# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 19:14:01 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-[[6-(3,5-dimethylpyridin-2-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(Oc4ncc(C)cc4C)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
 RTF  RTF  '3-[[6-(3,5-dimethylpyridin-2-yl)oxy-1-methyl-benzimidazol-2-yl]methoxy]benzoic acid'  ligand  50  30  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RTF
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
 RTF  C1   C  CR6    0   0.363  -3.3732  -1.1480  -0.0216
 RTF  C2   C  CR16   0  -0.391  -2.2651  -0.9581   0.7779
 RTF  C3   C  CR16   0  -0.332  -2.0819  -2.1463  -1.8062
 RTF  C4   C  CR16   0  -0.326  -3.2951  -1.7310  -1.2939
 RTF  C5   C  CR56   0   0.132  -0.9408  -1.9636  -1.0255
 RTF  C6   C  CR56   0   0.359  -1.0511  -1.3780   0.2446
 RTF  N7   N  NR5    0  -0.534   0.2245  -1.3388   0.7374
 RTF  C8   C  CR5    0   0.438   1.0247  -1.8889  -0.2201
 RTF  N9   N  N      0  -0.468   0.3718  -2.2685  -1.2834
 RTF  C10  C  CH3    0  -0.545   0.6010  -0.8883   2.0587
 RTF  C11  C  CH2    0  -0.305   2.4981  -2.0302  -0.0603
 RTF  O12  O  O2     0  -0.482   3.0527  -0.7289  -0.0399
 RTF  O13  O  O2     0  -0.524  -4.6111  -0.8052   0.4738
 RTF  C14  C  CR6    0   0.411   4.3863  -0.6017   0.1715
 RTF  C15  C  CR16   0  -0.397   4.8581   0.7019   0.3122
 RTF  C16  C  CR6    0  -0.087   6.2063   0.9531   0.5205
 RTF  C17  C  CR16   0  -0.312   7.0922  -0.1227   0.5928
 RTF  C18  C  CR16   0  -0.233   6.6217  -1.4171   0.4585
 RTF  C19  C  CR16   0  -0.382   5.2701  -1.6730   0.2464
 RTF  C20  C  C      0   0.401   6.7038   2.3881   0.6727
 RTF  O21  O  OC    -1  -0.592   7.9292   2.5356   0.8382
 RTF  O22  O  O      0  -0.591   5.8432   3.2870   0.6193
 RTF  C23  C  CR6    0   0.468  -5.1304   0.4055   0.1562
 RTF  C24  C  CR6    0  -0.032  -6.4106   0.6813   0.6604
 RTF  C25  C  CR16   0  -0.214  -6.9248   1.9218   0.3374
 RTF  C26  C  CR6    0   0.008  -6.2049   2.8315  -0.4446
 RTF  C27  C  CR16   0  -0.119  -4.9585   2.4179  -0.8734
 RTF  N28  N  N      0  -0.435  -4.4303   1.2292  -0.5771
 RTF  C29  C  CH3    0  -0.719  -7.1582  -0.3135   1.4918
 RTF  C30  C  CH3    0  -0.725  -6.7544   4.1819  -0.7909
 RTF  H1   H  HCR6   0   0.281  -2.3504  -0.5081   1.7588
 RTF  H2   H  HCR6   0   0.262  -2.0193  -2.6002  -2.7865
 RTF  H3   H  HCR6   0   0.266  -4.2016  -1.8574  -1.8716
 RTF  H4   H  HCH3   0   0.265   0.4780  -1.6833   2.7931
 RTF  H5   H  HCH3   0   0.275   1.6334  -0.5545   2.0639
 RTF  H6   H  HCH3   0   0.269  -0.0222  -0.0441   2.3455
 RTF  H7   H  HCH2   0   0.256   2.7413  -2.5731   0.8606
 RTF  H8   H  HCH2   0   0.269   2.8727  -2.6157  -0.9043
