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
28.1 kcal/mol
Protein clashes
0
Internal clashes
1
Native overlap
contact recall 0.59, Jaccard 0.59, H-bond role recall 0.33
Reason: no major geometry red flags detected
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.733 kcal/mol/HA)
✓ Good fit quality (FQ -7.07)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (77% SASA buried)
✓ Lipophilic contacts well-matched (72%)
✗ High strain energy (28.1 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-21.990
kcal/mol
LE
-0.733
kcal/mol/HA
Fit Quality
-7.07
FQ (Leeson)
HAC
30
heavy atoms
MW
461
Da
LogP
4.98
cLogP
Interaction summary
HB 7
HY 22
PI 4
CLASH 1
Interaction summary
HB 7
HY 22
PI 4
CLASH 1
| Final rank | 3.989 | Score | -21.990 |
|---|---|---|---|
| Inter norm | -0.947 | Intra norm | 0.214 |
| Top1000 | no | Excluded | no |
| Contacts | 10 | H-bonds | 7 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes; 2 cofactor-context clashes; moderate strain Δ 28.0 | ||
| Residues |
ARG17
GLY225
HIS241
LEU188
LEU229
MET233
NDP302
PHE113
TYR194
VAL230
| ||
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 | 10 | Native recall | 0.59 |
| Jaccard | 0.59 | RMSD | - |
| HB strict | 2 | Strict recall | 0.29 |
| HB same residue+role | 2 | HB role recall | 0.33 |
| HB same residue | 3 | HB residue recall | 0.60 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 491 | 0.6568242934034779 | -0.855812 | -26.9155 | 1 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 461 | 1.4757152030497325 | -0.727168 | -18.8759 | 4 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 419 | 2.301587904267888 | -0.810249 | -24.2859 | 5 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 482 | 2.4509505637358693 | -0.954137 | -28.3986 | 5 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 2.6910133316567784 | -1.10832 | -33.2889 | 9 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 433 | 3.1237119935793745 | -1.03561 | -30.7711 | 8 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 403 | 3.806388656164234 | -0.820277 | -23.8419 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 434 | 3.821146497143834 | -0.80197 | -21.889 | 8 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 396 | 3.989000081121798 | -0.947387 | -21.9904 | 7 | 10 | 10 | 0.59 | 0.33 | - | no | Current |
| 519 | 4.4009244236670835 | -0.83158 | -24.0403 | 6 | 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
-21.990kcal/mol
Ligand efficiency (LE)
-0.7330kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.071
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
461.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.98
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
28.10kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
74.21kcal/mol
Minimised FF energy
46.11kcal/mol
SASA & burial
✓ computed
SASA (unbound)
678.0Ų
Total solvent-accessible surface area of free ligand
BSA total
522.0Ų
Buried surface area upon binding
BSA apolar
373.4Ų
Hydrophobic contacts buried
BSA polar
148.6Ų
Polar contacts buried
Fraction buried
77.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1620.3Ų
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
1066.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)