 | 4 | 15 | 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
-25.434kcal/mol
Ligand efficiency (LE)
-1.0598kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.497
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
337.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.36
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.32kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
108.86kcal/mol
Minimised FF energy
80.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
569.9Ų
Total solvent-accessible surface area of free ligand
BSA total
497.8Ų
Buried surface area upon binding
BSA apolar
401.6Ų
Hydrophobic contacts buried
BSA polar
96.2Ų
Polar contacts buried
Fraction buried
87.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1584.8Ų
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
2179.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1064.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)