 RTF  H9   H  HCR6   0   0.251   4.1587   1.5265   0.2585
 RTF  H10  H  HCR6   0   0.241   8.1461   0.0581   0.7526
 RTF  H11  H  HCR6   0   0.253   7.3087  -2.2519   0.5165
 RTF  H12  H  HCR6   0   0.279   4.9374  -2.6968   0.1388
 RTF  H14  H  HCR6   0   0.258  -7.9108   2.1900   0.7012
 RTF  H15  H  HCR6   0   0.254  -4.3469   3.0703  -1.4884
 RTF  H16  H  HCH3   0   0.250  -6.6150  -0.5660   2.4037
 RTF  H17  H  HCH3   0   0.247  -8.1298   0.0827   1.7815
 RTF  H18  H  HCH3   0   0.250  -7.3265  -1.2459   0.9509
 RTF  H19  H  HCH3   0   0.247  -6.8695   4.8032   0.0988
 RTF  H20  H  HCH3   0   0.245  -6.0968   4.7099  -1.4805
 RTF  H21  H  HCH3   0   0.246  -7.7367   4.1047  -1.2588

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
 RTF  O22  C20  deloc     1.246  0.020  1.246
 RTF  O21  C20  deloc     1.245  0.020  1.245
 RTF  C20  C16  single    1.526  0.020  1.526
 RTF  C17  C16  aromatic  1.395  0.020  1.395
 RTF  C17  C18  aromatic  1.384  0.020  1.384
 RTF  C16  C15  aromatic  1.387  0.020  1.387
 RTF  C18  C19  aromatic  1.392  0.020  1.392
 RTF  C15  C14  aromatic  1.393  0.020  1.393
 RTF  C19  C14  aromatic  1.391  0.020  1.391
 RTF  C14  O12  single    1.356  0.020  1.356
 RTF  O12  C11  single    1.415  0.020  1.415
 RTF  C11  C8   single    1.489  0.020  1.489
 RTF  C8   N9   aromatic  1.304  0.020  1.304
 RTF  C8   N7   aromatic  1.364  0.020  1.364
 RTF  N9   C5   aromatic  1.372  0.020  1.372
 RTF  C10  N7   single    1.446  0.020  1.446
 RTF  N7   C6   aromatic  1.368  0.020  1.368
 RTF  C5   C6   aromatic  1.403  0.020  1.403
 RTF  C5   C3   aromatic  1.395  0.020  1.395
 RTF  C6   C2   aromatic  1.391  0.020  1.391
 RTF  C3   C4   aromatic  1.381  0.020  1.381
 RTF  C2   C1   aromatic  1.380  0.020  1.380
 RTF  C4   C1   aromatic  1.402  0.020  1.402
 RTF  C1   O13  single    1.377  0.020  1.377
 RTF  O13  C23  single    1.355  0.020  1.355
 RTF  N28  C23  aromatic  1.306  0.020  1.306
 RTF  N28  C27  aromatic  1.334  0.020  1.334
 RTF  C23  C24  aromatic  1.403  0.020  1.403
 RTF  C27  C26  aromatic  1.382  0.020  1.382
 RTF  C24  C29  single    1.497  0.020  1.497
 RTF  C24  C25  aromatic  1.381  0.020  1.381
 RTF  C26  C25  aromatic  1.399  0.020  1.399
 RTF  C26  C30  single    1.498  0.020  1.498
 RTF  C2   H1   single    0.930  0.020  1.080
 RTF  C3   H2   single    0.930  0.020  1.080
 RTF  C4   H3   single    0.930  0.020  1.080
 RTF  C10  H4   single    0.970  0.020  1.090
 RTF  C10  H5   single    0.970  0.020  1.090
 RTF  C10  H6   single    0.970  0.020  1.090
 RTF  C11  H7   single    0.970  0.020  1.090
 RTF  C11  H8   single    0.970  0.020  1.090
 RTF  C15  H9   single    0.930  0.020  1.080
