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 mixed
SASA done
Strain ΔE
12.9 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.53, Jaccard 0.40, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
71% of hydrophobic surface is solvent-exposed (12/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.900 kcal/mol/HA)
✓ Good fit quality (FQ -8.29)
✓ Good H-bonds (3 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (71%)
✗ Moderate strain (12.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-23.396
kcal/mol
LE
-0.900
kcal/mol/HA
Fit Quality
-8.29
FQ (Leeson)
HAC
26
heavy atoms
MW
367
Da
LogP
2.95
cLogP
Interaction summary
HB 3
HY 2
PI 0
CLASH 1
⚠ Exposure 70%
Interaction summary
HB 3
HY 2
PI 0
CLASH 1
⚠ Exposure 70%
Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (12/17 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 17
Buried (contacted) 5
Exposed 12
LogP 2.95
H-bonds 3
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 3.886 | Score | -23.396 |
|---|---|---|---|
| Inter norm | -0.912 | Intra norm | 0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 3 |
| Artifact reason | geometry warning; 10 clashes; 3 protein clashes | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
ASP47
GLU384
LEU339
LYS51
PHE383
SER282
THR241
VAL335
VAL336
| ||
Protein summary
398 residues
| Protein target | T14 | Atoms | 6140 |
|---|---|---|---|
| Residues | 398 | Chains | 1 |
| Residue summary | VAL:592; LEU:513; LYS:484; ARG:432; PHE:420; ILE:418; ASP:349; THR:322; TYR:315; PRO:308; GLU:301; ALA:290; SER:253; GLY:217; ASN:210; GLN:170 | ||
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:ORX602
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 1NJJ | Contacts | 15 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ARG22
ARG242
ARG337
ARG342
ASP243
ASP385
GLN341
GLU384
LEU25
LEU339
LEU382
PRO340
PRO344
SER282
THR241
| ||
| Current overlap | 8 | Native recall | 0.53 |
| Jaccard | 0.40 | RMSD | - |
| HB strict | 0 | Strict recall | 0.00 |
| HB same residue+role | 0 | HB role recall | 0.00 |
| HB same residue | 1 | HB residue recall | 0.20 |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 313 | 0.8712913457919358 | -1.07999 | -25.8552 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 259 | 1.0887783330232708 | -1.16095 | -30.3355 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 310 | 1.5345591015763724 | -0.726221 | -16.5713 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 229 | 2.0704697110349266 | -0.998736 | -19.793 | 2 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 256 | 2.3416472278121194 | -1.03745 | -25.3269 | 2 | 11 | 0 | 0.00 | 0.00 | - | no | Open |
| 245 | 2.6468222692756207 | -1.26083 | -33.0935 | 10 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 191 | 3.0336689687352054 | -1.09429 | -28.6535 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 277 | 3.806776809599375 | -0.815034 | -16.965 | 6 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 214 | 3.8581501940359018 | -1.22756 | -28.0706 | 10 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 297 | 3.8864053339831193 | -0.911524 | -23.3962 | 3 | 13 | 8 | 0.53 | 0.00 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-23.396kcal/mol
Ligand efficiency (LE)
-0.8999kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.291
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
367.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.95
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.94kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-71.34kcal/mol
Minimised FF energy
-84.28kcal/mol
SASA & burial
✓ computed
SASA (unbound)
597.3Ų
Total solvent-accessible surface area of free ligand
BSA total
468.1Ų
Buried surface area upon binding
BSA apolar
333.5Ų
Hydrophobic contacts buried
BSA polar
134.5Ų
Polar contacts buried
Fraction buried
78.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
71.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2395.9Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1390.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)