# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 05:49:59 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: 1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCn1c(C)[n+](Cc2cnccn2)c3C(=O)c4ccccc4C(=O)c13
#
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
 GXU  GXU  1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione  ligand  46  27  .  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_GXU
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
 GXU  N5   N  NR5   1  -0.499  66.1636  -26.9756  11.7749
 GXU  N7   N  N     0  -0.344  65.0812  -25.7327  16.2207
 GXU  C8   C  CR56  0   0.204  65.0264  -26.5714   9.9469
 GXU  C10  C  CR5   0   0.630  66.9670  -26.3069  10.9413
 GXU  C12  C  CH2   0  -0.404  66.5032  -27.3259  13.1448
 GXU  C13  C  CR6   0   0.369  63.9103  -26.5678   8.9918
 GXU  C14  C  CR6   0   0.370  63.7317  -27.7477  11.7242
 GXU  C15  C  CR66  0  -0.036  62.6759  -27.2294   9.4902
 GXU  C16  C  CR66  0  -0.034  62.5890  -27.7811  10.7795
 GXU  C17  C  CH3   0  -0.768  68.3615  -25.9427  11.2579
 GXU  C18  C  CH2   0  -0.141  66.4210  -23.8108   8.8817
 GXU  C19  C  CR6   0   0.211  65.9479  -26.2962  14.0914
 GXU  C21  C  CR16  0  -0.260  61.4044  -28.3734  11.1966
 GXU  C22  C  CR16  0  -0.227  60.3981  -27.8862   9.0694
 GXU  C23  C  CR16  0  -0.228  60.3122  -28.4274  10.3432
 GXU  C24  C  CR16  0  -0.087  65.5397  -26.6412  15.3743
 GXU  C9   C  CR56  0   0.223  64.9453  -27.1321  11.1791
 GXU  C20  C  CR16  0  -0.260  61.5755  -27.2869   8.6452
 GXU  C25  C  CH3   0  -0.393  66.5411  -22.0780  10.4551
 GXU  C26  C  CR16  0  -0.108  65.4187  -24.1377  14.5035
 GXU  C27  C  CR16  0  -0.094  65.0198  -24.4811  15.7876
 GXU  N4   N  NR5   0  -0.506  66.2949  -26.0693   9.8121
 GXU  N6   N  N     0  -0.366  65.8839  -25.0473  13.6603
 GXU  O1   O  O     0  -0.348  63.9905  -26.0677   7.8940
 GXU  O2   O  O     0  -0.347  63.6784  -28.1763  12.8538
 GXU  O3   O  O2    0  -0.478  66.9187  -23.3908  10.1195
 GXU  H1   H  HCH2  0   0.331  66.1301  -28.3225  13.3638
 GXU  H2   H  HCH2  0   0.335  67.5894  -27.3700  13.2250
 GXU  H3   H  HCH3  0   0.303  68.3857  -25.3230  12.1534
 GXU  H4   H  HCH3  0   0.304  68.9468  -26.8436  11.4434
 GXU  H5   H  HCH3  0   0.305  68.8335  -25.3893  10.4549
 GXU  H6   H  HCH2  0   0.239  66.8500  -23.2420   8.0464
 GXU  H7   H  HCH2  0   0.224  65.3305  -23.6922   8.8273
 GXU  H8   H  HCR6  0   0.283  61.3344  -28.7949  12.1902
 GXU  H9   H  HCR6  0   0.283  59.5469  -27.9268   8.4033
 GXU  H10  H  HCR6  0   0.283  59.3937  -28.8917  10.6760
 GXU  H11  H  HCR6  0   0.282  65.5847  -27.6696  15.7154
 GXU  H12  H  HCH2  0   0.318  66.3759  -25.6555   7.7717
 GXU  H13  H  HCH2  0   0.305  67.8726  -25.3982   8.6396
 GXU  H14  H  HCR6  0   0.283  61.6360  -26.8612   7.6529
 GXU  H15  H  HCH3  0   0.239  66.9405  -21.8613  11.4445