 RTF  C17  H10  single    0.930  0.020  1.080
 RTF  C18  H11  single    0.930  0.020  1.080
 RTF  C19  H12  single    0.930  0.020  1.080
 RTF  C25  H14  single    0.930  0.020  1.080
 RTF  C27  H15  single    0.930  0.020  1.080
 RTF  C29  H16  single    0.970  0.020  1.090
 RTF  C29  H17  single    0.970  0.020  1.090
 RTF  C29  H18  single    0.970  0.020  1.090
 RTF  C30  H19  single    0.970  0.020  1.090
 RTF  C30  H20  single    0.970  0.020  1.090
 RTF  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
 RTF  O13  C1   C4   118.71  3.000
 RTF  O13  C1   C2   118.65  3.000
 RTF  C4   C1   C2   122.58  3.000
 RTF  H1   C2   C6   122.80  3.000
 RTF  H1   C2   C1   121.27  3.000
 RTF  C6   C2   C1   115.93  3.000
 RTF  H2   C3   C5   120.98  3.000
 RTF  H2   C3   C4   120.86  3.000
 RTF  C5   C3   C4   118.15  3.000
 RTF  H3   C4   C3   120.18  3.000
 RTF  H3   C4   C1   119.10  3.000
 RTF  C3   C4   C1   120.72  3.000
 RTF  N9   C5   C6   109.76  3.000
 RTF  C6   C5   C3   119.81  3.000
 RTF  N9   C5   C3   130.42  3.000
 RTF  N7   C6   C5   105.35  3.000
 RTF  C5   C6   C2   122.80  3.000
 RTF  N7   C6   C2   131.84  3.000
 RTF  C10  N7   C8   127.92  3.000
 RTF  C10  N7   C6   125.51  3.000
 RTF  C8   N7   C6   106.42  3.000
 RTF  C11  C8   N9   123.73  3.000
 RTF  N9   C8   N7   113.33  3.000
 RTF  C11  C8   N7   122.94  3.000
 RTF  C8   N9   C5   105.13  3.000
 RTF  H6   C10  H5   107.77  3.000
 RTF  H6   C10  H4   108.91  3.000
 RTF  H5   C10  H4   109.19  3.000
 RTF  H6   C10  N7   109.49  3.000
 RTF  H5   C10  N7   110.36  3.000
 RTF  H4   C10  N7   111.06  3.000
 RTF  H8   C11  H7   107.89  3.000
 RTF  H8   C11  O12  111.68  3.000
 RTF  H7   C11  O12  110.88  3.000
 RTF  H8   C11  C8   107.89  3.000
 RTF  H7   C11  C8   110.90  3.000
 RTF  O12  C11  C8   107.59  3.000
 RTF  C14  O12  C11  118.30  3.000
 RTF  C23  O13  C1   118.86  3.000
 RTF  C19  C14  C15  120.00  3.000
 RTF  C19  C14  O12  124.12  3.000
 RTF  C15  C14  O12  115.88  3.000
 RTF  H9   C15  C16  119.83  3.000
 RTF  H9   C15  C14  119.26  3.000
 RTF  C16  C15  C14  120.91  3.000
 RTF  C20  C16  C17  120.84  3.000
 RTF  C17  C16  C15  119.02  3.000
 RTF  C20  C16  C15  120.13  3.000
 RTF  H10  C17  C18  120.15  3.000
 RTF  H10  C17  C16  119.84  3.000
 RTF  C18  C17  C16  120.02  3.000
 RTF  H11  C18  C19  118.86  3.000
 RTF  H11  C18  C17  120.02  3.000
 RTF  C19  C18  C17  121.12  3.000
 RTF  H12  C19  C18  119.19  3.000
 RTF  H12  C19  C14  121.88  3.000
 RTF  C18  C19  C14  118.93  3.000
 RTF  O22  C20  O21  126.88  3.000
 RTF  O21  C20  C16  116.44  3.000
 RTF  O22  C20  C16  116.68  3.000
 RTF  N28  C23  C24  124.52  3.000
