Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
16.2 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.65, Jaccard 0.61, H-bond role recall 0.50
Reason: no major geometry red flags detected
53% of hydrophobic surface appears solvent-exposed (10/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.985 kcal/mol/HA)
✓ Good fit quality (FQ -9.07)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (80%)
✗ Moderate strain (16.2 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-25.607
kcal/mol
LE
-0.985
kcal/mol/HA
Fit Quality
-9.07
FQ (Leeson)
HAC
26
heavy atoms
MW
356
Da
LogP
0.89
cLogP
Interaction summary
HB 6
HY 8
PI 1
CLASH 1
⚠ Exposure 52%
Interaction summary
HB 6
HY 8
PI 1
CLASH 1
⚠ Exposure 52%
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
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (10/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 9
Exposed 10
LogP 0.89
H-bonds 6
Exposed fragments:
phenyl (4/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 1.023 | Score | -25.607 |
|---|---|---|---|
| Inter norm | -1.100 | Intra norm | 0.115 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 6 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; 1 severe cofactor-context clash | ||
| Residues |
ARG17
GLY225
LEU188
LEU226
LEU229
NDP302
PHE113
SER111
SER112
TYR194
VAL230
ARG287
| ||
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 | 11 | Native recall | 0.65 |
| Jaccard | 0.61 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 3 | HB role recall | 0.50 |
| HB same residue | 3 | HB residue recall | 0.60 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 416 | 0.23475121758339515 | -0.88829 | -21.2441 | 0 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 395 | 1.0230333012145574 | -1.09972 | -25.6067 | 6 | 12 | 11 | 0.65 | 0.50 | - | no | Current |
| 429 | 1.1342574424919623 | -1.03555 | -26.3926 | 2 | 12 | 11 | 0.65 | 0.17 | - | no | Open |
| 458 | 1.7325280487707913 | -0.789146 | -19.3483 | 5 | 13 | 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
-25.607kcal/mol
Ligand efficiency (LE)
-0.9849kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.074
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
356.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.89
Lipinski: ≤ 5
Rotatable bonds
4
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.21kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
17.64kcal/mol
Minimised FF energy
1.43kcal/mol
SASA & burial
✓ computed
SASA (unbound)
604.9Ų
Total solvent-accessible surface area of free ligand
BSA total
525.4Ų
Buried surface area upon binding
BSA apolar
420.8Ų
Hydrophobic contacts buried
BSA polar
104.5Ų
Polar contacts buried
Fraction buried
86.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
80.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1632.8Ų
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
1030.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)