# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 08:45:19 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-[[6-(2,6-dimethylpyridin-3-yl)oxy-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c(COc2cccc(c2)C(O)=O)nc3ccc(Oc4ccc(C)nc4C)cc13
#
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
 B0X  B0X  '3-[[6-(2,6-dimethylpyridin-3-yl)oxy-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid'  ligand  50  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B0X
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
 B0X  C1   C  CR6    0   0.411   4.5986  -0.6105   0.0270
 B0X  C2   C  CR16   0  -0.397   5.3161   0.5311   0.3796
 B0X  C3   C  CR6    0  -0.087   6.6566   0.4508   0.7261
 B0X  C4   C  CR16   0  -0.312   7.2845  -0.7955   0.7211
 B0X  C5   C  CR16   0  -0.232   6.5726  -1.9275   0.3660
 B0X  C6   C  CR16   0  -0.383   5.2283  -1.8505   0.0140
 B0X  C7   C  CR56   0   0.133  -0.8014  -0.6223  -1.5793
 B0X  C8   C  CR56   0   0.363  -0.8393  -0.1858  -0.2467
 B0X  N9   N  NR5    0  -0.534   0.3866  -0.4988   0.2717
 B0X  C10  C  CR5    0   0.443   1.0962  -1.0774  -0.7390
 B0X  N11  N  N      0  -0.469   0.4253  -1.1716  -1.8533
 B0X  C12  C  CR6    0   0.309  -3.0447   0.5780  -0.5179
 B0X  C13  C  CR16   0  -0.394  -1.9581   0.4186   0.3182
 B0X  C14  C  CR16   0  -0.325  -1.9185  -0.4495  -2.3963
 B0X  C15  C  CR16   0  -0.319  -3.0360   0.1551  -1.8566
 B0X  C16  C  C1     0  -0.334  -6.6019  -1.4707   0.3986
 B0X  C17  C  C      0   0.216  -7.7263  -0.6756   0.5590
 B0X  N18  N  N      0  -0.435  -7.6409   0.6553   0.5269
 B0X  C19  C  C      0   0.158  -6.4754   1.2523   0.3305
 B0X  C20  C  C      0   0.266  -5.3021   0.5081   0.1542
 B0X  C21  C  C1     0  -0.228  -5.3661  -0.8724   0.1952
 B0X  O22  O  O2     0  -0.513  -4.1537   1.2173  -0.0194
 B0X  C24  C  CH2    0  -0.309   2.4958  -1.5498  -0.5646
 B0X  O25  O  O2     0  -0.479   3.2949  -0.4163  -0.2919
 B0X  C26  C  C      0   0.402   7.4285   1.7117   1.1049
 B0X  O27  O  O      0  -0.591   6.8028   2.7874   1.0536
 B0X  O28  O  OC    -1  -0.593   8.6205   1.5548   1.4302
 B0X  H1   H  HCR6   0   0.250   4.8161   1.4917   0.3805
 B0X  H2   H  HCR6   0   0.241   8.3287  -0.8723   0.9908
 B0X  H3   H  HCR6   0   0.253   7.0598  -2.8944   0.3583
 B0X  H4   H  HCR6   0   0.279   4.7061  -2.7558  -0.2641
 B0X  H5   H  HCR6   0   0.284  -1.9894   0.7542   1.3469
 B0X  H6   H  HCR6   0   0.265  -1.9090  -0.7725  -3.4290
 B0X  H7   H  HCR6   0   0.275  -3.9143   0.3136  -2.4696
 B0X  H8   H  H      0   0.265  -6.6816  -2.5490   0.4311
 B0X  H9   H  H      0   0.287  -4.4817  -1.4844   0.0740
 B0X  H10  H  HCH3   0   0.265   0.0045  -0.3553   2.3086
