# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 13:43:45 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 3-cyclopropyl-5-[(3R)-pyrrolidin-3-yl]-1,2,4-oxadiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C[C@H](CN1)c2onc(n2)C3CC3
#
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
 WOD  WOD  3-cyclopropyl-5-[(3R)-pyrrolidin-3-yl]-1,2,4-oxadiazole  ligand  26  13  .  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_WOD
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
 WOD  C10  C  CH2   0  -0.466  -29.5975  31.9494  -23.5419
 WOD  N12  N  NH1   0  -0.580  -28.2548  31.5936  -25.5358
 WOD  C13  C  CH2   0  -0.296  -29.5430  30.9696  -25.7504
 WOD  C01  C  CH2   0  -0.472  -35.1004  32.0527  -26.2215
 WOD  C02  C  CH2   0  -0.471  -35.1466  32.8336  -24.9566
 WOD  C03  C  CH1   0  -0.374  -34.9606  31.3405  -24.9012
 WOD  C04  C  CR5   0   0.364  -33.6540  30.8020  -24.5259
 WOD  C07  C  CR5   0   0.564  -31.5941  30.6059  -24.3229
 WOD  C09  C  CH1   0  -0.425  -30.1201  30.7311  -24.3361
 WOD  C11  C  CH2   0  -0.318  -28.4702  32.5266  -24.4350
 WOD  N05  N  N     0  -0.181  -33.5148  29.6858  -23.8759
 WOD  N08  N  N     0  -0.469  -32.4704  31.4115  -24.8264
 WOD  O06  O  O     0  -0.335  -32.1530  29.5541  -23.7424
 WOD  H1   H  HCH2  0   0.251  -30.3839  32.6872  -23.3803
 WOD  H2   H  HCH2  0   0.256  -29.2330  31.6419  -22.5628
 WOD  H3   H  HNH1  0   0.351  -27.5977  30.8822  -25.2397
 WOD  H5   H  HCH2  0   0.235  -30.1961  31.6508  -26.3035
 WOD  H6   H  HCH2  0   0.260  -29.4504  30.0495  -26.3264
 WOD  H8   H  HCH2  0   0.261  -34.2161  32.1318  -26.8401
 WOD  H9   H  HCH2  0   0.261  -34.2944  33.4524  -24.7073
 WOD  H10  H  HCH2  0   0.268  -36.0998  33.2170  -24.6183
 WOD  H11  H  HCH1  0   0.283  -35.8020  30.7471  -24.5666
 WOD  H12  H  HCH1  0   0.290  -29.6914  29.8126  -23.9302
 WOD  H13  H  HCH2  0   0.243  -27.5415  32.6868  -23.8888
 WOD  H14  H  HCH2  0   0.231  -28.7817  33.4932  -24.8370
 WOD  H7   H  HCH2  0   0.268  -36.0212  31.8906  -26.7655

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
 WOD  C01  C02  single    1.487  0.020  1.487
 WOD  C01  C03  single    1.507  0.020  1.507
 WOD  C13  N12  single    1.447  0.020  1.447
 WOD  C13  C09  single    1.546  0.020  1.546
 WOD  N12  C11  single    1.459  0.020  1.459
 WOD  C02  C03  single    1.506  0.020  1.506
 WOD  C03  C04  single    1.462  0.020  1.462
 WOD  N08  C04  aromatic  1.365  0.020  1.365
 WOD  N08  C07  aromatic  1.292  0.020  1.292
 WOD  C09  C07  single    1.479  0.020  1.479
 WOD  C09  C10  single    1.545  0.020  1.545
 WOD  C11  C10  single    1.550  0.020  1.550
 WOD  C04  N05  aromatic  1.299  0.020  1.299
 WOD  C07  O06  aromatic  1.325  0.020  1.325
 WOD  N05  O06  aromatic  1.375  0.020  1.375
 WOD  C10  H1   single    0.970  0.020  1.090
 WOD  C10  H2   single    0.970  0.020  1.090
 WOD  N12  H3   single    0.890  0.020  1.040
 WOD  C13  H5   single    0.970  0.020  1.090
 WOD  C13  H6   single    0.970  0.020  1.090
 WOD  C01  H7   single    0.970  0.020  1.090
 WOD  C01  H8   single    0.970  0.020  1.090
 WOD  C02  H9   single    0.970  0.020  1.090
 WOD  C02  H10  single    0.970  0.020  1.090
