# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 07:42:57 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCCOc1ccnc(C[S@@](=O)c2[nH]c3ccccc3n2)c1C
#
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
 RZX  RZX  2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole  ligand  46  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RZX
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
 RZX  C1    C  CR16  0  -0.322    5.8903   2.1392   0.1941
 RZX  C2    C  CR56  0   0.135    5.0299   1.0704  -0.0611
 RZX  C3    C  CR56  0   0.347    5.4757  -0.2499   0.1187
 RZX  C4    C  CR16  0  -0.299    6.7627  -0.5543   0.5498
 RZX  C5    C  CR16  0  -0.273    7.5986   0.5184   0.7972
 RZX  C6    C  CR16  0  -0.268    7.1700   1.8454   0.6225
 RZX  N7    N  NR15  0  -0.674    4.4015  -1.0306  -0.2196
 RZX  C8    C  CR5   0   0.185    3.4053  -0.1803  -0.5632
 RZX  N9    N  N     0  -0.411    3.7226   1.0734  -0.4905
 RZX  S10   S  S3    0   0.784    1.8088  -0.7703  -1.1202
 RZX  C11   C  CH2   0  -0.704    1.0659  -0.8982   0.5531
 RZX  C12   C  CR6   0   0.209   -0.3753  -1.2681   0.3807
 RZX  N13   N  N     0  -0.423   -0.5837  -2.5807   0.2340
 RZX  C14   C  CR16  0  -0.081   -1.8224  -2.9968   0.0531
 RZX  C15   C  CR16  0  -0.439   -2.9213  -2.1530   0.0157
 RZX  C16   C  CR6   0   0.470   -2.6982  -0.7913   0.1707
 RZX  C17   C  CR6   0  -0.072   -1.3847  -0.3125   0.3412
 RZX  O18   O  O     0  -0.730    1.1489   0.3831  -1.8081
 RZX  O19   O  O2    0  -0.456   -3.6597   0.1333   0.1673
 RZX  C20   C  CH2   0  -0.182   -5.0153  -0.2705   0.0215
 RZX  C21   C  CH2   0  -0.501   -5.8831   0.9601   0.1796
 RZX  C22   C  CH2   0  -0.127   -7.3462   0.6136  -0.0230
 RZX  O23   O  O2    0  -0.485   -8.1190   1.7673   0.1893
 RZX  C24   C  CH3   0  -0.398   -9.4914   1.5376  -0.0017
 RZX  C25   C  CH3   0  -0.717   -1.1689   1.1657   0.4697
 RZX  H1    H  HCR6  0   0.262    5.5604   3.1609   0.0596
 RZX  H4    H  HCR6  0   0.274    7.0943  -1.5750   0.6858
 RZX  H5    H  HCR6  0   0.262    8.6096   0.3315   1.1344
 RZX  H6    H  HCR6  0   0.258    7.8613   2.6517   0.8291
 RZX  HN7   H  HNR5  0   0.432    4.3735  -2.0388  -0.2412
 RZX  H11   H  HCH2  0   0.322    1.6054  -1.6950   1.0668
 RZX  H11A  H  HCH2  0   0.325    1.2319   0.0436   1.0717
 RZX  H14   H  HCR6  0   0.265   -1.9659  -4.0650  -0.0658
 RZX  H15   H  HCR6  0   0.291   -3.9070  -2.5700  -0.1339
 RZX  H20   H  HCH2  0   0.234   -5.1649  -0.7291  -0.9621
 RZX  H20A  H  HCH2  0   0.234   -5.2698  -1.0175   0.7806
 RZX  H21   H  HCH2  0   0.244   -5.7409   1.3792   1.1788
 RZX  H21A  H  HCH2  0   0.244   -5.5825   1.7195  -0.5466
 RZX  H22   H  HCH2  0   0.200   -7.5037   0.2229  -1.0393
 RZX  H22A  H  HCH2  0   0.199   -7.6462  -0.1868   0.6698
 RZX  H24   H  HCH3  0   0.204   -9.7143   1.2097  -1.0242
 RZX  H24A  H  HCH3  0   0.204   -9.8808   0.7769   0.6857
 RZX  H24B  H  HCH3  0   0.234  -10.0195   2.4722   0.1843
