# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 12:04:01 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-(6-imidazolidin-2-yl-1H,3'H-2,5'-bibenzimidazol-2'-yl)phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)c2[nH]c3cc(ccc3n2)c4[nH]c5cc(ccc5n4)C6NCCN6
#
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
 IBB  IBB  4-(6-imidazolidin-2-yl-1H,3'H-2,5'-bibenzimidazol-2'-yl)phenol  ligand  50  30  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IBB
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
 IBB  C1    C  CH1   0   0.019  -0.3921  -0.2556  -7.2790
 IBB  C2    C  CH2   0  -0.349  -0.4612   1.2914  -8.9774
 IBB  C3    C  CH2   0  -0.299   1.0180   1.0457  -8.6704
 IBB  C4    C  CR6   0   0.059  -0.5768  -0.4239  -5.7899
 IBB  C5    C  CR16  0  -0.297  -1.7531  -1.0397  -5.3234
 IBB  C6    C  CR16  0  -0.334  -2.0269  -1.1776  -3.9764
 IBB  C7    C  CR56  0   0.148  -1.0941  -0.6778  -3.0665
 IBB  C8    C  CR56  0   0.361   0.0768  -0.0677  -3.5439
 IBB  C9    C  CR16  0  -0.373   0.3604   0.0683  -4.8972
 IBB  C10   C  CR5   0   0.486   0.0125  -0.0826  -1.3407
 IBB  C11   C  CR56  0   0.379  -0.0529  -0.0073   2.3599
 IBB  C12   C  CR56  0   0.159   1.1695   0.6088   2.6833
 IBB  C13   C  CR16  0  -0.326   2.0298   1.0038   1.6599
 IBB  C14   C  CR16  0  -0.312   1.6425   0.7698   0.3559
 IBB  C15   C  CR5   0   0.491   0.2065   0.1847   4.5387
 IBB  C16   C  CR6   0  -0.014  -0.0788   0.0776   5.9633
 IBB  C17   C  CR16  0  -0.273   0.8990   0.4521   6.8863
 IBB  C18   C  CR16  0  -0.367   0.6694   0.3639   8.2456
 IBB  C19   C  CR6   0   0.358  -0.5570  -0.1043   8.7178
 IBB  C20   C  CR16  0  -0.321  -1.5438  -0.4790   7.8066
 IBB  C21   C  CR16  0  -0.288  -1.3025  -0.3870   6.4493
 IBB  C22   C  CR6   0  -0.009   0.4143   0.1530   0.0436
 IBB  C23   C  CR16  0  -0.367  -0.4531  -0.2456   1.0583
 IBB  N1    N  NH1   0  -0.585  -1.1496   0.8929  -7.7562
 IBB  N2    N  NH1   0  -0.620   1.0026  -0.0393  -7.6869
 IBB  N3    N  NR15  0  -0.743   0.7587   0.2972  -2.4153
 IBB  N4    N  N     0  -0.489  -1.1017  -0.6726  -1.6967
 IBB  N5    N  N     0  -0.486   1.2984   0.7132   4.0397
 IBB  N6    N  NR15  0  -0.742  -0.6397  -0.2610   3.5694
 IBB  O1    O  OH1   0  -0.620  -0.8381  -0.2134  10.0251
 IBB  H1    H  HCH1  0   0.225  -0.7887  -1.1516  -7.7756
 IBB  H21A  H  HCH2  0   0.228  -0.7946   0.6596  -9.8056
 IBB  H22   H  HCH2  0   0.247  -0.6912   2.3254  -9.2326
 IBB  H31   H  HCH2  0   0.228   1.5959   0.7757  -9.5555
 IBB  H32   H  HCH2  0   0.211   1.4714   1.9471  -8.2464
 IBB  H5    H  HCR6  0   0.243  -2.4625  -1.4210  -6.0486
 IBB  H6    H  HCR6  0   0.251  -2.9350  -1.6581  -3.6357
