# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:31:36 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: 4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](c1c[nH]cn1)c2cccc(C)c2C
#
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
 CZX  CZX  4-[(1~{S})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole  ligand  31  15  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CZX
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
 CZX  C10  C  CH3   0  -0.767  106.9133  105.4946  143.8141
 CZX  C13  C  CR15  0  -0.128  111.4330  106.3009  142.5001
 CZX  C15  C  CR15  0   0.082  112.1493  107.5624  140.8654
 CZX  C03  C  CH1   0  -0.424  108.9860  107.0827  142.4742
 CZX  C04  C  CR6   0   0.123  108.0994  106.1338  141.6830
 CZX  C05  C  CR6   0  -0.001  107.1014  105.3839  142.3233
 CZX  C06  C  CR5   0   0.189  110.4124  107.0707  142.0119
 CZX  C07  C  CH3   0  -0.636  108.3913  108.4934  142.4445
 CZX  C08  C  CR6   0   0.082  106.2836  104.5288  141.5663
 CZX  C09  C  CR16  0  -0.316  108.2479  106.0462  140.3010
 CZX  C11  C  CR16  0  -0.321  106.4624  104.4546  140.1877
 CZX  C12  C  CR16  0  -0.244  107.4335  105.2129  139.5531
 CZX  C14  C  CH3   0  -0.750  105.2173  103.6841  142.2093
 CZX  N01  N  N     0  -0.462  110.8789  107.8558  140.9925
 CZX  N02  N  NR15  0  -0.562  112.5286  106.6271  141.7541
 CZX  H1   H  HCH3  0   0.248  107.7651  105.0816  144.3589
 CZX  H2   H  HCH3  0   0.246  106.8088  106.5330  144.1329
 CZX  H3   H  HCH3  0   0.261  106.0285  104.9662  144.1592
 CZX  H5   H  HCR5  0   0.275  112.8338  107.9987  140.1543
 CZX  H6   H  HCH1  0   0.253  109.0026  106.7499  143.5138
 CZX  H7   H  HCH3  0   0.229  108.9793  109.1823  143.0523
 CZX  H8   H  HCH3  0   0.227  108.3638  108.8782  141.4256
 CZX  H9   H  HCH3  0   0.229  107.3711  108.4885  142.8299
 CZX  H10  H  HCR6  0   0.245  109.0108  106.6359  139.8078
 CZX  H11  H  HCR6  0   0.240  105.8320  103.7939  139.6046
 CZX  H12  H  HCR6  0   0.245  107.5577  105.1505  138.4792
 CZX  H13  H  HCH3  0   0.243  105.6311  103.0075  142.9590
 CZX  H14  H  HCH3  0   0.243  104.4611  104.2910  142.7109
 CZX  H15  H  HCH3  0   0.249  104.7039  103.0746  141.4668
 CZX  H17  H  HNR5  0   0.419  113.4549  106.2453  141.8589
 CZX  H4   H  HCR5  0   0.282  111.4684  105.5705  143.2909

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
 CZX  C12  C11  aromatic  1.386  0.020  1.386
 CZX  C12  C09  aromatic  1.385  0.020  1.385
 CZX  C11  C08  aromatic  1.392  0.020  1.392
 CZX  C09  C04  aromatic  1.393  0.020  1.393
 CZX  C15  N01  aromatic  1.310  0.020  1.310
 CZX  C15  N02  aromatic  1.345  0.020  1.345
 CZX  N01  C06  aromatic  1.369  0.020  1.369
 CZX  C08  C14  single    1.505  0.020  1.505
 CZX  C08  C05  aromatic  1.405  0.020  1.405
 CZX  N02  C13  aromatic  1.365  0.020  1.365
 CZX  C04  C05  aromatic  1.403  0.020  1.403
 CZX  C04  C03  single    1.521  0.020  1.521
 CZX  C06  C13  aromatic  1.368  0.020  1.368
 CZX  C06  C03  single    1.499  0.020  1.499
 CZX  C07  C03  single    1.531  0.020  1.531
 CZX  C05  C10  single    1.507  0.020  1.507
 CZX  C10  H1   single    0.970  0.020  1.090
 CZX  C10  H2   single    0.970  0.020  1.090
 CZX  C10  H3   single    0.970  0.020  1.090
 CZX  C13  H4   single    0.930  0.020  1.080
 CZX  C15  H5   single    0.930  0.020  1.080
 CZX  C03  H6   single    0.970  0.020  1.090
 CZX  C07  H7   single    0.970  0.020  1.090
 CZX  C07  H8   single    0.970  0.020  1.090
 CZX  C07  H9   single    0.970  0.020  1.090
 CZX  C09  H10  single    0.930  0.020  1.080
 CZX  C11  H11  single    0.930  0.020  1.080
 CZX  C12  H12  single    0.930  0.020  1.080
 CZX  C14  H13  single    0.970  0.020  1.090
 CZX  C14  H14  single    0.970  0.020  1.090
 CZX  C14  H15  single    0.970  0.020  1.090
 CZX  N02  H17  single    0.860  0.020  1.020

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
 CZX  H3   C10  H2   106.97  3.000
 CZX  H3   C10  H1   107.02  3.000