 RTF  C24  C23  O13  116.17  3.000
 RTF  N28  C23  O13  119.31  3.000
 RTF  C29  C24  C25  122.75  3.000
 RTF  C25  C24  C23  115.61  3.000
 RTF  C29  C24  C23  121.65  3.000
 RTF  H14  C25  C26  119.63  3.000
 RTF  H14  C25  C24  118.82  3.000
 RTF  C26  C25  C24  121.55  3.000
 RTF  C30  C26  C27  121.93  3.000
 RTF  C30  C26  C25  121.77  3.000
 RTF  C27  C26  C25  116.30  3.000
 RTF  H15  C27  N28  116.00  3.000
 RTF  H15  C27  C26  120.29  3.000
 RTF  N28  C27  C26  123.71  3.000
 RTF  C27  N28  C23  118.32  3.000
 RTF  H18  C29  H17  107.78  3.000
 RTF  H18  C29  H16  107.06  3.000
 RTF  H17  C29  H16  107.83  3.000
 RTF  H18  C29  C24  111.70  3.000
 RTF  H17  C29  C24  110.60  3.000
 RTF  H16  C29  C24  111.68  3.000
 RTF  H21  C30  H20  107.84  3.000
 RTF  H21  C30  H19  107.16  3.000
 RTF  H20  C30  H19  107.69  3.000
 RTF  H21  C30  C26  111.44  3.000
 RTF  H20  C30  C26  111.21  3.000
 RTF  H19  C30  C26  111.31  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
 RTF  CONST_01  N7   C6   C2   C1    180.00   0.0  0
 RTF  CONST_02  C5   C6   C2   C1      0.00   0.0  0
 RTF  CONST_03  C5   C3   C4   C1      0.00   0.0  0
 RTF  CONST_04  C8   N7   C6   C2    180.00   0.0  0
 RTF  CONST_05  N9   C5   C6   C2    180.00   0.0  0
 RTF  CONST_06  C3   C5   C6   C2      0.00   0.0  0
 RTF  CONST_07  C3   C4   C1   C2      0.00   0.0  0
 RTF  CONST_08  C8   N9   C5   C3    180.00   0.0  0
 RTF  CONST_09  N7   C6   C5   C3    180.00   0.0  0
 RTF  CONST_10  N9   C5   C3   C4    180.00   0.0  0
 RTF  CONST_11  C6   C5   C3   C4      0.00   0.0  0
 RTF  CONST_12  C6   C2   C1   C4      0.00   0.0  0
 RTF  CONST_13  N7   C8   N9   C5      0.00   0.0  0
 RTF  CONST_14  C8   N7   C6   C5      0.00   0.0  0
 RTF  CONST_15  N9   C8   N7   C6      0.00   0.0  0
 RTF  CONST_16  C8   N9   C5   C6      0.00   0.0  0
 RTF  CONST_17  N9   C5   C6   N7      0.00   0.0  0
 RTF  CONST_18  C17  C16  C15  C14     0.00   0.0  0
 RTF  CONST_19  C17  C18  C19  C14     0.00   0.0  0
 RTF  CONST_20  C18  C17  C16  C15     0.00   0.0  0
 RTF  CONST_21  C18  C19  C14  C15     0.00   0.0  0
 RTF  CONST_22  C19  C18  C17  C16     0.00   0.0  0
 RTF  CONST_23  C19  C14  C15  C16     0.00   0.0  0
 RTF  CONST_24  C26  C27  N28  C23     0.00   0.0  0
 RTF  CONST_25  C26  C25  C24  C23     0.00   0.0  0
 RTF  CONST_26  C27  N28  C23  C24     0.00   0.0  0
 RTF  CONST_27  C27  C26  C25  C24     0.00   0.0  0
 RTF  CONST_28  N28  C23  C24  C25     0.00   0.0  0
 RTF  CONST_29  N28  C27  C26  C25     0.00   0.0  0
 RTF  CONST_30  C10  N7   C6   C2      0.00   0.0  0
 RTF  CONST_31  O13  C1   C4   C3    180.00   0.0  0
 RTF  CONST_32  C11  C8   N9   C5    180.00   0.0  0