 IBB  H9    H  HCR6  0   0.257   1.2740   0.5247  -5.2546
 IBB  H13   H  HCR6  0   0.261   2.9758   1.4803   1.8805
 IBB  H14   H  HCR6  0   0.241   2.3177   1.0742  -0.4330
 IBB  H17   H  HCR6  0   0.264   1.8541   0.8164   6.5329
 IBB  H18   H  HCR6  0   0.279   1.4474   0.6575   8.9410
 IBB  H20   H  HCR6  0   0.274  -2.4987  -0.8405   8.1653
 IBB  H21   H  HCR6  0   0.249  -2.0975  -0.6801   5.7757
 IBB  H23   H  HCR6  0   0.268  -1.3966  -0.7193   0.8233
 IBB  HN1   H  HNH1  0   0.347  -1.0622   1.6410  -7.0760
 IBB  HN2   H  HNH1  0   0.354   1.3806  -0.8878  -8.0833
 IBB  HN3   H  HNR5  0   0.422   1.6430   0.7788  -2.3986
 IBB  HN6   H  HNR5  0   0.425  -1.5221  -0.7276   3.7058
 IBB  HO1   H  HOH1  0   0.479  -0.0896   0.0756  10.5595

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
 IBB  C1   C4    single    1.510  0.020  1.510
 IBB  C1   N1    single    1.456  0.020  1.456
 IBB  C1   N2    single    1.469  0.020  1.469
 IBB  C1   H1    single    0.970  0.020  1.090
 IBB  C2   C3    single    1.531  0.020  1.531
 IBB  C2   N1    single    1.457  0.020  1.457
 IBB  C2   H21A  single    0.970  0.020  1.090
 IBB  C2   H22   single    0.970  0.020  1.090
 IBB  C3   N2    single    1.465  0.020  1.465
 IBB  C3   H31   single    0.970  0.020  1.090
 IBB  C3   H32   single    0.970  0.020  1.090
 IBB  C4   C5    aromatic  1.407  0.020  1.407
 IBB  C4   C9    aromatic  1.385  0.020  1.385
 IBB  C5   C6    aromatic  1.381  0.020  1.381
 IBB  C5   H5    single    0.930  0.020  1.080
 IBB  C6   C7    aromatic  1.396  0.020  1.396
 IBB  C6   H6    single    0.930  0.020  1.080
 IBB  C7   C8    aromatic  1.404  0.020  1.404
 IBB  C7   N4    aromatic  1.370  0.020  1.370
 IBB  C8   C9    aromatic  1.389  0.020  1.389
 IBB  C8   N3    aromatic  1.368  0.020  1.368
 IBB  C9   H9    single    0.930  0.020  1.080
 IBB  C10  C22   single    1.461  0.020  1.461
 IBB  C10  N3    aromatic  1.362  0.020  1.362
 IBB  C10  N4    aromatic  1.310  0.020  1.310
 IBB  C11  C12   aromatic  1.407  0.020  1.407
 IBB  C11  C23   aromatic  1.382  0.020  1.382
 IBB  C11  N6    aromatic  1.368  0.020  1.368
 IBB  C12  C13   aromatic  1.394  0.020  1.394
 IBB  C12  N5    aromatic  1.366  0.020  1.366
 IBB  C13  C14   aromatic  1.380  0.020  1.380
 IBB  C13  H13   single    0.930  0.020  1.080
 IBB  C14  C22   aromatic  1.409  0.020  1.409
 IBB  C14  H14   single    0.930  0.020  1.080
 IBB  C15  C16   single    1.457  0.020  1.457
 IBB  C15  N5    aromatic  1.312  0.020  1.312
 IBB  C15  N6    aromatic  1.362  0.020  1.362
 IBB  C16  C17   aromatic  1.396  0.020  1.396
 IBB  C16  C21   aromatic  1.396  0.020  1.396