 WOD  C03  H11  single    0.970  0.020  1.090
 WOD  C09  H12  single    0.970  0.020  1.090
 WOD  C11  H13  single    0.970  0.020  1.090
 WOD  C11  H14  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
 WOD  H2   C10  H1   107.41  3.000
 WOD  H2   C10  C11  112.32  3.000
 WOD  H1   C10  C11  110.98  3.000
 WOD  H2   C10  C09  110.65  3.000
 WOD  H1   C10  C09  111.45  3.000
 WOD  C11  C10  C09  104.09  3.000
 WOD  H3   N12  C11  108.93  3.000
 WOD  H3   N12  C13  108.54  3.000
 WOD  C11  N12  C13  104.84  3.000
 WOD  H6   C13  H5   108.02  3.000
 WOD  H6   C13  C09  112.65  3.000
 WOD  H5   C13  C09  109.62  3.000
 WOD  H6   C13  N12  111.52  3.000
 WOD  H5   C13  N12  109.75  3.000
 WOD  C09  C13  N12  105.25  3.000
 WOD  H8   C01  H7   114.78  3.000
 WOD  H8   C01  C03  117.37  3.000
 WOD  H7   C01  C03  116.67  3.000
 WOD  H8   C01  C02  118.24  3.000
 WOD  H7   C01  C02  118.69  3.000
 WOD  C03  C01  C02   60.38  3.000
 WOD  H10  C02  H9   114.79  3.000
 WOD  H10  C02  C03  116.67  3.000
 WOD  H9   C02  C03  117.47  3.000
 WOD  H10  C02  C01  118.65  3.000
 WOD  H9   C02  C01  118.14  3.000
 WOD  C03  C02  C01   60.45  3.000
 WOD  H11  C03  C04  114.41  3.000
 WOD  H11  C03  C02  117.32  3.000
 WOD  C04  C03  C02  119.02  3.000
 WOD  H11  C03  C01  117.24  3.000
 WOD  C04  C03  C01  118.81  3.000
 WOD  C02  C03  C01   59.17  3.000
 WOD  N08  C04  N05  113.64  3.000
 WOD  N05  C04  C03  122.72  3.000
 WOD  N08  C04  C03  123.64  3.000
 WOD  O06  C07  N08  112.30  3.000
 WOD  O06  C07  C09  119.43  3.000
 WOD  N08  C07  C09  128.26  3.000
 WOD  H12  C09  C07  108.46  3.000
 WOD  H12  C09  C13  108.86  3.000
 WOD  C07  C09  C13  113.15  3.000
 WOD  H12  C09  C10  109.84  3.000
 WOD  C07  C09  C10  113.52  3.000
 WOD  C13  C09  C10  102.84  3.000
 WOD  H14  C11  H13  107.31  3.000
 WOD  H14  C11  N12  109.29  3.000
 WOD  H13  C11  N12  110.27  3.000
 WOD  H14  C11  C10  109.53  3.000
 WOD  H13  C11  C10  112.71  3.000
 WOD  N12  C11  C10  107.70  3.000
 WOD  O06  N05  C04  103.71  3.000
 WOD  C07  N08  C04  102.93  3.000
 WOD  N05  O06  C07  107.41  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
 WOD  CONST_01  O06  C07  N08  C04    0.00   0.0  0
 WOD  CONST_02  C07  O06  N05  C04    0.00   0.0  0
 WOD  CONST_03  N05  C04  N08  C07    0.00   0.0  0
 WOD  CONST_04  N08  C07  O06  N05    0.00   0.0  0
 WOD  CONST_05  O06  N05  C04  N08    0.00   0.0  0
 WOD  CONST_06  C07  N08  C04  C03  180.00   0.0  0
 WOD  CONST_07  O06  N05  C04  C03  180.00   0.0  0
 WOD  CONST_08  C09  C07  N08  C04  180.00   0.0  0
 WOD  CONST_09  N05  O06  C07  C09  180.00   0.0  0
 WOD  Var_01    C13  N12  C11  C10   29.63  30.0  1
 WOD  Var_02    C09  C10  C11  N12   -7.55  30.0  1
 WOD  Var_03    C04  C03  C02  C01  108.10  30.0  1
 WOD  Var_04    N08  C04  C03  C01   35.96  30.0  2
 WOD  Var_05    C11  N12  C13  C09  -40.03  30.0  1

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
 WOD  chir_02  C09  C13  C07  C10  positiv
 WOD  chir_03  C03  C01  C02  C04  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
 WOD  plan-1  C03  0.020
 WOD  plan-1  C04  0.020
 WOD  plan-1  C07  0.020
 WOD  plan-1  C09  0.020
 WOD  plan-1  N05  0.020
 WOD  plan-1  N08  0.020
 WOD  plan-1  O06  0.020

