# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 11:14:00 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: N-cycloheptyl-5-methyl-1,3,4-oxadiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1oc(NC2CCCCCC2)nn1
#
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
 LJJ  LJJ  N-cycloheptyl-5-methyl-1,3,4-oxadiazol-2-amine  ligand  31  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LJJ
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
 LJJ  N1   N  N     0  -0.319   2.9597  -1.1269  -0.6492
 LJJ  N3   N  NH1   0  -0.688   0.3534   0.9947   0.1415
 LJJ  C4   C  CH1   0  -0.068  -0.9591   0.4039  -0.1014
 LJJ  C5   C  CH2   0  -0.449  -1.3511  -0.5818   1.0081
 LJJ  C6   C  CH2   0  -0.431  -2.2978  -1.7055   0.5875
 LJJ  C7   C  CH2   0  -0.444  -3.4694  -1.3141  -0.3176
 LJJ  C8   C  CH2   0  -0.436  -4.0749   0.0658  -0.0613
 LJJ  C10  C  CH2   0  -0.441  -1.9543   1.5576  -0.2310
 LJJ  C2   C  CR5   0   0.448   3.5421  -0.1402  -0.0848
 LJJ  C3   C  CR5   0   0.681   1.4659   0.2768  -0.0596
 LJJ  C9   C  CH2   0  -0.435  -3.3295   1.1911  -0.7759
 LJJ  N2   N  N     0  -0.389   1.6012  -0.8761  -0.6348
 LJJ  O1   O  O     0  -0.433   2.6440   0.7969   0.3194
 LJJ  H1   H  HNH1  0   0.401   0.4061   1.7271   0.8346
 LJJ  H2   H  HCH1  0   0.243  -0.8873  -0.1250  -1.0570
 LJJ  H3   H  HCH2  0   0.241  -0.4485  -1.0468   1.4104
 LJJ  H4   H  HCH2  0   0.221  -1.7876  -0.0129   1.8353
 LJJ  H5   H  HCH2  0   0.222  -1.7193  -2.4854   0.0849
 LJJ  H6   H  HCH2  0   0.224  -2.6874  -2.1636   1.5004
 LJJ  H7   H  HCH2  0   0.215  -3.1574  -1.3574  -1.3658
 LJJ  H8   H  HCH2  0   0.231  -4.2433  -2.0785  -0.2159
 LJJ  H9   H  HCH2  0   0.230  -5.1054   0.0666  -0.4249
 LJJ  H10  H  HCH2  0   0.216  -4.1398   0.2686   1.0129
 LJJ  H11  H  HCH2  0   0.221  -2.0668   2.0216   0.7557
 LJJ  H12  H  HCH2  0   0.238  -1.5215   2.3199  -0.8841
 LJJ  H13  H  HCH3  0   0.269   5.3259   0.9903  -0.3472
 LJJ  H14  H  HCH3  0   0.269   5.1793   0.2127   1.2285
 LJJ  H15  H  HCH3  0   0.270   5.5487  -0.7572  -0.2030
 LJJ  H16  H  HCH2  0   0.214  -3.2346   0.9199  -1.8327
 LJJ  H17  H  HCH2  0   0.231  -3.9413   2.0966  -0.7541
 LJJ  C1   C  CH3   0  -0.752   4.9780   0.0920   0.1637