 GXU  H16  H  HCH3  0   0.212  66.9417  -21.3436   9.7479
 GXU  H17  H  HCH3  0   0.211  65.4519  -21.9632  10.4849
 GXU  H18  H  HCR6  0   0.284  65.3605  -23.1139  14.1550
 GXU  H19  H  HCR6  0   0.283  64.6421  -23.7298  16.4701
 GXU  C11  C  CH2   0  -0.391  66.7949  -25.2671   8.6939

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
 GXU  O1   C13  double    1.209  0.020  1.209
 GXU  C20  C22  aromatic  1.388  0.020  1.388
 GXU  C20  C15  aromatic  1.389  0.020  1.389
 GXU  C11  C18  single    1.515  0.020  1.515
 GXU  C11  N4   single    1.464  0.020  1.464
 GXU  C18  O3   single    1.399  0.020  1.399
 GXU  C13  C15  single    1.487  0.020  1.487
 GXU  C13  C8   single    1.469  0.020  1.469
 GXU  C22  C23  aromatic  1.387  0.020  1.387
 GXU  C15  C16  aromatic  1.405  0.020  1.405
 GXU  N4   C8   aromatic  1.371  0.020  1.371
 GXU  N4   C10  aromatic  1.335  0.020  1.335
 GXU  C8   C9   aromatic  1.356  0.020  1.356
 GXU  O3   C25  single    1.407  0.020  1.407
 GXU  C23  C21  aromatic  1.387  0.020  1.387
 GXU  C16  C21  aromatic  1.389  0.020  1.389
 GXU  C16  C14  single    1.483  0.020  1.483
 GXU  C10  C17  single    1.476  0.020  1.476
 GXU  C10  N5   aromatic  1.337  0.020  1.337
 GXU  C9   C14  single    1.466  0.020  1.466
 GXU  C9   N5   aromatic  1.365  0.020  1.365
 GXU  C14  O2   double    1.209  0.020  1.209
 GXU  N5   C12  single    1.454  0.020  1.454
 GXU  C12  C19  single    1.505  0.020  1.505
 GXU  N6   C19  aromatic  1.323  0.020  1.323
 GXU  N6   C26  aromatic  1.325  0.020  1.325
 GXU  C19  C24  aromatic  1.390  0.020  1.390
 GXU  C26  C27  aromatic  1.388  0.020  1.388
 GXU  C24  N7   aromatic  1.324  0.020  1.324
 GXU  C27  N7   aromatic  1.326  0.020  1.326
 GXU  C12  H1   single    0.970  0.020  1.090
 GXU  C12  H2   single    0.970  0.020  1.090
 GXU  C17  H3   single    0.970  0.020  1.090
 GXU  C17  H4   single    0.970  0.020  1.090
 GXU  C17  H5   single    0.970  0.020  1.090
 GXU  C18  H6   single    0.970  0.020  1.090
 GXU  C18  H7   single    0.970  0.020  1.090
 GXU  C21  H8   single    0.930  0.020  1.080
 GXU  C22  H9   single    0.930  0.020  1.080
 GXU  C23  H10  single    0.930  0.020  1.080
 GXU  C24  H11  single    0.930  0.020  1.080
 GXU  C11  H12  single    0.970  0.020  1.090
 GXU  C11  H13  single    0.970  0.020  1.090
 GXU  C20  H14  single    0.930  0.020  1.080
 GXU  C25  H15  single    0.970  0.020  1.090
 GXU  C25  H16  single    0.970  0.020  1.090
 GXU  C25  H17  single    0.970  0.020  1.090
 GXU  C26  H18  single    0.930  0.020  1.080
 GXU  C27  H19  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
 GXU  C9   N5   C12  126.29  3.000
 GXU  C12  N5   C10  124.58  3.000
 GXU  C9   N5   C10  108.76  3.000
 GXU  C27  N7   C24  117.07  3.000
 GXU  N4   C8   C9   107.23  3.000
 GXU  C9   C8   C13  123.12  3.000
