# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 02:46:11 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: 1-[(4-chlorophenyl)methyl]-2-(pyrrolidin-1-ylmethyl)benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Cn2c(CN3CCCC3)nc4ccccc24)cc1
#
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
 GX0  GX0  1-[(4-chlorophenyl)methyl]-2-(pyrrolidin-1-ylmethyl)benzimidazole  ligand  43  23  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GX0
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
 GX0  C7   C   CH2   0  -0.405  162.0022  177.8953  156.0825
 GX0  N2   N   N     0  -0.472  165.3141  177.5888  154.6453
 GX0  C    C   CH2   0  -0.281  165.7295  174.5127  155.5937
 GX0  N    N   NT    0  -0.422  164.8047  174.8048  154.5101
 GX0  CL   CL  CL    0  -0.128  161.6703  178.3284  162.0766
 GX0  C1   C   CH2   0  -0.274  164.3522  173.5024  154.0504
 GX0  N1   N   NR5   0  -0.552  163.3376  178.0541  155.5557
 GX0  C2   C   CH2   0  -0.465  166.5359  173.3165  155.0807
 GX0  C3   C   CH2   0  -0.464  165.6375  172.6808  153.9983
 GX0  C4   C   CH2   0  -0.382  163.7254  175.6809  154.8713
 GX0  C5   C   CR5   0   0.465  164.1634  177.1048  155.0194
 GX0  C6   C   CR56  0   0.344  164.0264  179.2418  155.5270
 GX0  C8   C   CR56  0   0.129  165.2654  178.9287  154.9507
 GX0  C9   C   CR6   0   0.118  161.9453  178.0147  157.5856
 GX0  C10  C   CR16  0  -0.305  163.6884  180.5267  155.9321
 GX0  C11  C   CR16  0  -0.335  166.2174  179.9298  154.7680
 GX0  C12  C   CR16  0  -0.276  164.6468  181.5090  155.7404
 GX0  C13  C   CR16  0  -0.271  165.8926  181.2148  155.1686
 GX0  C14  C   CR16  0  -0.310  160.9121  178.7254  158.1844
 GX0  C15  C   CR16  0  -0.290  162.8948  177.4014  158.3970
 GX0  C16  C   CR16  0  -0.195  160.8159  178.8239  159.5651
 GX0  C17  C   CR16  0  -0.193  162.8174  177.4940  159.7779
 GX0  C18  C   CR6   0  -0.052  161.7739  178.2055  160.3508
 GX0  H1   H   HCH2  0   0.292  161.3546  178.6461  155.6255
 GX0  H2   H   HCH2  0   0.303  161.6136  176.9267  155.7663
 GX0  H4   H   HCH2  0   0.194  165.1859  174.2359  156.5132
 GX0  H6   H   HCH2  0   0.236  163.8508  173.5829  153.0835
 GX0  H7   H   HCH2  0   0.194  163.6373  173.0468  154.7563
 GX0  H8   H   HCH2  0   0.234  166.7617  172.6227  155.8897
 GX0  H9   H   HCH2  0   0.235  167.4878  173.6367  154.6574
 GX0  H10  H   HCH2  0   0.234  165.4453  171.6239  154.1791
 GX0  H11  H   HCH2  0   0.234  166.1021  172.7608  153.0153
 GX0  H12  H   HCH2  0   0.281  162.9593  175.6425  154.0885
 GX0  H13  H   HCH2  0   0.230  163.2247  175.3511  155.7989
 GX0  H14  H   HCR6  0   0.267  162.7288  180.7593  156.3761
 GX0  H15  H   HCR6  0   0.250  167.1796  179.7069  154.3249
 GX0  H16  H   HCR6  0   0.252  164.4294  182.5259  156.0400
 GX0  H17  H   HCR6  0   0.249  166.6132  182.0118  155.0384
 GX0  H18  H   HCR6  0   0.267  160.1683  179.2182  157.5698