 B0X  H11  H  HCH3   0   0.270   1.6263  -0.8925   1.9048
 B0X  H12  H  HCH3   0   0.265   1.1917   0.8116   1.7026
 B0X  H13  H  HCH2   0   0.255   2.5580  -2.2802   0.2513
 B0X  H14  H  HCH2   0   0.272   2.8038  -2.0534  -1.4851
 B0X  H16  H  HCH3   0   0.247  -9.4809  -0.9846   1.7575
 B0X  H17  H  HCH3   0   0.246  -9.7940  -0.9026   0.0317
 B0X  H18  H  HCH3   0   0.241  -9.0657  -2.3521   0.7249
 B0X  H19  H  HCH3   0   0.249  -5.7744   3.1498   1.0730
 B0X  H20  H  HCH3   0   0.249  -6.0902   3.1302  -0.6525
 B0X  H21  H  HCH3   0   0.248  -7.4402   3.1430   0.4873
 B0X  C29  C  CH3    0  -0.715  -9.0868  -1.2649   0.7790
 B0X  C23  C  CH3    0  -0.534   0.8309  -0.2120   1.6164
 B0X  C30  C  CH3    0  -0.724  -6.4421   2.7498   0.3081

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
 B0X  C4   C5   aromatic  1.384  0.020  1.384
 B0X  C4   C3   aromatic  1.396  0.020  1.396
 B0X  C5   C6   aromatic  1.392  0.020  1.392
 B0X  O27  C26  deloc     1.246  0.020  1.246
 B0X  C26  C3   single    1.526  0.020  1.526
 B0X  C26  O28  deloc     1.245  0.020  1.245
 B0X  C3   C2   aromatic  1.387  0.020  1.387
 B0X  C6   C1   aromatic  1.391  0.020  1.391
 B0X  C2   C1   aromatic  1.394  0.020  1.394
 B0X  C1   O25  single    1.356  0.020  1.356
 B0X  O25  C24  single    1.413  0.020  1.413
 B0X  C24  C10  single    1.487  0.020  1.487
 B0X  C10  N11  aromatic  1.304  0.020  1.304
 B0X  C10  N9   aromatic  1.364  0.020  1.364
 B0X  N11  C7   aromatic  1.372  0.020  1.372
 B0X  N9   C23  single    1.445  0.020  1.445
 B0X  N9   C8   aromatic  1.367  0.020  1.367
 B0X  C7   C8   aromatic  1.403  0.020  1.403
 B0X  C7   C14  aromatic  1.395  0.020  1.395
 B0X  C8   C13  aromatic  1.391  0.020  1.391
 B0X  C14  C15  aromatic  1.380  0.020  1.380
 B0X  C13  C12  aromatic  1.380  0.020  1.380
 B0X  C15  C12  aromatic  1.404  0.020  1.404
 B0X  C12  O22  single    1.374  0.020  1.374
 B0X  O22  C20  single    1.361  0.020  1.361
 B0X  C21  C20  aromatic  1.383  0.020  1.383
 B0X  C21  C16  aromatic  1.388  0.020  1.388
 B0X  C20  C19  aromatic  1.401  0.020  1.401
 B0X  C16  C17  aromatic  1.386  0.020  1.386
 B0X  C19  C30  single    1.498  0.020  1.498
 B0X  C19  N18  aromatic  1.324  0.020  1.324
 B0X  C17  N18  aromatic  1.334  0.020  1.334
 B0X  C17  C29  single    1.499  0.020  1.499
 B0X  C2   H1   single    0.930  0.020  1.080
 B0X  C4   H2   single    0.930  0.020  1.080
 B0X  C5   H3   single    0.930  0.020  1.080
 B0X  C6   H4   single    0.930  0.020  1.080
 B0X  C13  H5   single    0.930  0.020  1.080
 B0X  C14  H6   single    0.930  0.020  1.080
 B0X  C15  H7   single    0.930  0.020  1.080
 B0X  C16  H8   single    0.930  0.020  1.080
