# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:14:38 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@]12CCC(=C)[C@@H]1C2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 SNE  SNE  (1S,5S)-4-methylidene-1-(propan-2-yl)bicyclo[3.1.0]hexane  ligand  26  10  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SNE
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 SNE  C6   C  C2    0  -0.652   3.0455   0.9247  -0.0664
 SNE  C1   C  C     0   0.272   1.9274   0.2080   0.0123
 SNE  C7   C  CH1   0  -0.363   0.7367   0.5397   0.8211
 SNE  C9   C  CH2   0  -0.472   0.0852  -0.6046   1.5680
 SNE  C4   C  CH2   0  -0.547   1.6087  -1.0385  -0.7771
 SNE  C3   C  CH2   0  -0.430   0.0789  -1.0215  -0.9360
 SNE  C8   C  CT    0   0.029  -0.4431  -0.1993   0.2346
 SNE  C2   C  CH1   0  -0.254  -1.8052   0.4557   0.1497
 SNE  C    C  CH3   0  -0.655  -1.8774   1.4879  -0.9717
 SNE  C5   C  CH3   0  -0.655  -2.9115  -0.5878   0.0244
 SNE  H1   H  H     0   0.227   3.1934   1.8130   0.5357
 SNE  H2   H  H     0   0.227   3.8501   0.6479  -0.7366
 SNE  H4   H  HCH1  0   0.247   0.6310   1.5405   1.2249
 SNE  H5   H  HCH2  0   0.245   0.6243  -1.5387   1.6805
 SNE  H6   H  HCH2  0   0.255  -0.4988  -0.3297   2.4386
 SNE  H7   H  HCH2  0   0.254   2.1341  -1.0722  -1.7317
 SNE  H8   H  HCH2  0   0.235  -0.1910  -0.5355  -1.8767
 SNE  H9   H  HCH2  0   0.233  -0.3421  -2.0285  -0.9629
 SNE  H10  H  HCH1  0   0.217  -1.9582   0.9886   1.0955
 SNE  H11  H  HCH3  0   0.227  -1.0694   2.2166  -0.8884
 SNE  H12  H  HCH3  0   0.214  -1.8086   1.0243  -1.9575
 SNE  H13  H  HCH3  0   0.228  -2.8227   2.0324  -0.9384
 SNE  H14  H  HCH3  0   0.227  -2.8720  -1.3047   0.8463
 SNE  H15  H  HCH3  0   0.227  -3.8967  -0.1185   0.0373
 SNE  H16  H  HCH3  0   0.218  -2.8292  -1.1473  -0.9102
 SNE  H3   H  HCH2  0   0.248   1.9274  -1.9229  -0.2178

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 SNE  C6  C1   double  1.330  0.020  1.330
 SNE  C4  C1   single  1.509  0.020  1.509
 SNE  C4  C3   single  1.538  0.020  1.538
 SNE  C1  C7   single  1.477  0.020  1.477
 SNE  C9  C7   single  1.514  0.020  1.514
 SNE  C9  C8   single  1.490  0.020  1.490
 SNE  C3  C8   single  1.523  0.020  1.523
 SNE  C7  C8   single  1.511  0.020  1.511
 SNE  C8  C2   single  1.514  0.020  1.514
 SNE  C2  C5   single  1.526  0.020  1.526
 SNE  C2  C    single  1.526  0.020  1.526
 SNE  C6  H1   single  0.930  0.020  1.080
 SNE  C6  H2   single  0.930  0.020  1.080
 SNE  C7  H4   single  0.970  0.020  1.090
 SNE  C9  H5   single  0.970  0.020  1.090
 SNE  C9  H6   single  0.970  0.020  1.090
 SNE  C4  H7   single  0.970  0.020  1.090
 SNE  C3  H8   single  0.970  0.020  1.090
 SNE  C3  H9   single  0.970  0.020  1.090
 SNE  C2  H10  single  0.970  0.020  1.090
 SNE  C   H11  single  0.970  0.020  1.090
 SNE  C   H12  single  0.970  0.020  1.090