 GX0  H19  H   HCR6  0   0.266  163.7130  176.8412  157.9602
 GX0  H20  H   HCR6  0   0.280  160.0078  179.3828  160.0173
 GX0  H21  H   HCR6  0   0.280  163.5623  177.0142  160.3982
 GX0  H3   H   HCH2  0   0.236  166.3496  175.3777  155.8287

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
 GX0  C1   C3   single    1.526  0.020  1.526
 GX0  C1   N    single    1.453  0.020  1.453
 GX0  C3   C2   single    1.544  0.020  1.544
 GX0  N    C    single    1.454  0.020  1.454
 GX0  N    C4   single    1.436  0.020  1.436
 GX0  C2   C    single    1.531  0.020  1.531
 GX0  C11  C13  aromatic  1.385  0.020  1.385
 GX0  C11  C8   aromatic  1.394  0.020  1.394
 GX0  C13  C12  aromatic  1.402  0.020  1.402
 GX0  N2   C8   aromatic  1.375  0.020  1.375
 GX0  N2   C5   aromatic  1.303  0.020  1.303
 GX0  C8   C6   aromatic  1.402  0.020  1.402
 GX0  C5   C4   single    1.497  0.020  1.497
 GX0  C5   N1   aromatic  1.368  0.020  1.368
 GX0  C12  C10  aromatic  1.386  0.020  1.386
 GX0  C6   C10  aromatic  1.389  0.020  1.389
 GX0  C6   N1   aromatic  1.373  0.020  1.373
 GX0  N1   C7   single    1.444  0.020  1.444
 GX0  C7   C9   single    1.509  0.020  1.509
 GX0  C9   C14  aromatic  1.390  0.020  1.390
 GX0  C9   C15  aromatic  1.391  0.020  1.391
 GX0  C14  C16  aromatic  1.388  0.020  1.388
 GX0  C15  C17  aromatic  1.386  0.020  1.386
 GX0  C16  C18  aromatic  1.385  0.020  1.385
 GX0  C17  C18  aromatic  1.387  0.020  1.387
 GX0  C18  CL   single    1.733  0.020  1.733
 GX0  C7   H1   single    0.970  0.020  1.090
 GX0  C7   H2   single    0.970  0.020  1.090
 GX0  C    H3   single    0.970  0.020  1.090
 GX0  C    H4   single    0.970  0.020  1.090
 GX0  C1   H6   single    0.970  0.020  1.090
 GX0  C1   H7   single    0.970  0.020  1.090
 GX0  C2   H8   single    0.970  0.020  1.090
 GX0  C2   H9   single    0.970  0.020  1.090
 GX0  C3   H10  single    0.970  0.020  1.090
 GX0  C3   H11  single    0.970  0.020  1.090
 GX0  C4   H12  single    0.970  0.020  1.090
 GX0  C4   H13  single    0.970  0.020  1.090
 GX0  C10  H14  single    0.930  0.020  1.080
 GX0  C11  H15  single    0.930  0.020  1.080
 GX0  C12  H16  single    0.930  0.020  1.080
 GX0  C13  H17  single    0.930  0.020  1.080
 GX0  C14  H18  single    0.930  0.020  1.080
 GX0  C15  H19  single    0.930  0.020  1.080
 GX0  C16  H20  single    0.930  0.020  1.080
 GX0  C17  H21  single    0.930  0.020  1.080

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
 GX0  H2   C7   H1   106.15  3.000
 GX0  H2   C7   C9   110.22  3.000
 GX0  H1   C7   C9   109.89  3.000
 GX0  H2   C7   N1   108.74  3.000
 GX0  H1   C7   N1   108.67  3.000
 GX0  C9   C7   N1   112.92  3.000
 GX0  C8   N2   C5   105.47  3.000
 GX0  H4   C    H3   107.44  3.000
 GX0  H4   C    C2   110.04  3.000
 GX0  H3   C    C2   113.12  3.000
 GX0  H4   C    N    110.98  3.000
 GX0  H3   C    N    111.29  3.000
