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
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native mixed
SASA done
Strain ΔE
52.0 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.41, Jaccard 0.39, H-bond role recall 0.33
Reason: strain 52.0 kcal/mol
strain ΔE 52.0 kcal/mol
2 protein-contact clashes
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-2.107 kcal/mol/HA)
✓ Good fit quality (FQ -15.07)
✓ Strong H-bond network (14 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Extreme strain energy (52.0 kcal/mol)
✗ Geometry warnings
Score
-29.500
kcal/mol
LE
-2.107
kcal/mol/HA
Fit Quality
-15.07
FQ (Leeson)
HAC
14
heavy atoms
MW
208
Da
LogP
-4.68
cLogP
Interaction summary
HB 14
HY 6
PI 0
CLASH 2
Interaction summary
HB 14
HY 6
PI 0
CLASH 2
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
| Final rank | 1.307 | Score | -29.500 |
|---|---|---|---|
| Inter norm | -2.311 | Intra norm | 0.204 |
| Top1000 | no | Excluded | no |
| Contacts | 8 | H-bonds | 14 |
| Artifact reason | geometry warning; 1 clash; 2 protein clashes; 3 severe cofactor-context clashes; high strain Δ 52.0 | ||
| Residues |
ARG17
LEU229
NDP302
PHE113
SER227
TYR194
VAL228
VAL230
| ||
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 | 7 | Native recall | 0.41 |
| Jaccard | 0.39 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 657 | 1.3070008823646198 | -2.31148 | -29.4997 | 14 | 8 | 7 | 0.41 | 0.33 | - | no | Current |
| 662 | 2.481543155138736 | -2.23948 | -30.4848 | 12 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 648 | 2.7801507953753766 | -1.734 | -24.3155 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 660 | 2.9632763288987976 | -1.63935 | -23.3336 | 11 | 14 | 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
-29.500kcal/mol
Ligand efficiency (LE)
-2.1071kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-15.066
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
14HA
Physicochemical properties
Molecular weight
208.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-4.68
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
52.03kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
169.31kcal/mol
Minimised FF energy
117.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
389.1Ų
Total solvent-accessible surface area of free ligand
BSA total
362.5Ų
Buried surface area upon binding
BSA apolar
249.7Ų
Hydrophobic contacts buried
BSA polar
112.8Ų
Polar contacts buried
Fraction buried
93.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
68.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1431.8Ų
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
1018.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)