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
29.3 kcal/mol
Protein clashes
0
Internal clashes
3
Native overlap
contact recall 0.76, Jaccard 0.62, H-bond role recall 0.33
Reason: no major geometry red flags detected
3 intramolecular clashes
41% of hydrophobic surface appears solvent-exposed (11/27 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.654 kcal/mol/HA)
✓ Good fit quality (FQ -6.49)
✓ Good H-bonds (3 bonds)
✓ Deep burial (81% SASA buried)
✓ Lipophilic contacts well-matched (87%)
✗ High strain energy (29.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-21.573
kcal/mol
LE
-0.654
kcal/mol/HA
Fit Quality
-6.49
FQ (Leeson)
HAC
33
heavy atoms
MW
458
Da
LogP
5.09
cLogP
Final rank
0.3338
rank score
Inter norm
-0.891
normalised
Contacts
17
H-bonds 3
Interaction summary
HBD 1
HBA 2
HY 4
PI 2
CLASH 3
Interaction summary
HBD 1
HBA 2
HY 4
PI 2
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 2.
PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.
HY · Hydrophobic contacts
CLASH · Clashes
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 | 0.62 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 675 | 0.3337750167214599 | -0.890521 | -21.5732 | 3 | 17 | 13 | 0.76 | 0.33 | - | no | Current |
| 676 | 0.4249133577225625 | -0.878992 | -20.6441 | 2 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 674 | 2.6269909235535014 | -0.678815 | -16.1497 | 3 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 669 | 2.9795616679579218 | -0.854641 | -23.1495 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 677 | 3.7848854898616273 | -0.846089 | -22.353 | 8 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 675 | 3.8084641497204013 | -0.750838 | -20.6879 | 9 | 16 | 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
-21.573kcal/mol
Ligand efficiency (LE)
-0.6537kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.486
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.09
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.26kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
6.48kcal/mol
Minimised FF energy
-22.78kcal/mol
SASA & burial
✓ computed
SASA (unbound)
738.9Ų
Total solvent-accessible surface area of free ligand
BSA total
599.5Ų
Buried surface area upon binding
BSA apolar
519.9Ų
Hydrophobic contacts buried
BSA polar
79.6Ų
Polar contacts buried
Fraction buried
81.1%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
86.7%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1774.2Ų
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
1063.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)