 GX0  C2   C    N    104.01  3.000
 GX0  C4   N    C1   113.09  3.000
 GX0  C4   N    C    114.39  3.000
 GX0  C1   N    C    104.69  3.000
 GX0  H7   C1   H6   107.43  3.000
 GX0  H7   C1   C3   110.20  3.000
 GX0  H6   C1   C3   113.33  3.000
 GX0  H7   C1   N    111.68  3.000
 GX0  H6   C1   N    110.91  3.000
 GX0  C3   C1   N    103.35  3.000
 GX0  C6   N1   C5   106.82  3.000
 GX0  C6   N1   C7   124.50  3.000
 GX0  C5   N1   C7   128.68  3.000
 GX0  H9   C2   H8   107.13  3.000
 GX0  H9   C2   C3   110.92  3.000
 GX0  H8   C2   C3   112.28  3.000
 GX0  H9   C2   C    111.13  3.000
 GX0  H8   C2   C    110.97  3.000
 GX0  C3   C2   C    104.49  3.000
 GX0  H11  C3   H10  107.22  3.000
 GX0  H11  C3   C2   110.74  3.000
 GX0  H10  C3   C2   112.70  3.000
 GX0  H11  C3   C1   110.49  3.000
 GX0  H10  C3   C1   111.59  3.000
 GX0  C2   C3   C1   104.15  3.000
 GX0  H13  C4   H12  105.81  3.000
 GX0  H13  C4   C5   109.49  3.000
 GX0  H12  C4   C5   107.97  3.000
 GX0  H13  C4   N    111.70  3.000
 GX0  H12  C4   N    108.92  3.000
 GX0  C5   C4   N    112.66  3.000
 GX0  C4   C5   N1   121.49  3.000
 GX0  N1   C5   N2   112.83  3.000
 GX0  C4   C5   N2   125.67  3.000
 GX0  C10  C6   C8   122.79  3.000
 GX0  C10  C6   N1   132.22  3.000
 GX0  C8   C6   N1   104.99  3.000
 GX0  C11  C8   C6   119.82  3.000
 GX0  C6   C8   N2   109.89  3.000
 GX0  C11  C8   N2   130.29  3.000
 GX0  C15  C9   C14  118.79  3.000
 GX0  C15  C9   C7   121.35  3.000
 GX0  C14  C9   C7   119.85  3.000
 GX0  H14  C10  C12  121.16  3.000
 GX0  H14  C10  C6   122.28  3.000
 GX0  C12  C10  C6   116.56  3.000
 GX0  H15  C11  C13  121.19  3.000
 GX0  H15  C11  C8   120.86  3.000
 GX0  C13  C11  C8   117.94  3.000
 GX0  H16  C12  C13  119.25  3.000
 GX0  H16  C12  C10  119.27  3.000
 GX0  C13  C12  C10  121.48  3.000
 GX0  H17  C13  C12  119.09  3.000
 GX0  H17  C13  C11  119.50  3.000
 GX0  C12  C13  C11  121.41  3.000
 GX0  H18  C14  C16  118.98  3.000
 GX0  H18  C14  C9   119.91  3.000
 GX0  C16  C14  C9   121.11  3.000
 GX0  H19  C15  C17  118.58  3.000
 GX0  H19  C15  C9   120.54  3.000
 GX0  C17  C15  C9   120.88  3.000
 GX0  H20  C16  C18  120.69  3.000
 GX0  H20  C16  C14  120.30  3.000
 GX0  C18  C16  C14  119.00  3.000
 GX0  H21  C17  C18  120.59  3.000
 GX0  H21  C17  C15  120.21  3.000
 GX0  C18  C17  C15  119.20  3.000
 GX0  C17  C18  C16  121.02  3.000
 GX0  C17  C18  CL   119.51  3.000
 GX0  C16  C18  CL   119.47  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
 GX0  CONST_01  C13  C11  C8   N2   180.00   0.0  0
 GX0  CONST_02  C10  C6   C8   N2   180.00   0.0  0
 GX0  CONST_03  N1   C6   C8   N2     0.00   0.0  0
 GX0  CONST_04  C6   N1   C5   N2     0.00   0.0  0
 GX0  CONST_05  C8   N2   C5   N1     0.00   0.0  0
 GX0  CONST_06  C11  C8   C6   N1   180.00   0.0  0
 GX0  CONST_07  C12  C10  C6   N1   180.00   0.0  0