 RZX  H25   H  HCH3  0   0.252   -1.5060   1.6852  -0.4280
 RZX  H25A  H  HCH3  0   0.246   -1.7356   1.5714   1.3085
 RZX  H25B  H  HCH3  0   0.245   -0.1264   1.4287   0.6150

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
 RZX  C1   C2    aromatic  1.396  0.020  1.396
 RZX  C1   C6    aromatic  1.381  0.020  1.381
 RZX  C2   C3    aromatic  1.405  0.020  1.405
 RZX  C2   N9    aromatic  1.376  0.020  1.376
 RZX  C3   C4    aromatic  1.391  0.020  1.391
 RZX  C3   N7    aromatic  1.370  0.020  1.370
 RZX  C4   C5    aromatic  1.382  0.020  1.382
 RZX  C5   C6    aromatic  1.405  0.020  1.405
 RZX  N7   C8    aromatic  1.354  0.020  1.354
 RZX  C8   N9    aromatic  1.295  0.020  1.295
 RZX  C8   S10   single    1.791  0.020  1.791
 RZX  S10  C11   single    1.835  0.020  1.835
 RZX  S10  O18   double    1.496  0.020  1.496
 RZX  C11  C12   single    1.498  0.020  1.498
 RZX  C12  N13   aromatic  1.337  0.020  1.337
 RZX  C12  C17   aromatic  1.391  0.020  1.391
 RZX  N13  C14   aromatic  1.319  0.020  1.319
 RZX  C14  C15   aromatic  1.386  0.020  1.386
 RZX  C15  C16   aromatic  1.389  0.020  1.389
 RZX  C16  C17   aromatic  1.408  0.020  1.408
 RZX  C16  O19   single    1.334  0.020  1.334
 RZX  C17  C25   single    1.499  0.020  1.499
 RZX  O19  C20   single    1.422  0.020  1.422
 RZX  C20  C21   single    1.514  0.020  1.514
 RZX  C21  C22   single    1.517  0.020  1.517
 RZX  C22  O23   single    1.405  0.020  1.405
 RZX  O23  C24   single    1.405  0.020  1.405
 RZX  C1   H1    single    0.930  0.020  1.080
 RZX  C4   H4    single    0.930  0.020  1.080
 RZX  C5   H5    single    0.930  0.020  1.080
 RZX  C6   H6    single    0.930  0.020  1.080
 RZX  N7   HN7   single    0.860  0.020  1.020
 RZX  C11  H11   single    0.970  0.020  1.090
 RZX  C11  H11A  single    0.970  0.020  1.090
 RZX  C14  H14   single    0.930  0.020  1.080
 RZX  C15  H15   single    0.930  0.020  1.080
 RZX  C20  H20   single    0.970  0.020  1.090
 RZX  C20  H20A  single    0.970  0.020  1.090
 RZX  C21  H21   single    0.970  0.020  1.090
 RZX  C21  H21A  single    0.970  0.020  1.090
 RZX  C22  H22   single    0.970  0.020  1.090
 RZX  C22  H22A  single    0.970  0.020  1.090
 RZX  C24  H24   single    0.970  0.020  1.090
 RZX  C24  H24A  single    0.970  0.020  1.090
 RZX  C24  H24B  single    0.970  0.020  1.090
 RZX  C25  H25   single    0.970  0.020  1.090
 RZX  C25  H25A  single    0.970  0.020  1.090
 RZX  C25  H25B  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
 RZX  H1    C1   C6    121.47  3.000
 RZX  H1    C1   C2    120.83  3.000
 RZX  C6    C1   C2    117.71  3.000
 RZX  N9    C2   C3    110.09  3.000
 RZX  N9    C2   C1    129.87  3.000
 RZX  C3    C2   C1    120.04  3.000
 RZX  N7    C3   C4    132.63  3.000
 RZX  N7    C3   C2    104.77  3.000
 RZX  C4    C3   C2    122.60  3.000
 RZX  H4    C4   C5    121.63  3.000
 RZX  H4    C4   C3    121.93  3.000