 RTF  CONST_33  C10  N7   C6   C5    180.00   0.0  0
 RTF  CONST_34  C11  C8   N7   C6    180.00   0.0  0
 RTF  CONST_35  O13  C1   C2   C6    180.00   0.0  0
 RTF  CONST_36  C10  N7   C8   N9    180.00   0.0  0
 RTF  CONST_37  C16  C15  C14  O12   180.00   0.0  0
 RTF  CONST_38  C18  C19  C14  O12   180.00   0.0  0
 RTF  CONST_39  C27  N28  C23  O13   180.00   0.0  0
 RTF  CONST_40  C25  C24  C23  O13   180.00   0.0  0
 RTF  CONST_41  C20  C16  C15  C14   180.00   0.0  0
 RTF  CONST_42  C20  C16  C17  C18   180.00   0.0  0
 RTF  CONST_43  C30  C26  C25  C24   180.00   0.0  0
 RTF  CONST_44  C29  C24  C25  C26   180.00   0.0  0
 RTF  CONST_45  C29  C24  C23  N28   180.00   0.0  0
 RTF  CONST_46  C30  C26  C27  N28   180.00   0.0  0
 RTF  CONST_47  H2   C3   C4   C1    180.00   0.0  0
 RTF  CONST_48  H3   C4   C1   C2    180.00   0.0  0
 RTF  CONST_49  H1   C2   C1   C4    180.00   0.0  0
 RTF  CONST_50  H11  C18  C19  C14   180.00   0.0  0
 RTF  CONST_51  H10  C17  C16  C15   180.00   0.0  0
 RTF  CONST_52  H12  C19  C14  C15   180.00   0.0  0
 RTF  CONST_53  H9   C15  C16  C17   180.00   0.0  0
 RTF  CONST_54  H15  C27  N28  C23   180.00   0.0  0
 RTF  CONST_55  H14  C25  C24  C23   180.00   0.0  0
 RTF  Var_01    N28  C23  O13  C1     -1.95  30.0  2
 RTF  Var_02    O12  C11  C8   N7    -66.78  30.0  1
 RTF  Var_03    C15  C14  O12  C11  -173.95  30.0  2
 RTF  Var_04    O22  C20  C16  C15     1.02  30.0  2
 RTF  Var_05    H4   C10  N7   C6     83.04  30.0  2
 RTF  Var_06    H16  C29  C24  C23    60.19  30.0  2
 RTF  Var_07    H19  C30  C26  C25    65.29  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
 RTF  plan-1  O12  0.020
 RTF  plan-1  C14  0.020
 RTF  plan-1  C15  0.020
 RTF  plan-1  C16  0.020
 RTF  plan-1  C17  0.020
 RTF  plan-1  C18  0.020
 RTF  plan-1  C19  0.020
 RTF  plan-1  C20  0.020
 RTF  plan-1  H9   0.020
 RTF  plan-1  H10  0.020
 RTF  plan-1  H11  0.020
 RTF  plan-1  H12  0.020
 RTF  plan-2  O13  0.020
 RTF  plan-2  C23  0.020
 RTF  plan-2  C24  0.020
 RTF  plan-2  C25  0.020
 RTF  plan-2  C26  0.020
 RTF  plan-2  C27  0.020
 RTF  plan-2  N28  0.020
 RTF  plan-2  C29  0.020
 RTF  plan-2  C30  0.020
 RTF  plan-2  H14  0.020
 RTF  plan-2  H15  0.020
 RTF  plan-3  C1   0.020
 RTF  plan-3  C2   0.020
 RTF  plan-3  C3   0.020
 RTF  plan-3  C4   0.020
 RTF  plan-3  C5   0.020
 RTF  plan-3  C6   0.020
 RTF  plan-3  N7   0.020
 RTF  plan-3  C8   0.020
 RTF  plan-3  N9   0.020
 RTF  plan-3  C10  0.020
 RTF  plan-3  C11  0.020
 RTF  plan-3  O13  0.020
 RTF  plan-3  H1   0.020
 RTF  plan-3  H2   0.020
 RTF  plan-3  H3   0.020
 RTF  plan-4  C16  0.020
 RTF  plan-4  C20  0.020
 RTF  plan-4  O21  0.020
 RTF  plan-4  O22  0.020