 GX0  CONST_08  C11  C8   N2   C5   180.00   0.0  0
 GX0  CONST_09  C6   C8   N2   C5     0.00   0.0  0
 GX0  CONST_10  C8   C6   N1   C5     0.00   0.0  0
 GX0  CONST_11  C10  C6   N1   C5   180.00   0.0  0
 GX0  CONST_12  C13  C11  C8   C6     0.00   0.0  0
 GX0  CONST_13  C13  C12  C10  C6     0.00   0.0  0
 GX0  CONST_14  C12  C13  C11  C8     0.00   0.0  0
 GX0  CONST_15  C12  C10  C6   C8     0.00   0.0  0
 GX0  CONST_16  C18  C16  C14  C9     0.00   0.0  0
 GX0  CONST_17  C18  C17  C15  C9     0.00   0.0  0
 GX0  CONST_18  C11  C13  C12  C10    0.00   0.0  0
 GX0  CONST_19  C11  C8   C6   C10    0.00   0.0  0
 GX0  CONST_20  C17  C15  C9   C14    0.00   0.0  0
 GX0  CONST_21  C17  C18  C16  C14    0.00   0.0  0
 GX0  CONST_22  C16  C14  C9   C15    0.00   0.0  0
 GX0  CONST_23  C16  C18  C17  C15    0.00   0.0  0
 GX0  CONST_24  N2   C5   N1   C7   180.00   0.0  0
 GX0  CONST_25  C8   C6   N1   C7   180.00   0.0  0
 GX0  CONST_26  C10  C6   N1   C7     0.00   0.0  0
 GX0  CONST_27  C16  C14  C9   C7   180.00   0.0  0
 GX0  CONST_28  C17  C15  C9   C7   180.00   0.0  0
 GX0  CONST_29  C14  C16  C18  CL   180.00   0.0  0
 GX0  CONST_30  C15  C17  C18  CL   180.00   0.0  0
 GX0  CONST_31  C8   N2   C5   C4   180.00   0.0  0
 GX0  CONST_32  C6   N1   C5   C4   180.00   0.0  0
 GX0  CONST_33  H15  C11  C8   N2     0.00   0.0  0
 GX0  CONST_34  H14  C10  C6   N1     0.00   0.0  0
 GX0  CONST_35  H16  C12  C10  C6   180.00   0.0  0
 GX0  CONST_36  H17  C13  C11  C8   180.00   0.0  0
 GX0  CONST_37  H20  C16  C14  C9   180.00   0.0  0
 GX0  CONST_38  H21  C17  C15  C9   180.00   0.0  0
 GX0  CONST_39  H19  C15  C9   C14  180.00   0.0  0
 GX0  CONST_40  H18  C14  C9   C15  180.00   0.0  0
 GX0  Var_01    C3   C1   N    C    -44.02  30.0  1
 GX0  Var_02    C1   C3   C2   C     -3.93  30.0  1
 GX0  Var_03    C2   C3   C1   N     28.58  30.0  1
 GX0  Var_04    C3   C2   C    N    -22.08  30.0  1
 GX0  Var_05    C2   C    N    C1    41.44  30.0  1
 GX0  Var_06    N    C4   C5   N2    11.81  30.0  2
 GX0  Var_07    C5   C4   N    C     74.27  30.0  3
 GX0  Var_08    C14  C9   C7   N1   138.09  30.0  2
 GX0  Var_09    C9   C7   N1   C5   108.23  30.0  2

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
 GX0  plan-1  C7   0.020
 GX0  plan-1  CL   0.020
 GX0  plan-1  C9   0.020
 GX0  plan-1  C14  0.020
 GX0  plan-1  C15  0.020
 GX0  plan-1  C16  0.020
 GX0  plan-1  C17  0.020
 GX0  plan-1  C18  0.020
 GX0  plan-1  H18  0.020
 GX0  plan-1  H19  0.020
 GX0  plan-1  H20  0.020
 GX0  plan-1  H21  0.020
 GX0  plan-2  C7   0.020
 GX0  plan-2  N2   0.020
 GX0  plan-2  N1   0.020
 GX0  plan-2  C4   0.020
 GX0  plan-2  C5   0.020
 GX0  plan-2  C6   0.020
 GX0  plan-2  C8   0.020
 GX0  plan-2  C10  0.020
 GX0  plan-2  C11  0.020
 GX0  plan-2  C12  0.020
 GX0  plan-2  C13  0.020
 GX0  plan-2  H14  0.020
 GX0  plan-2  H15  0.020
 GX0  plan-2  H16  0.020
 GX0  plan-2  H17  0.020