 GXU  N4   C8   C13  129.65  3.000
 GXU  N4   C10  C17  127.82  3.000
 GXU  C17  C10  N5   123.89  3.000
 GXU  N4   C10  N5   108.28  3.000
 GXU  H2   C12  H1   106.88  3.000
 GXU  H2   C12  C19  110.43  3.000
 GXU  H1   C12  C19  111.97  3.000
 GXU  H2   C12  N5   108.16  3.000
 GXU  H1   C12  N5   109.31  3.000
 GXU  C19  C12  N5   109.97  3.000
 GXU  O1   C13  C15  122.93  3.000
 GXU  C15  C13  C8   114.32  3.000
 GXU  O1   C13  C8   122.75  3.000
 GXU  O2   C14  C9   122.18  3.000
 GXU  O2   C14  C16  123.58  3.000
 GXU  C9   C14  C16  114.24  3.000
 GXU  C20  C15  C16  119.55  3.000
 GXU  C16  C15  C13  122.26  3.000
 GXU  C20  C15  C13  118.19  3.000
 GXU  C21  C16  C15  119.73  3.000
 GXU  C21  C16  C14  118.40  3.000
 GXU  C15  C16  C14  121.87  3.000
 GXU  H5   C17  H4   108.32  3.000
 GXU  H5   C17  H3   108.00  3.000
 GXU  H4   C17  H3   108.56  3.000
 GXU  H5   C17  C10  112.26  3.000
 GXU  H4   C17  C10  109.88  3.000
 GXU  H3   C17  C10  109.74  3.000
 GXU  H7   C18  H6   107.12  3.000
 GXU  H7   C18  O3   111.39  3.000
 GXU  H6   C18  O3   112.25  3.000
 GXU  H7   C18  C11  110.04  3.000
 GXU  H6   C18  C11  107.89  3.000
 GXU  O3   C18  C11  108.09  3.000
 GXU  N6   C19  C24  121.40  3.000
 GXU  C24  C19  C12  121.28  3.000
 GXU  N6   C19  C12  117.32  3.000
 GXU  H8   C21  C23  119.94  3.000
 GXU  H8   C21  C16  119.83  3.000
 GXU  C23  C21  C16  120.23  3.000
 GXU  H9   C22  C20  119.72  3.000
 GXU  H9   C22  C23  120.15  3.000
 GXU  C20  C22  C23  120.13  3.000
 GXU  H10  C23  C22  120.18  3.000
 GXU  H10  C23  C21  119.74  3.000
 GXU  C22  C23  C21  120.07  3.000
 GXU  H11  C24  C19  120.90  3.000
 GXU  H11  C24  N7   117.65  3.000
 GXU  C19  C24  N7   121.45  3.000
 GXU  C14  C9   C8   124.12  3.000
 GXU  C14  C9   N5   128.66  3.000
 GXU  C8   C9   N5   107.20  3.000
 GXU  H14  C20  C22  119.86  3.000
 GXU  H14  C20  C15  119.86  3.000
 GXU  C22  C20  C15  120.28  3.000
 GXU  H17  C25  H16  108.11  3.000
 GXU  H17  C25  H15  108.61  3.000
 GXU  H16  C25  H15  108.61  3.000
 GXU  H17  C25  O3   111.79  3.000
 GXU  H16  C25  O3   111.93  3.000
 GXU  H15  C25  O3   107.71  3.000
 GXU  H18  C26  N6   117.59  3.000
 GXU  H18  C26  C27  121.08  3.000
 GXU  N6   C26  C27  121.33  3.000
 GXU  H19  C27  C26  120.77  3.000
 GXU  H19  C27  N7   117.72  3.000
 GXU  C26  C27  N7   121.51  3.000
 GXU  C11  N4   C10  124.84  3.000
 GXU  C10  N4   C8   108.50  3.000
 GXU  C11  N4   C8   126.28  3.000
 GXU  C26  N6   C19  117.25  3.000
 GXU  C25  O3   C18  113.32  3.000
 GXU  H13  C11  H12  107.29  3.000
 GXU  H13  C11  N4   108.10  3.000
 GXU  H12  C11  N4   108.73  3.000
 GXU  H13  C11  C18  111.52  3.000
 GXU  H12  C11  C18  110.75  3.000
 GXU  N4   C11  C18  110.34  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
 GXU  CONST_01  C8   N4   C10  N5     0.00   0.0  0
 GXU  CONST_02  N4   C8   C9   N5     0.00   0.0  0
