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 high
Native strong
SASA done
Strain ΔE
18.6 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.68, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.424 kcal/mol/HA)
✓ Good fit quality (FQ -12.76)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Moderate strain (18.6 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Many internal clashes (12)
Score
-34.176
kcal/mol
LE
-1.424
kcal/mol/HA
Fit Quality
-12.76
FQ (Leeson)
HAC
24
heavy atoms
MW
338
Da
LogP
1.85
cLogP
Interaction summary
HB 8
HY 24
PI 5
CLASH 1
Interaction summary
HB 8
HY 24
PI 5
CLASH 1
| Final rank | 0.801 | Score | -34.176 |
|---|---|---|---|
| Inter norm | -1.460 | Intra norm | 0.036 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 8 |
| Artifact reason | geometry warning; 12 clashes; 5 protein contact clashes; 1 severe cofactor-context clash | ||
| Residues |
ARG17
ASP181
GLY225
HIS241
LEU188
LEU226
LYS198
NDP302
PHE113
SER111
SER112
TYR191
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 | 5 | Strict recall | 0.71 |
| HB same residue+role | 4 | HB role recall | 0.67 |
| HB same residue | 4 | HB residue recall | 0.80 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 173 | 0.7297662232967618 | -1.1223 | -25.4623 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 166 | 0.7619998499724264 | -1.12236 | -21.9231 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 124 | 0.8007085204419594 | -1.45986 | -34.1762 | 8 | 15 | 13 | 0.76 | 0.67 | - | no | Current |
| 176 | 1.465631046449186 | -1.34406 | -32.047 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 156 | 1.9477162826235883 | -1.0966 | -22.0804 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 142 | 1.9889542389045647 | -1.07786 | -25.6529 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 165 | 2.619897110181579 | -0.985905 | -19.201 | 5 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 97 | 3.761259210392481 | -0.998031 | -20.1356 | 14 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 187 | 4.198272735387158 | -0.88192 | -20.6453 | 5 | 12 | 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
-34.176kcal/mol
Ligand efficiency (LE)
-1.4240kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.762
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
338.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
18.56kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-150.42kcal/mol
Minimised FF energy
-168.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
574.9Ų
Total solvent-accessible surface area of free ligand
BSA total
500.6Ų
Buried surface area upon binding
BSA apolar
390.7Ų
Hydrophobic contacts buried
BSA polar
109.9Ų
Polar contacts buried
Fraction buried
87.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
78.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1628.6Ų
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
1013.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)