 IBB  C17  C18   aromatic  1.381  0.020  1.381
 IBB  C17  H17   single    0.930  0.020  1.080
 IBB  C18  C19   aromatic  1.395  0.020  1.395
 IBB  C18  H18   single    0.930  0.020  1.080
 IBB  C19  C20   aromatic  1.394  0.020  1.394
 IBB  C19  O1    single    1.342  0.020  1.342
 IBB  C20  C21   aromatic  1.382  0.020  1.382
 IBB  C20  H20   single    0.930  0.020  1.080
 IBB  C21  H21   single    0.930  0.020  1.080
 IBB  C22  C23   aromatic  1.393  0.020  1.393
 IBB  C23  H23   single    0.930  0.020  1.080
 IBB  N1   HN1   single    0.890  0.020  1.040
 IBB  N2   HN2   single    0.890  0.020  1.040
 IBB  N3   HN3   single    0.860  0.020  1.020
 IBB  N6   HN6   single    0.860  0.020  1.020
 IBB  O1   HO1   single    0.850  0.020  0.980

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
 IBB  H1    C1   N2    109.71  3.000
 IBB  H1    C1   N1    107.91  3.000
 IBB  N2    C1   N1    106.66  3.000
 IBB  H1    C1   C4    108.10  3.000
 IBB  N2    C1   C4    113.97  3.000
 IBB  N1    C1   C4    110.33  3.000
 IBB  H22   C2   H21A  107.85  3.000
 IBB  H22   C2   N1    110.86  3.000
 IBB  H21A  C2   N1    109.43  3.000
 IBB  H22   C2   C3    113.78  3.000
 IBB  H21A  C2   C3    110.72  3.000
 IBB  N1    C2   C3    104.15  3.000
 IBB  H32   C3   H31   107.38  3.000
 IBB  H32   C3   N2    110.75  3.000
 IBB  H31   C3   N2    111.54  3.000
 IBB  H32   C3   C2    110.23  3.000
 IBB  H31   C3   C2    112.89  3.000
 IBB  N2    C3   C2    104.09  3.000
 IBB  C9    C4   C5    120.50  3.000
 IBB  C9    C4   C1    120.89  3.000
 IBB  C5    C4   C1    118.55  3.000
 IBB  H5    C5   C6    119.19  3.000
 IBB  H5    C5   C4    118.63  3.000
 IBB  C6    C5   C4    122.18  3.000
 IBB  H6    C6   C7    120.97  3.000
 IBB  H6    C6   C5    121.16  3.000
 IBB  C7    C6   C5    117.87  3.000
 IBB  N4    C7   C8    110.06  3.000
 IBB  N4    C7   C6    130.51  3.000
 IBB  C8    C7   C6    119.43  3.000
 IBB  N3    C8   C9    132.50  3.000
 IBB  N3    C8   C7    104.54  3.000
 IBB  C9    C8   C7    122.96  3.000
 IBB  H9    C9   C8    122.38  3.000
 IBB  H9    C9   C4    120.56  3.000
 IBB  C8    C9   C4    117.06  3.000
 IBB  N4    C10  N3    112.15  3.000
 IBB  N4    C10  C22   124.34  3.000
 IBB  N3    C10  C22   123.50  3.000
 IBB  N6    C11  C23   132.55  3.000
 IBB  N6    C11  C12   104.52  3.000
 IBB  C23   C11  C12   122.93  3.000
 IBB  N5    C12  C13   130.45  3.000
 IBB  N5    C12  C11   110.11  3.000
 IBB  C13   C12  C11   119.45  3.000
 IBB  H13   C13  C14   120.84  3.000
 IBB  H13   C13  C12   120.98  3.000
 IBB  C14   C13  C12   118.18  3.000
 IBB  H14   C14  C22   120.35  3.000
 IBB  H14   C14  C13   117.77  3.000
 IBB  C22   C14  C13   121.87  3.000
