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
9.8 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.82, Jaccard 0.78, H-bond role recall 0.27
Reason: no major geometry red flags detected
2 protein-contact clashes
71% of hydrophobic surface is solvent-exposed (15/21 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 (-1.008 kcal/mol/HA)
✓ Good fit quality (FQ -9.16)
✓ Strong H-bond network (7 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (9.8 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-25.196
kcal/mol
LE
-1.008
kcal/mol/HA
Fit Quality
-9.16
FQ (Leeson)
HAC
25
heavy atoms
MW
342
Da
LogP
4.31
cLogP
Interaction summary
HB 7
HY 1
PI 1
CLASH 2
⚠ Exposure 71%
Interaction summary
HB 7
HY 1
PI 1
CLASH 2
⚠ Exposure 71%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
71% of hydrophobic surface is solvent-exposed (15/21 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 21
Buried (contacted) 6
Exposed 15
LogP 4.31
H-bonds 7
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)aliphatic chain/group (6 atoms exposed)
| Final rank | 3.361 | Score | -25.196 |
|---|---|---|---|
| Inter norm | -1.066 | Intra norm | 0.058 |
| Top1000 | no | Excluded | no |
| Contacts | 15 | H-bonds | 7 |
| Artifact reason | geometry warning; 11 clashes; 2 protein clashes | ||
| Residues |
ARG116
ARG140
ARG144
ASN106
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
SER46
THR74
TYR49
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | 6FXW | Contacts | 17 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA15
ARG116
ARG140
ARG144
ASN106
ASP13
CYS72
GLY73
GLY75
GLY77
HIS105
HIS14
HIS141
ILE76
LEU101
THR74
TYR49
| ||
| Current overlap | 14 | Native recall | 0.82 |
| Jaccard | 0.78 | RMSD | - |
| HB strict | 3 | Strict recall | 0.23 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 5 | HB residue recall | 0.45 |
Protein summary
155 residues
| Protein target | T10 | Atoms | 4590 |
|---|---|---|---|
| Residues | 155 | Chains | 1 |
| Residue summary | ILE:494; ARG:384; ALA:360; VAL:352; LEU:304; GLU:300; THR:280; MET:272; LYS:220; ASP:216; TYR:210; HIS:204; GLY:182; SER:176; GLN:170; ASN:140 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 180 | 1.2753405841528704 | -1.12179 | -25.6351 | 7 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 300 | 2.22332971551258 | -1.14752 | -26.0885 | 5 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 203 | 2.7620845826778937 | -1.19377 | -25.0678 | 8 | 19 | 5 | 0.29 | 0.18 | - | no | Open |
| 380 | 2.8934951626599332 | -1.02286 | -21.1841 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 301 | 3.273343699463647 | -0.792808 | -17.732 | 6 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 189 | 3.361396722874519 | -1.0661 | -25.1956 | 7 | 15 | 14 | 0.82 | 0.27 | - | no | Current |
| 247 | 3.6688427296143553 | -1.35024 | -30.2174 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 249 | 4.150411199346974 | -1.466 | -32.3181 | 6 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 283 | 4.185532692114118 | -0.915922 | -20.4383 | 7 | 9 | 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
-25.196kcal/mol
Ligand efficiency (LE)
-1.0078kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.162
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
342.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.31
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
9.76kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
45.75kcal/mol
Minimised FF energy
35.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
612.5Ų
Total solvent-accessible surface area of free ligand
BSA total
410.2Ų
Buried surface area upon binding
BSA apolar
336.6Ų
Hydrophobic contacts buried
BSA polar
73.7Ų
Polar contacts buried
Fraction buried
67.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
82.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2296.1Ų
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
2417.4Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
657.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)