Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
14.7 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.59, Jaccard 0.50, H-bond role recall 0.67
Reason: no major geometry red flags detected
1 protein-contact clashes
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.041 kcal/mol/HA)
✓ Good fit quality (FQ -9.19)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (76%)
✗ Moderate strain (14.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-23.944
kcal/mol
LE
-1.041
kcal/mol/HA
Fit Quality
-9.19
FQ (Leeson)
HAC
23
heavy atoms
MW
314
Da
LogP
1.19
cLogP
Interaction summary
HB 9
HY 7
PI 1
CLASH 1
⚠ Exposure 52%
Interaction summary
HB 9
HY 7
PI 1
CLASH 1
⚠ Exposure 52%
Partial hydrophobic solvent exposure
53% of hydrophobic surface appears solvent-exposed (9/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 8
Exposed 9
LogP 1.19
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (3 atoms exposed)
| Final rank | 2.579 | Score | -23.944 |
|---|---|---|---|
| Inter norm | -1.224 | Intra norm | 0.183 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 9 |
| Artifact reason | geometry warning; 8 clashes; 2 protein clashes; 2 cofactor-context clashes | ||
| Residues |
ARG17
ASP181
GLY225
LEU188
LEU226
MET183
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 | 10 | Native recall | 0.59 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 3 | Strict recall | 0.43 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 628 | 0.18702354902015306 | -1.17891 | -22.6406 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 616 | 0.6285692150163996 | -1.03442 | -15.6318 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 617 | 2.579057013340084 | -1.22393 | -23.9439 | 9 | 13 | 10 | 0.59 | 0.67 | - | no | Current |
| 636 | 2.6212597648646407 | -1.27144 | -23.7154 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 635 | 2.628679045735035 | -1.08796 | -19.974 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 639 | 2.942909683415412 | -1.07862 | -18.8879 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 626 | 4.096418414128663 | -1.32544 | -25.1928 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 622 | 4.311340728481773 | -1.06258 | -19.8805 | 8 | 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
-23.944kcal/mol
Ligand efficiency (LE)
-1.0410kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.188
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
23HA
Physicochemical properties
Molecular weight
314.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.19
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
36.32kcal/mol
Minimised FF energy
21.62kcal/mol
SASA & burial
✓ computed
SASA (unbound)
588.1Ų
Total solvent-accessible surface area of free ligand
BSA total
512.6Ų
Buried surface area upon binding
BSA apolar
392.2Ų
Hydrophobic contacts buried
BSA polar
120.4Ų
Polar contacts buried
Fraction buried
87.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1594.5Ų
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
1044.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)