 RZX  C5    C4   C3    116.44  3.000
 RZX  H5    C5   C6    119.13  3.000
 RZX  H5    C5   C4    119.13  3.000
 RZX  C6    C5   C4    121.74  3.000
 RZX  H6    C6   C5    119.01  3.000
 RZX  H6    C6   C1    119.52  3.000
 RZX  C5    C6   C1    121.47  3.000
 RZX  HN7   N7   C8    126.99  3.000
 RZX  HN7   N7   C3    126.61  3.000
 RZX  C8    N7   C3    106.36  3.000
 RZX  S10   C8   N9    123.69  3.000
 RZX  S10   C8   N7    121.87  3.000
 RZX  N9    C8   N7    114.42  3.000
 RZX  C8    N9   C2    104.36  3.000
 RZX  O18   S10  C11   107.12  3.000
 RZX  O18   S10  C8    106.39  3.000
 RZX  C11   S10  C8     95.75  3.000
 RZX  H11A  C11  H11   109.42  3.000
 RZX  H11A  C11  C12   114.55  3.000
 RZX  H11   C11  C12   110.47  3.000
 RZX  H11A  C11  S10   108.21  3.000
 RZX  H11   C11  S10   106.27  3.000
 RZX  C12   C11  S10   107.56  3.000
 RZX  C17   C12  N13   123.94  3.000
 RZX  C17   C12  C11   122.14  3.000
 RZX  N13   C12  C11   113.89  3.000
 RZX  C14   N13  C12   118.11  3.000
 RZX  H14   C14  C15   119.46  3.000
 RZX  H14   C14  N13   116.75  3.000
 RZX  C15   C14  N13   123.79  3.000
 RZX  H15   C15  C16   122.72  3.000
 RZX  H15   C15  C14   119.47  3.000
 RZX  C16   C15  C14   117.81  3.000
 RZX  O19   C16  C17   115.91  3.000
 RZX  O19   C16  C15   124.30  3.000
 RZX  C17   C16  C15   119.79  3.000
 RZX  C25   C17  C16   118.67  3.000
 RZX  C25   C17  C12   124.79  3.000
 RZX  C16   C17  C12   116.54  3.000
 RZX  C20   O19  C16   119.39  3.000
 RZX  H20A  C20  H20   107.76  3.000
 RZX  H20A  C20  C21   110.42  3.000
 RZX  H20   C20  C21   110.84  3.000
 RZX  H20A  C20  O19   110.13  3.000
 RZX  H20   C20  O19   109.94  3.000
 RZX  C21   C20  O19   107.76  3.000
 RZX  H21A  C21  H21   107.78  3.000
 RZX  H21A  C21  C22   109.58  3.000
 RZX  H21   C21  C22   109.58  3.000
 RZX  H21A  C21  C20   109.74  3.000
 RZX  H21   C21  C20   109.42  3.000
 RZX  C22   C21  C20   110.68  3.000
 RZX  H22A  C22  H22   106.52  3.000
 RZX  H22A  C22  O23   110.63  3.000
 RZX  H22   C22  O23   110.64  3.000
 RZX  H22A  C22  C21   110.18  3.000
 RZX  H22   C22  C21   110.03  3.000
 RZX  O23   C22  C21   108.83  3.000
 RZX  C24   O23  C22   112.50  3.000
 RZX  H24B  C24  H24A  108.41  3.000
 RZX  H24B  C24  H24   108.49  3.000
 RZX  H24A  C24  H24   107.75  3.000
 RZX  H24B  C24  O23   108.07  3.000
 RZX  H24A  C24  O23   112.03  3.000
 RZX  H24   C24  O23   111.98  3.000
 RZX  H25B  C25  H25A  107.83  3.000
 RZX  H25B  C25  H25   106.97  3.000
 RZX  H25A  C25  H25   107.17  3.000
 RZX  H25B  C25  C17   112.88  3.000
 RZX  H25A  C25  C17   110.97  3.000
 RZX  H25   C25  C17   110.77  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
 RZX  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 RZX  CONST_02  N7   C3   C2   C1   180.00   0.0  0
 RZX  CONST_03  C8   N9   C2   C1   180.00   0.0  0
 RZX  CONST_04  C4   C5   C6   C1     0.00   0.0  0
 RZX  CONST_05  C5   C6   C1   C2     0.00   0.0  0