 GXU  CONST_03  N6   C19  C24  N7     0.00   0.0  0
 GXU  CONST_04  N6   C26  C27  N7     0.00   0.0  0
 GXU  CONST_05  C10  N5   C9   C8     0.00   0.0  0
 GXU  CONST_06  C9   C8   N4   C10    0.00   0.0  0
 GXU  CONST_07  C23  C22  C20  C15    0.00   0.0  0
 GXU  CONST_08  C23  C21  C16  C15    0.00   0.0  0
 GXU  CONST_09  C22  C20  C15  C16    0.00   0.0  0
 GXU  CONST_10  C22  C23  C21  C16    0.00   0.0  0
 GXU  CONST_11  C27  C26  N6   C19    0.00   0.0  0
 GXU  CONST_12  C27  N7   C24  C19    0.00   0.0  0
 GXU  CONST_13  C20  C22  C23  C21    0.00   0.0  0
 GXU  CONST_14  C20  C15  C16  C21    0.00   0.0  0
 GXU  CONST_15  C26  N6   C19  C24    0.00   0.0  0
 GXU  CONST_16  C26  C27  N7   C24    0.00   0.0  0
 GXU  CONST_17  N4   C10  N5   C9     0.00   0.0  0
 GXU  CONST_18  C11  N4   C10  N5   180.00   0.0  0
 GXU  CONST_19  C12  C19  C24  N7   180.00   0.0  0
 GXU  CONST_20  C17  C10  N4   C8   180.00   0.0  0
 GXU  CONST_21  C12  N5   C9   C8   180.00   0.0  0
 GXU  CONST_22  N4   C10  N5   C12  180.00   0.0  0
 GXU  CONST_23  C14  C9   N5   C12    0.00   0.0  0
 GXU  CONST_24  C26  N6   C19  C12  180.00   0.0  0
 GXU  CONST_25  C11  N4   C8   C13    0.00   0.0  0
 GXU  CONST_26  C9   N5   C10  C17  180.00   0.0  0
 GXU  CONST_27  C11  N4   C8   C9   180.00   0.0  0
 GXU  CONST_28  H18  C26  C27  N7   180.00   0.0  0
 GXU  CONST_29  H14  C20  C15  C13    0.00   0.0  0
 GXU  CONST_30  H8   C21  C16  C14    0.00   0.0  0
 GXU  CONST_31  H9   C22  C20  C15  180.00   0.0  0
 GXU  CONST_32  H10  C23  C21  C16  180.00   0.0  0
 GXU  CONST_33  H19  C27  N7   C24  180.00   0.0  0
 GXU  CONST_34  H11  C24  N7   C27  180.00   0.0  0
 GXU  Var_01    N6   C19  C12  N5   -32.73  30.0  2
 GXU  Var_02    C19  C12  N5   C10   95.78  30.0  2
 GXU  Var_03    C18  C11  N4   C8    82.84  30.0  2
 GXU  Var_04    H3   C17  C10  N5   -58.95  30.0  2
 GXU  Var_05    O3   C18  C11  N4    56.05  30.0  3
 GXU  Var_06    H15  C25  O3   C18  177.76  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
 GXU  plan-1  N7   0.020
 GXU  plan-1  C12  0.020
 GXU  plan-1  C19  0.020
 GXU  plan-1  C24  0.020
 GXU  plan-1  C26  0.020
 GXU  plan-1  C27  0.020
 GXU  plan-1  N6   0.020
 GXU  plan-1  H11  0.020
 GXU  plan-1  H18  0.020
 GXU  plan-1  H19  0.020
 GXU  plan-2  N5   0.020
 GXU  plan-2  C8   0.020
 GXU  plan-2  C10  0.020
 GXU  plan-2  C12  0.020
 GXU  plan-2  C13  0.020
 GXU  plan-2  C14  0.020
 GXU  plan-2  C15  0.020
 GXU  plan-2  C16  0.020
 GXU  plan-2  C17  0.020
 GXU  plan-2  C21  0.020
 GXU  plan-2  C22  0.020
 GXU  plan-2  C23  0.020
 GXU  plan-2  C9   0.020
 GXU  plan-2  C20  0.020
 GXU  plan-2  N4   0.020
 GXU  plan-2  O1   0.020
 GXU  plan-2  O2   0.020
 GXU  plan-2  H8   0.020
 GXU  plan-2  H9   0.020
 GXU  plan-2  H10  0.020
 GXU  plan-2  H14  0.020
 GXU  plan-2  C11  0.020

