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
25.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.40, Jaccard 0.30, H-bond role recall 0.00
Reason: no major geometry red flags detected
1 protein-contact clashes
78% of hydrophobic surface is solvent-exposed (14/18 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 (-0.786 kcal/mol/HA)
✓ Good fit quality (FQ -7.24)
✓ Good H-bonds (3 bonds)
✓ Deep burial (66% SASA buried)
✓ Lipophilic contacts well-matched (64%)
✗ High strain energy (25.8 kcal/mol)
✗ Geometry warnings
✗ Protein-contact clashes (5)
✗ Internal clashes (9)
Score
-20.439
kcal/mol
LE
-0.786
kcal/mol/HA
Fit Quality
-7.24
FQ (Leeson)
HAC
26
heavy atoms
MW
399
Da
LogP
4.85
cLogP
Interaction summary
HB 3
HY 5
PI 0
CLASH 1
⚠ Exposure 77%
Interaction summary
HB 3
HY 5
PI 0
CLASH 1
⚠ Exposure 77%
Solvent-exposed hydrophobic surface — desolvation penalty likely
78% of hydrophobic surface is solvent-exposed (14/18 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 18
Buried (contacted) 4
Exposed 14
LogP 4.85
H-bonds 3
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (3/5 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 1.091 | Score | -20.439 |
|---|---|---|---|
| Inter norm | -0.855 | Intra norm | 0.069 |
| Top1000 | no | Excluded | no |
| Contacts | 11 | H-bonds | 3 |
| Artifact reason | geometry warning; 9 clashes; 5 protein contact clashes; moderate strain Δ 25.8 | ||
| Residues |
ARG242
ARG337
ASP243
ASP385
GLU384
LEU339
LYS247
PHE383
PRO245
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 | 6 | Native recall | 0.40 |
| Jaccard | 0.30 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 415 | 0.7067403089329425 | -1.2582 | -30.6077 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 1.0913425355892699 | -0.855067 | -20.4389 | 3 | 11 | 6 | 0.40 | 0.00 | - | no | Current |
| 414 | 1.1639069284048813 | -1.1191 | -26.8464 | 3 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 462 | 1.841593328223823 | -0.854383 | -22.2042 | 5 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 401 | 1.97218672047719 | -1.08105 | -22.5838 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 441 | 2.322335104540528 | -0.789116 | -18.7871 | 5 | 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
-20.439kcal/mol
Ligand efficiency (LE)
-0.7861kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.243
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
398.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
25.79kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
51.99kcal/mol
Minimised FF energy
26.21kcal/mol
SASA & burial
✓ computed
SASA (unbound)
643.4Ų
Total solvent-accessible surface area of free ligand
BSA total
425.6Ų
Buried surface area upon binding
BSA apolar
272.8Ų
Hydrophobic contacts buried
BSA polar
152.8Ų
Polar contacts buried
Fraction buried
66.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2378.9Ų
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
1426.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)