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
 LJJ  N1   N2   aromatic  1.382  0.020  1.382
 LJJ  N1   C2   aromatic  1.277  0.020  1.277
 LJJ  N2   C3   aromatic  1.295  0.020  1.295
 LJJ  C2   C1   single    1.476  0.020  1.476
 LJJ  C2   O1   aromatic  1.359  0.020  1.359
 LJJ  C3   O1   aromatic  1.342  0.020  1.342
 LJJ  C3   N3   single    1.339  0.020  1.339
 LJJ  N3   C4   single    1.460  0.020  1.460
 LJJ  C5   C4   single    1.535  0.020  1.535
 LJJ  C5   C6   single    1.528  0.020  1.528
 LJJ  C4   C10  single    1.529  0.020  1.529
 LJJ  C6   C7   single    1.531  0.020  1.531
 LJJ  C10  C9   single    1.524  0.020  1.524
 LJJ  C7   C8   single    1.529  0.020  1.529
 LJJ  C8   C9   single    1.527  0.020  1.527
 LJJ  N3   H1   single    0.890  0.020  1.040
 LJJ  C4   H2   single    0.970  0.020  1.090
 LJJ  C5   H3   single    0.970  0.020  1.090
 LJJ  C5   H4   single    0.970  0.020  1.090
 LJJ  C6   H5   single    0.970  0.020  1.090
 LJJ  C6   H6   single    0.970  0.020  1.090
 LJJ  C7   H7   single    0.970  0.020  1.090
 LJJ  C7   H8   single    0.970  0.020  1.090
 LJJ  C8   H9   single    0.970  0.020  1.090
 LJJ  C8   H10  single    0.970  0.020  1.090
 LJJ  C10  H11  single    0.970  0.020  1.090
 LJJ  C10  H12  single    0.970  0.020  1.090
 LJJ  C1   H13  single    0.970  0.020  1.090
 LJJ  C1   H14  single    0.970  0.020  1.090
 LJJ  C1   H15  single    0.970  0.020  1.090
 LJJ  C9   H16  single    0.970  0.020  1.090
 LJJ  C9   H17  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
 LJJ  N2   N1   C2   107.67  3.000
 LJJ  H1   N3   C3   116.65  3.000
 LJJ  H1   N3   C4   117.05  3.000
 LJJ  C3   N3   C4   120.33  3.000
 LJJ  H2   C4   C10  109.46  3.000
 LJJ  H2   C4   C5   109.73  3.000
 LJJ  C10  C4   C5   112.30  3.000
 LJJ  H2   C4   N3   106.37  3.000
 LJJ  C10  C4   N3   107.09  3.000
 LJJ  C5   C4   N3   111.68  3.000
 LJJ  H4   C5   H3   105.81  3.000
 LJJ  H4   C5   C6   110.07  3.000
 LJJ  H3   C5   C6   107.47  3.000
 LJJ  H4   C5   C4   108.32  3.000
 LJJ  H3   C5   C4   109.18  3.000
 LJJ  C6   C5   C4   115.56  3.000
 LJJ  H6   C6   H5   105.88  3.000
 LJJ  H6   C6   C7   109.15  3.000
 LJJ  H5   C6   C7   108.39  3.000
 LJJ  H6   C6   C5   107.40  3.000
 LJJ  H5   C6   C5   108.86  3.000
 LJJ  C7   C6   C5   116.65  3.000
 LJJ  H8   C7   H7   105.27  3.000
 LJJ  H8   C7   C8   109.60  3.000
 LJJ  H7   C7   C8   108.01  3.000
 LJJ  H8   C7   C6   107.94  3.000
 LJJ  H7   C7   C6   109.74  3.000
 LJJ  C8   C7   C6   115.77  3.000
 LJJ  H10  C8   H9   105.69  3.000
 LJJ  H10  C8   C9   110.58  3.000
 LJJ  H9   C8   C9   107.70  3.000
 LJJ  H10  C8   C7   110.80  3.000
 LJJ  H9   C8   C7   108.57  3.000
 LJJ  C9   C8   C7   113.16  3.000
 LJJ  H12  C10  H11  106.45  3.000
 LJJ  H12  C10  C9   108.15  3.000
 LJJ  H11  C10  C9   109.33  3.000
 LJJ  H12  C10  C4   108.61  3.000
 LJJ  H11  C10  C4   108.05  3.000
 LJJ  C9   C10  C4   115.86  3.000
 LJJ  O1   C2   C1   118.97  3.000
 LJJ  O1   C2   N1   111.27  3.000
 LJJ  C1   C2   N1   129.76  3.000
 LJJ  O1   C3   N2   112.24  3.000
 LJJ  O1   C3   N3   118.61  3.000
 LJJ  N2   C3   N3   129.09  3.000
 LJJ  H17  C9   H16  105.83  3.000
 LJJ  H17  C9   C10  107.39  3.000
 LJJ  H16  C9   C10  109.04  3.000
 LJJ  H17  C9   C8   109.14  3.000
 LJJ  H16  C9   C8   108.14  3.000
 LJJ  C10  C9   C8   116.76  3.000
 LJJ  C3   N2   N1   105.60  3.000
 LJJ  C3   O1   C2   103.22  3.000
 LJJ  H15  C1   H14  108.60  3.000
 LJJ  H15  C1   H13  108.54  3.000
 LJJ  H14  C1   H13  107.90  3.000
 LJJ  H15  C1   C2   109.35  3.000
 LJJ  H14  C1   C2   111.20  3.000
 LJJ  H13  C1   C2   111.17  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
 LJJ  CONST_01  O1   C3  N2  N1    0.00   0.0  0
 LJJ  CONST_02  C3   O1  C2  N1    0.00   0.0  0
 LJJ  CONST_03  C3   N2  N1  C2    0.00   0.0  0
 LJJ  CONST_04  N2   C3  O1  C2    0.00   0.0  0
 LJJ  CONST_05  O1   C2  N1  N2    0.00   0.0  0
 LJJ  CONST_06  N3   C3  N2  N1  180.00   0.0  0
 LJJ  CONST_07  C2   O1  C3  N3  180.00   0.0  0
 LJJ  CONST_08  N2   N1  C2  C1  180.00   0.0  0
 LJJ  CONST_09  C3   O1  C2  C1  180.00   0.0  0
 LJJ  CONST_10  N2   C3  N3  C4    0.00   0.0  0
 LJJ  CONST_11  O1   C3  N3  C4  180.00   0.0  0
 LJJ  Var_01    H13  C1  C2  N1  118.67  30.0  2

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
 LJJ  chir_01  C4  N3  C5  C10  negativ

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
 LJJ  plan-1  N1  0.020
 LJJ  plan-1  N3  0.020
 LJJ  plan-1  C2  0.020
 LJJ  plan-1  C3  0.020
 LJJ  plan-1  N2  0.020
 LJJ  plan-1  O1  0.020
 LJJ  plan-1  C1  0.020
 LJJ  plan-2  N3  0.020
 LJJ  plan-2  C4  0.020
 LJJ  plan-2  C3  0.020
 LJJ  plan-2  H1  0.020