 B0X  C21  H9   single    0.930  0.020  1.080
 B0X  C23  H10  single    0.970  0.020  1.090
 B0X  C23  H11  single    0.970  0.020  1.090
 B0X  C23  H12  single    0.970  0.020  1.090
 B0X  C24  H13  single    0.970  0.020  1.090
 B0X  C24  H14  single    0.970  0.020  1.090
 B0X  C29  H16  single    0.970  0.020  1.090
 B0X  C29  H17  single    0.970  0.020  1.090
 B0X  C29  H18  single    0.970  0.020  1.090
 B0X  C30  H19  single    0.970  0.020  1.090
 B0X  C30  H20  single    0.970  0.020  1.090
 B0X  C30  H21  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
 B0X  O25  C1   C6   124.11  3.000
 B0X  O25  C1   C2   115.92  3.000
 B0X  C6   C1   C2   119.97  3.000
 B0X  H1   C2   C3   119.83  3.000
 B0X  H1   C2   C1   119.28  3.000
 B0X  C3   C2   C1   120.89  3.000
 B0X  C26  C3   C4   120.74  3.000
 B0X  C26  C3   C2   120.20  3.000
 B0X  C4   C3   C2   119.06  3.000
 B0X  H2   C4   C5   120.19  3.000
 B0X  H2   C4   C3   119.81  3.000
 B0X  C5   C4   C3   120.00  3.000
 B0X  H3   C5   C6   118.83  3.000
 B0X  H3   C5   C4   120.06  3.000
 B0X  C6   C5   C4   121.11  3.000
 B0X  H4   C6   C5   119.02  3.000
 B0X  H4   C6   C1   122.01  3.000
 B0X  C5   C6   C1   118.97  3.000
 B0X  C14  C7   N11  130.46  3.000
 B0X  C14  C7   C8   119.76  3.000
 B0X  N11  C7   C8   109.79  3.000
 B0X  C13  C8   N9   131.80  3.000
 B0X  C13  C8   C7   122.85  3.000
 B0X  N9   C8   C7   105.35  3.000
 B0X  C23  N9   C10  127.88  3.000
 B0X  C23  N9   C8   125.66  3.000
 B0X  C10  N9   C8   106.42  3.000
 B0X  C24  C10  N11  124.15  3.000
 B0X  N11  C10  N9   113.35  3.000
 B0X  C24  C10  N9   122.51  3.000
 B0X  C10  N11  C7   105.10  3.000
 B0X  O22  C12  C15  119.42  3.000
 B0X  O22  C12  C13  118.00  3.000
 B0X  C15  C12  C13  122.54  3.000
 B0X  H5   C13  C12  121.14  3.000
 B0X  H5   C13  C8   122.93  3.000
 B0X  C12  C13  C8   115.93  3.000
 B0X  H6   C14  C15  120.73  3.000
 B0X  H6   C14  C7   121.00  3.000
 B0X  C15  C14  C7   118.27  3.000
 B0X  H7   C15  C14  119.96  3.000
 B0X  H7   C15  C12  119.39  3.000
 B0X  C14  C15  C12  120.65  3.000
 B0X  H8   C16  C21  119.98  3.000
 B0X  H8   C16  C17  120.55  3.000
 B0X  C21  C16  C17  119.46  3.000
 B0X  C29  C17  N18  117.00  3.000
 B0X  C29  C17  C16  121.85  3.000
 B0X  N18  C17  C16  121.16  3.000
 B0X  C19  N18  C17  120.65  3.000
 B0X  C30  C19  C20  120.71  3.000
 B0X  C30  C19  N18  118.20  3.000
 B0X  C20  C19  N18  121.09  3.000
 B0X  O22  C20  C21  124.28  3.000
 B0X  C21  C20  C19  119.21  3.000
 B0X  O22  C20  C19  116.49  3.000
 B0X  H9   C21  C20  121.56  3.000
 B0X  H9   C21  C16  120.02  3.000
 B0X  C20  C21  C16  118.42  3.000
 B0X  C20  O22  C12  119.02  3.000