 CZX  H2   C10  H1   106.78  3.000
 CZX  H3   C10  C05  112.34  3.000
 CZX  H2   C10  C05  111.77  3.000
 CZX  H1   C10  C05  111.62  3.000
 CZX  H4   C13  N02  122.47  3.000
 CZX  H4   C13  C06  131.91  3.000
 CZX  N02  C13  C06  105.62  3.000
 CZX  H5   C15  N02  122.53  3.000
 CZX  H5   C15  N01  126.05  3.000
 CZX  N02  C15  N01  111.42  3.000
 CZX  H6   C03  C07  107.77  3.000
 CZX  H6   C03  C06  106.06  3.000
 CZX  C07  C03  C06  111.77  3.000
 CZX  H6   C03  C04  108.31  3.000
 CZX  C07  C03  C04  109.77  3.000
 CZX  C06  C03  C04  112.91  3.000
 CZX  C09  C04  C05  119.68  3.000
 CZX  C05  C04  C03  120.72  3.000
 CZX  C09  C04  C03  119.56  3.000
 CZX  C08  C05  C04  119.58  3.000
 CZX  C04  C05  C10  120.07  3.000
 CZX  C08  C05  C10  120.35  3.000
 CZX  N01  C06  C03  123.32  3.000
 CZX  C03  C06  C13  127.15  3.000
 CZX  N01  C06  C13  109.53  3.000
 CZX  H9   C07  H8   107.97  3.000
 CZX  H9   C07  H7   108.07  3.000
 CZX  H8   C07  H7   108.16  3.000
 CZX  H9   C07  C03  110.63  3.000
 CZX  H8   C07  C03  110.69  3.000
 CZX  H7   C07  C03  111.20  3.000
 CZX  C14  C08  C11  118.97  3.000
 CZX  C14  C08  C05  121.61  3.000
 CZX  C11  C08  C05  119.43  3.000
 CZX  H10  C09  C12  119.73  3.000
 CZX  H10  C09  C04  119.52  3.000
 CZX  C12  C09  C04  120.74  3.000
 CZX  H11  C11  C12  119.66  3.000
 CZX  H11  C11  C08  119.39  3.000
 CZX  C12  C11  C08  120.95  3.000
 CZX  H12  C12  C11  120.19  3.000
 CZX  H12  C12  C09  120.20  3.000
 CZX  C11  C12  C09  119.61  3.000
 CZX  H15  C14  H14  107.32  3.000
 CZX  H15  C14  H13  107.46  3.000
 CZX  H14  C14  H13  106.96  3.000
 CZX  H15  C14  C08  110.91  3.000
 CZX  H14  C14  C08  112.04  3.000
 CZX  H13  C14  C08  111.89  3.000
 CZX  C06  N01  C15  105.92  3.000
 CZX  H17  N02  C15  126.27  3.000
 CZX  H17  N02  C13  126.20  3.000
 CZX  C15  N02  C13  107.52  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
 CZX  CONST_01  N01  C15  N02  C13    0.00   0.0  0
 CZX  CONST_02  C15  N01  C06  C13    0.00   0.0  0
 CZX  CONST_03  C06  C13  N02  C15    0.00   0.0  0
 CZX  CONST_04  C11  C12  C09  C04    0.00   0.0  0
 CZX  CONST_05  C11  C08  C05  C04    0.00   0.0  0
 CZX  CONST_06  C12  C11  C08  C05    0.00   0.0  0
 CZX  CONST_07  C12  C09  C04  C05    0.00   0.0  0
 CZX  CONST_08  N02  C15  N01  C06    0.00   0.0  0
 CZX  CONST_09  C09  C12  C11  C08    0.00   0.0  0
 CZX  CONST_10  C09  C04  C05  C08    0.00   0.0  0
 CZX  CONST_11  N02  C13  C06  N01    0.00   0.0  0
 CZX  CONST_12  C11  C08  C05  C10  180.00   0.0  0
 CZX  CONST_13  C09  C04  C05  C10  180.00   0.0  0
 CZX  CONST_14  C03  C06  N01  C15  180.00   0.0  0
 CZX  CONST_15  C12  C09  C04  C03  180.00   0.0  0
 CZX  CONST_16  C08  C05  C04  C03  180.00   0.0  0
 CZX  CONST_17  N02  C13  C06  C03  180.00   0.0  0
 CZX  CONST_18  C14  C08  C05  C04  180.00   0.0  0
 CZX  CONST_19  C14  C08  C11  C12  180.00   0.0  0
 CZX  CONST_20  H5   C15  N02  C13  180.00   0.0  0
 CZX  CONST_21  H4   C13  N02  C15  180.00   0.0  0
 CZX  CONST_22  H12  C12  C09  C04  180.00   0.0  0
 CZX  CONST_23  H11  C11  C08  C05  180.00   0.0  0
 CZX  CONST_24  H10  C09  C04  C05  180.00   0.0  0
 CZX  CONST_25  H17  N02  C13  C06  180.00   0.0  0
 CZX  Var_01    H1   C10  C05  C04  -67.36  30.0  2
 CZX  Var_02    H13  C14  C08  C05  -58.84  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
 CZX  chir_01  C03  C04  C06  C07  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
 CZX  plan-1  C13  0.020
 CZX  plan-1  C15  0.020
 CZX  plan-1  C03  0.020
 CZX  plan-1  C06  0.020
 CZX  plan-1  N01  0.020
 CZX  plan-1  N02  0.020
 CZX  plan-1  H5   0.020
 CZX  plan-1  H17  0.020
 CZX  plan-1  H4   0.020
 CZX  plan-2  C10  0.020
 CZX  plan-2  C03  0.020
 CZX  plan-2  C04  0.020
 CZX  plan-2  C05  0.020
 CZX  plan-2  C08  0.020
 CZX  plan-2  C09  0.020
 CZX  plan-2  C11  0.020
 CZX  plan-2  C12  0.020
 CZX  plan-2  C14  0.020
 CZX  plan-2  H10  0.020
 CZX  plan-2  H11  0.020
 CZX  plan-2  H12  0.020

