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
32.1 kcal/mol
Protein clashes
2
Internal clashes
3
Native overlap
contact recall 0.71, Jaccard 0.60, H-bond role recall 0.33
Reason: no major geometry red flags detected
2 protein-contact clashes
3 intramolecular clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.301 kcal/mol/HA)
✓ Good fit quality (FQ -12.13)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (90% SASA buried)
✓ Lipophilic contacts well-matched (81%)
✗ Very high strain energy (32.1 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-35.119
kcal/mol
LE
-1.301
kcal/mol/HA
Fit Quality
-12.13
FQ (Leeson)
HAC
27
heavy atoms
MW
361
Da
LogP
2.25
cLogP
Interaction summary
HB 8
HY 24
PI 5
CLASH 3
Interaction summary
HB 8
HY 24
PI 5
CLASH 3
| Final rank | 2.995 | Score | -35.119 |
|---|---|---|---|
| Inter norm | -1.175 | Intra norm | -0.126 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes; 1 cofactor-context clash; high strain Δ 32.1 | ||
| Residues |
ARG17
ASP181
HIS241
LEU188
LEU226
LEU229
MET183
MET233
NDP302
PHE113
SER111
TYR194
VAL228
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 | 12 | Native recall | 0.71 |
| Jaccard | 0.60 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 283 | 1.2722808858315229 | -1.04799 | -30.721 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 224 | 1.830523606696722 | -0.98222 | -28.3408 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 277 | 2.1752208580813424 | -0.994771 | -27.113 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 256 | 2.4779460977723615 | -0.969468 | -28.731 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 281 | 2.8450958207030004 | -0.836675 | -24.0082 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 232 | 2.994935745466194 | -1.1746 | -35.1192 | 8 | 15 | 12 | 0.71 | 0.33 | - | no | Current |
| 339 | 4.32933961656478 | -0.843873 | -24.7753 | 8 | 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
-35.119kcal/mol
Ligand efficiency (LE)
-1.3007kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.135
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
27HA
Physicochemical properties
Molecular weight
361.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.25
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.11kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
81.36kcal/mol
Minimised FF energy
49.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
592.0Ų
Total solvent-accessible surface area of free ligand
BSA total
534.3Ų
Buried surface area upon binding
BSA apolar
433.2Ų
Hydrophobic contacts buried
BSA polar
101.2Ų
Polar contacts buried
Fraction buried
90.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1658.2Ų
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
1012.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)