 B0X  H14  C24  H13  107.67  3.000
 B0X  H14  C24  O25  111.86  3.000
 B0X  H13  C24  O25  111.01  3.000
 B0X  H14  C24  C10  108.21  3.000
 B0X  H13  C24  C10  110.61  3.000
 B0X  O25  C24  C10  107.46  3.000
 B0X  C24  O25  C1   118.30  3.000
 B0X  O28  C26  O27  126.90  3.000
 B0X  O28  C26  C3   116.41  3.000
 B0X  O27  C26  C3   116.69  3.000
 B0X  H18  C29  H17  108.07  3.000
 B0X  H18  C29  H16  107.94  3.000
 B0X  H17  C29  H16  107.15  3.000
 B0X  H18  C29  C17  111.57  3.000
 B0X  H17  C29  C17  110.93  3.000
 B0X  H16  C29  C17  111.00  3.000
 B0X  H12  C23  H11  108.99  3.000
 B0X  H12  C23  H10  108.98  3.000
 B0X  H11  C23  H10  107.76  3.000
 B0X  H12  C23  N9   111.24  3.000
 B0X  H11  C23  N9   110.37  3.000
 B0X  H10  C23  N9   109.42  3.000
 B0X  H21  C30  H20  108.35  3.000
 B0X  H21  C30  H19  108.26  3.000
 B0X  H20  C30  H19  106.97  3.000
 B0X  H21  C30  C19  109.79  3.000
 B0X  H20  C30  C19  111.64  3.000
 B0X  H19  C30  C19  111.69  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
 B0X  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 B0X  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 B0X  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 B0X  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 B0X  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 B0X  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 B0X  CONST_07  N9   C10  N11  C7     0.00   0.0  0
 B0X  CONST_08  C10  N9   C8   C7     0.00   0.0  0
 B0X  CONST_09  C12  C13  C8   C7     0.00   0.0  0
 B0X  CONST_10  C12  C15  C14  C7     0.00   0.0  0
 B0X  CONST_11  N11  C10  N9   C8     0.00   0.0  0
 B0X  CONST_12  C10  N11  C7   C8     0.00   0.0  0
 B0X  CONST_13  C15  C14  C7   C8     0.00   0.0  0
 B0X  CONST_14  C15  C12  C13  C8     0.00   0.0  0
 B0X  CONST_15  N11  C7   C8   N9     0.00   0.0  0
 B0X  CONST_16  C14  C7   C8   N9   180.00   0.0  0
 B0X  CONST_17  C12  C13  C8   N9   180.00   0.0  0
 B0X  CONST_18  C14  C7   N11  C10  180.00   0.0  0
 B0X  CONST_19  C13  C8   N9   C10  180.00   0.0  0
 B0X  CONST_20  C13  C8   C7   N11  180.00   0.0  0
 B0X  CONST_21  C15  C14  C7   N11  180.00   0.0  0
 B0X  CONST_22  C14  C7   C8   C13    0.00   0.0  0
 B0X  CONST_23  C14  C15  C12  C13    0.00   0.0  0
 B0X  CONST_24  C19  C20  C21  C16    0.00   0.0  0
 B0X  CONST_25  C19  N18  C17  C16    0.00   0.0  0
 B0X  CONST_26  C20  C21  C16  C17    0.00   0.0  0
 B0X  CONST_27  C20  C19  N18  C17    0.00   0.0  0
 B0X  CONST_28  C21  C20  C19  N18    0.00   0.0  0
 B0X  CONST_29  C21  C16  C17  N18    0.00   0.0  0
 B0X  CONST_30  C26  C3   C2   C1   180.00   0.0  0
 B0X  CONST_31  O25  C1   C2   C3   180.00   0.0  0