 SNE  C   H13  single  0.970  0.020  1.090
 SNE  C5  H14  single  0.970  0.020  1.090
 SNE  C5  H15  single  0.970  0.020  1.090
 SNE  C5  H16  single  0.970  0.020  1.090
 SNE  C4  H3   single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 SNE  H2   C6  H1   116.88  3.000
 SNE  H2   C6  C1   121.55  3.000
 SNE  H1   C6  C1   121.57  3.000
 SNE  C4   C1  C7   107.56  3.000
 SNE  C7   C1  C6   126.08  3.000
 SNE  C4   C1  C6   126.25  3.000
 SNE  H4   C7  C8   121.32  3.000
 SNE  H4   C7  C9   118.15  3.000
 SNE  C8   C7  C9    59.05  3.000
 SNE  H4   C7  C1   119.33  3.000
 SNE  C8   C7  C1   107.89  3.000
 SNE  C9   C7  C1   116.57  3.000
 SNE  H6   C9  H5   113.77  3.000
 SNE  H6   C9  C8   117.30  3.000
 SNE  H5   C9  C8   120.22  3.000
 SNE  H6   C9  C7   115.88  3.000
 SNE  H5   C9  C7   119.23  3.000
 SNE  C8   C9  C7    60.37  3.000
 SNE  H3   C4  H7   106.40  3.000
 SNE  H3   C4  C3   110.58  3.000
 SNE  H7   C4  C3   112.91  3.000
 SNE  H3   C4  C1   109.80  3.000
 SNE  H7   C4  C1   112.44  3.000
 SNE  C3   C4  C1   104.76  3.000
 SNE  H9   C3  H8   107.08  3.000
 SNE  H9   C3  C8   112.63  3.000
 SNE  H8   C3  C8   109.70  3.000
 SNE  H9   C3  C4   112.07  3.000
 SNE  H8   C3  C4   109.85  3.000
 SNE  C8   C3  C4   105.52  3.000
 SNE  C2   C8  C3   119.93  3.000
 SNE  C2   C8  C9   119.13  3.000
 SNE  C3   C8  C9   114.80  3.000
 SNE  C2   C8  C7   120.86  3.000
 SNE  C3   C8  C7   107.15  3.000
 SNE  C9   C8  C7    60.58  3.000
 SNE  H10  C2  C5   107.58  3.000
 SNE  H10  C2  C    107.37  3.000
 SNE  C5   C2  C    111.59  3.000
 SNE  H10  C2  C8   106.71  3.000
 SNE  C    C2  C8   112.12  3.000
 SNE  C5   C2  C8   111.17  3.000
 SNE  H13  C   H12  107.11  3.000
 SNE  H13  C   H11  107.80  3.000
 SNE  H12  C   H11  107.82  3.000
 SNE  H13  C   C2   110.86  3.000
 SNE  H12  C   C2   111.93  3.000
 SNE  H11  C   C2   111.13  3.000
 SNE  H16  C5  H15  107.36  3.000
 SNE  H16  C5  H14  107.77  3.000
 SNE  H15  C5  H14  107.83  3.000
 SNE  H16  C5  C2   111.46  3.000
 SNE  H15  C5  C2   111.07  3.000
 SNE  H14  C5  C2   111.18  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 SNE  Var_01  C8   C3  C4  C1   -25.11  30.0  1
 SNE  Var_02  C8   C9  C7  C1   -95.77  30.0  1
 SNE  Var_03  C3   C4  C1  C7    26.58  30.0  1
 SNE  Var_04  C4   C3  C8  C7    14.76  30.0  1
 SNE  Var_05  C4   C1  C7  C9    46.04  30.0  1
 SNE  Var_06  C5   C2  C8  C7  -159.01  30.0  3
 SNE  Var_07  H1   C6  C1  C7     4.17   0.0  2
 SNE  Var_08  H14  C5  C2  C8    55.75  30.0  3
 SNE  Var_09  H11  C   C2  C8   -53.22  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 SNE  chir_01  C7  C1  C9  C8  both
 SNE  chir_02  C8  C3  C7  C2  both

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 SNE  plan-1  C6  0.020
 SNE  plan-1  C1  0.020
 SNE  plan-1  C7  0.020
 SNE  plan-1  C4  0.020
 SNE  plan-1  H1  0.020
 SNE  plan-1  H2  0.020

