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
31.5 kcal/mol
Protein clashes
1
Internal clashes
2
Native overlap
contact recall 0.76, Jaccard 0.68, H-bond role recall 0.33
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.838 kcal/mol/HA)
✓ Good fit quality (FQ -8.31)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (82% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ Very high strain energy (31.5 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (13)
Score
-27.646
kcal/mol
LE
-0.838
kcal/mol/HA
Fit Quality
-8.31
FQ (Leeson)
HAC
33
heavy atoms
MW
460
Da
LogP
2.91
cLogP
Interaction summary
HB 6
HY 17
PI 2
CLASH 2
Interaction summary
HB 6
HY 17
PI 2
CLASH 2
| Final rank | 0.984 | Score | -27.646 |
|---|---|---|---|
| Inter norm | -0.858 | Intra norm | 0.021 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 13 clashes; 2 protein contact clashes; 2 cofactor-context clashes; high strain Δ 30.3 | ||
| Residues |
ARG17
GLY225
HIS241
LEU188
LEU226
LEU229
LYS16
MET233
NDP302
PHE113
SER111
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 | 13 | Native recall | 0.76 |
| Jaccard | 0.68 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 94 | 0.983913686264644 | -0.858335 | -27.6464 | 6 | 15 | 13 | 0.76 | 0.33 | - | no | Current |
| 151 | 2.273298104065473 | -0.846275 | -25.1995 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 142 | 2.946945609023217 | -0.993841 | -28.3916 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 122 | 3.1529463375870637 | -0.703753 | -17.4509 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 128 | 3.6405601809908945 | -0.837547 | -23.8296 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 115 | 3.9252777073304115 | -0.788301 | -27.0966 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 145 | 4.094128194450695 | -0.584234 | -18.7207 | 5 | 8 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 4.175623452188693 | -0.858805 | -25.7709 | 12 | 20 | 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
-27.646kcal/mol
Ligand efficiency (LE)
-0.8378kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.312
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
459.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.91
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.47kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-117.82kcal/mol
Minimised FF energy
-149.29kcal/mol
SASA & burial
✓ computed
SASA (unbound)
732.2Ų
Total solvent-accessible surface area of free ligand
BSA total
598.8Ų
Buried surface area upon binding
BSA apolar
432.3Ų
Hydrophobic contacts buried
BSA polar
166.4Ų
Polar contacts buried
Fraction buried
81.8%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
72.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1663.3Ų
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
1047.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)