 RZX  CONST_06  C5   C4   C3   C2     0.00   0.0  0
 RZX  CONST_07  C8   N7   C3   C2     0.00   0.0  0
 RZX  CONST_08  N7   C8   N9   C2     0.00   0.0  0
 RZX  CONST_09  C6   C1   C2   C3     0.00   0.0  0
 RZX  CONST_10  C8   N9   C2   C3     0.00   0.0  0
 RZX  CONST_11  C6   C5   C4   C3     0.00   0.0  0
 RZX  CONST_12  N9   C8   N7   C3     0.00   0.0  0
 RZX  CONST_13  N9   C2   C3   C4   180.00   0.0  0
 RZX  CONST_14  C8   N7   C3   C4   180.00   0.0  0
 RZX  CONST_15  N7   C3   C4   C5   180.00   0.0  0
 RZX  CONST_16  N9   C2   C1   C6   180.00   0.0  0
 RZX  CONST_17  N9   C2   C3   N7     0.00   0.0  0
 RZX  CONST_18  C15  C14  N13  C12    0.00   0.0  0
 RZX  CONST_19  C15  C16  C17  C12    0.00   0.0  0
 RZX  CONST_20  C16  C17  C12  N13    0.00   0.0  0
 RZX  CONST_21  C16  C15  C14  N13    0.00   0.0  0
 RZX  CONST_22  C17  C12  N13  C14    0.00   0.0  0
 RZX  CONST_23  C17  C16  C15  C14    0.00   0.0  0
 RZX  CONST_24  S10  C8   N9   C2   180.00   0.0  0
 RZX  CONST_25  S10  C8   N7   C3   180.00   0.0  0
 RZX  CONST_26  C14  N13  C12  C11  180.00   0.0  0
 RZX  CONST_27  C16  C17  C12  C11  180.00   0.0  0
 RZX  CONST_28  O19  C16  C17  C12  180.00   0.0  0
 RZX  CONST_29  C25  C17  C12  N13  180.00   0.0  0
 RZX  CONST_30  O19  C16  C15  C14  180.00   0.0  0
 RZX  CONST_31  C25  C17  C16  C15  180.00   0.0  0
 RZX  CONST_32  H5   C5   C6   C1   180.00   0.0  0
 RZX  CONST_33  H6   C6   C1   C2   180.00   0.0  0
 RZX  CONST_34  H4   C4   C3   C2   180.00   0.0  0
 RZX  CONST_35  HN7  N7   C3   C2   180.00   0.0  0
 RZX  CONST_36  H1   C1   C2   C3   180.00   0.0  0
 RZX  CONST_37  H14  C14  N13  C12  180.00   0.0  0
 RZX  CONST_38  H15  C15  C14  N13  180.00   0.0  0
 RZX  Var_01    C11  S10  C8   N7    87.95  30.0  2
 RZX  Var_02    C12  C11  S10  C8   174.78  30.0  3
 RZX  Var_03    N13  C12  C11  S10   84.02  30.0  2
 RZX  Var_04    H25  C25  C17  C12  119.05  30.0  2
 RZX  Var_05    C21  C20  O19  C16  174.92  30.0  3
 RZX  Var_06    C22  C21  C20  O19  177.60  30.0  3
 RZX  Var_07    O23  C22  C21  C20  177.46  30.0  3
 RZX  Var_08    H24  C24  O23  C22  -60.80  30.0  3

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
 RZX  plan-1  C11  0.020
 RZX  plan-1  C12  0.020
 RZX  plan-1  N13  0.020
 RZX  plan-1  C14  0.020
 RZX  plan-1  C15  0.020
 RZX  plan-1  C16  0.020
 RZX  plan-1  C17  0.020
 RZX  plan-1  O19  0.020
 RZX  plan-1  C25  0.020
 RZX  plan-1  H14  0.020
 RZX  plan-1  H15  0.020
 RZX  plan-2  C1   0.020
 RZX  plan-2  C2   0.020
 RZX  plan-2  C3   0.020
 RZX  plan-2  C4   0.020
 RZX  plan-2  C5   0.020
 RZX  plan-2  C6   0.020
 RZX  plan-2  N7   0.020
 RZX  plan-2  C8   0.020
 RZX  plan-2  N9   0.020
 RZX  plan-2  S10  0.020
 RZX  plan-2  H1   0.020
 RZX  plan-2  H4   0.020
 RZX  plan-2  H5   0.020
 RZX  plan-2  H6   0.020
 RZX  plan-2  HN7  0.020
 RZX  plan-3  C8   0.020
 RZX  plan-3  S10  0.020
 RZX  plan-3  C11  0.020
 RZX  plan-3  O18  0.020