 B0X  CONST_32  C26  C3   C4   C5   180.00   0.0  0
 B0X  CONST_33  O25  C1   C6   C5   180.00   0.0  0
 B0X  CONST_34  C24  C10  N11  C7   180.00   0.0  0
 B0X  CONST_35  C23  N9   C8   C7   180.00   0.0  0
 B0X  CONST_36  C24  C10  N9   C8   180.00   0.0  0
 B0X  CONST_37  O22  C12  C13  C8   180.00   0.0  0
 B0X  CONST_38  C23  N9   C10  N11  180.00   0.0  0
 B0X  CONST_39  C23  N9   C8   C13    0.00   0.0  0
 B0X  CONST_40  O22  C12  C15  C14  180.00   0.0  0
 B0X  CONST_41  O22  C20  C21  C16  180.00   0.0  0
 B0X  CONST_42  C30  C19  N18  C17  180.00   0.0  0
 B0X  CONST_43  O22  C20  C19  N18  180.00   0.0  0
 B0X  CONST_44  C29  C17  N18  C19  180.00   0.0  0
 B0X  CONST_45  C30  C19  C20  C21  180.00   0.0  0
 B0X  CONST_46  C29  C17  C16  C21  180.00   0.0  0
 B0X  CONST_47  H3   C5   C6   C1   180.00   0.0  0
 B0X  CONST_48  H2   C4   C3   C2   180.00   0.0  0
 B0X  CONST_49  H4   C6   C1   C2   180.00   0.0  0
 B0X  CONST_50  H1   C2   C3   C4   180.00   0.0  0
 B0X  CONST_51  H5   C13  C8   C7   180.00   0.0  0
 B0X  CONST_52  H7   C15  C14  C7   180.00   0.0  0
 B0X  CONST_53  H6   C14  C7   C8   180.00   0.0  0
 B0X  CONST_54  H9   C21  C16  C17  180.00   0.0  0
 B0X  CONST_55  H8   C16  C17  N18  180.00   0.0  0
 B0X  Var_01    C21  C20  O22  C12   17.35  30.0  2
 B0X  Var_02    C10  C24  O25  C1   174.06  30.0  3
 B0X  Var_03    O27  C26  C3   C2    -1.57  30.0  2
 B0X  Var_04    O25  C24  C10  N9   -64.19  30.0  2
 B0X  Var_05    H10  C23  N9   C8    38.01  30.0  2
 B0X  Var_06    H16  C29  C17  C16  116.57  30.0  2
 B0X  Var_07    H19  C30  C19  N18  121.28  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
 B0X  plan-1  C1   0.020
 B0X  plan-1  C2   0.020
 B0X  plan-1  C3   0.020
 B0X  plan-1  C4   0.020
 B0X  plan-1  C5   0.020
 B0X  plan-1  C6   0.020
 B0X  plan-1  O25  0.020
 B0X  plan-1  C26  0.020
 B0X  plan-1  H1   0.020
 B0X  plan-1  H2   0.020
 B0X  plan-1  H3   0.020
 B0X  plan-1  H4   0.020
 B0X  plan-2  C16  0.020
 B0X  plan-2  C17  0.020
 B0X  plan-2  N18  0.020
 B0X  plan-2  C19  0.020
 B0X  plan-2  C20  0.020
 B0X  plan-2  C21  0.020
 B0X  plan-2  O22  0.020
 B0X  plan-2  H8   0.020
 B0X  plan-2  H9   0.020
 B0X  plan-2  C29  0.020
 B0X  plan-2  C30  0.020
 B0X  plan-3  C7   0.020
 B0X  plan-3  C8   0.020
 B0X  plan-3  N9   0.020
 B0X  plan-3  C10  0.020
 B0X  plan-3  N11  0.020
 B0X  plan-3  C12  0.020
 B0X  plan-3  C13  0.020
 B0X  plan-3  C14  0.020
 B0X  plan-3  C15  0.020
 B0X  plan-3  O22  0.020
 B0X  plan-3  C24  0.020
 B0X  plan-3  H5   0.020
 B0X  plan-3  H6   0.020
 B0X  plan-3  H7   0.020
 B0X  plan-3  C23  0.020
 B0X  plan-4  C3   0.020
 B0X  plan-4  C26  0.020
 B0X  plan-4  O27  0.020
 B0X  plan-4  O28  0.020

