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
29.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.50, H-bond role recall 0.40
Reason: no major geometry red flags detected
2 protein-contact clashes
64% of hydrophobic surface is solvent-exposed (14/22 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 (-0.601 kcal/mol/HA)
✓ Good fit quality (FQ -5.79)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (79% SASA buried)
✓ Lipophilic contacts well-matched (79%)
✗ High strain energy (29.4 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (4)
✗ Many internal clashes (12)
Score
-18.014
kcal/mol
LE
-0.601
kcal/mol/HA
Fit Quality
-5.79
FQ (Leeson)
HAC
30
heavy atoms
MW
461
Da
LogP
5.64
cLogP
Interaction summary
HB 6
HY 7
PI 0
CLASH 2
⚠ Exposure 63%
Interaction summary
HB 6
HY 7
PI 0
CLASH 2
⚠ Exposure 63%
Solvent-exposed hydrophobic surface — desolvation penalty likely
64% of hydrophobic surface is solvent-exposed (14/22 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 22
Buried (contacted) 8
Exposed 14
LogP 5.64
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 1.324 | Score | -18.014 |
|---|---|---|---|
| Inter norm | -0.743 | Intra norm | 0.143 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 6 |
| Artifact reason | geometry warning; 12 clashes; 4 protein contact clashes; moderate strain Δ 29.4 | ||
| Residues |
ARG22
ARG242
ASN20
ASP243
ASP385
CYS26
GLN341
GLU384
LEU25
LEU382
PHE284
SER282
THR21
THR241
THR285
| ||
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 | 10 | Native recall | 0.67 |
| Jaccard | 0.50 | RMSD | - |
| HB strict | 1 | Strict recall | 0.17 |
| HB same residue+role | 2 | HB role recall | 0.40 |
| HB same residue | 2 | HB residue recall | 0.40 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 653 | 1.3244415791256103 | -0.743307 | -18.014 | 6 | 15 | 10 | 0.67 | 0.40 | - | no | Current |
| 642 | 1.5054588274908072 | -0.84976 | -24.6402 | 1 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 672 | 3.1280044484273932 | -1.19062 | -29.6046 | 9 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 643 | 3.468377420654051 | -0.844482 | -18.7227 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 661 | 3.5246286595051073 | -0.63605 | -17.0492 | 4 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 667 | 5.404155028206115 | -0.976484 | -25.0007 | 8 | 18 | 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
-18.014kcal/mol
Ligand efficiency (LE)
-0.6005kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-5.792
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
461.0Da
Lipinski: ≤ 500 Da
LogP (cLogP)
5.64
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
29.36kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
41.24kcal/mol
Minimised FF energy
11.88kcal/mol
SASA & burial
✓ computed
SASA (unbound)
732.2Ų
Total solvent-accessible surface area of free ligand
BSA total
576.4Ų
Buried surface area upon binding
BSA apolar
456.8Ų
Hydrophobic contacts buried
BSA polar
119.6Ų
Polar contacts buried
Fraction buried
78.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
79.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2529.2Ų
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
3349.0Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1416.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)