 IBB  N6    C15  N5    112.23  3.000
 IBB  N6    C15  C16   123.39  3.000
 IBB  N5    C15  C16   124.37  3.000
 IBB  C21   C16  C17   118.23  3.000
 IBB  C21   C16  C15   122.44  3.000
 IBB  C17   C16  C15   119.33  3.000
 IBB  H17   C17  C18   119.33  3.000
 IBB  H17   C17  C16   119.53  3.000
 IBB  C18   C17  C16   121.14  3.000
 IBB  H18   C18  C19   120.31  3.000
 IBB  H18   C18  C17   119.65  3.000
 IBB  C19   C18  C17   120.04  3.000
 IBB  O1    C19  C20   117.82  3.000
 IBB  O1    C19  C18   122.77  3.000
 IBB  C20   C19  C18   119.41  3.000
 IBB  H20   C20  C21   120.13  3.000
 IBB  H20   C20  C19   119.84  3.000
 IBB  C21   C20  C19   120.03  3.000
 IBB  H21   C21  C20   117.72  3.000
 IBB  H21   C21  C16   121.14  3.000
 IBB  C20   C21  C16   121.14  3.000
 IBB  C23   C22  C14   120.43  3.000
 IBB  C23   C22  C10   118.22  3.000
 IBB  C14   C22  C10   121.35  3.000
 IBB  H23   C23  C22   120.68  3.000
 IBB  H23   C23  C11   122.18  3.000
 IBB  C22   C23  C11   117.14  3.000
 IBB  HN1   N1   C2    108.63  3.000
 IBB  HN1   N1   C1    108.48  3.000
 IBB  C2    N1   C1    104.15  3.000
 IBB  HN2   N2   C3    110.78  3.000
 IBB  HN2   N2   C1    109.91  3.000
 IBB  C3    N2   C1    107.79  3.000
 IBB  HN3   N3   C10   126.96  3.000
 IBB  HN3   N3   C8    125.37  3.000
 IBB  C10   N3   C8    107.66  3.000
 IBB  C10   N4   C7    105.59  3.000
 IBB  C15   N5   C12   105.56  3.000
 IBB  HN6   N6   C15   126.83  3.000
 IBB  HN6   N6   C11   125.54  3.000
 IBB  C15   N6   C11   107.58  3.000
 IBB  HO1   O1   C19   110.68  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
 IBB  CONST_01  C7   C6   C5   C4     0.00   0.0  0
 IBB  CONST_02  C7   C8   C9   C4     0.00   0.0  0
 IBB  CONST_03  N3   C8   C9   C4   180.00   0.0  0
 IBB  CONST_04  C8   C9   C4   C5     0.00   0.0  0
 IBB  CONST_05  C8   C7   C6   C5     0.00   0.0  0
 IBB  CONST_06  N4   C7   C6   C5   180.00   0.0  0
 IBB  CONST_07  C9   C4   C5   C6     0.00   0.0  0
 IBB  CONST_08  C9   C8   C7   C6     0.00   0.0  0
 IBB  CONST_09  N3   C8   C7   C6   180.00   0.0  0
 IBB  CONST_10  C10  N4   C7   C6   180.00   0.0  0
 IBB  CONST_11  C10  N3   C8   C7     0.00   0.0  0
 IBB  CONST_12  C22  C10  N4   C7   180.00   0.0  0
 IBB  CONST_13  N3   C10  N4   C7     0.00   0.0  0
 IBB  CONST_14  C10  N4   C7   C8     0.00   0.0  0
 IBB  CONST_15  C22  C10  N3   C8   180.00   0.0  0
 IBB  CONST_16  N4   C10  N3   C8     0.00   0.0  0
 IBB  CONST_17  N4   C7   C8   C9   180.00   0.0  0
 IBB  CONST_18  C10  N3   C8   C9   180.00   0.0  0
 IBB  CONST_19  C13  C14  C22  C10  180.00   0.0  0
 IBB  CONST_20  C11  C23  C22  C10  180.00   0.0  0
 IBB  CONST_21  C14  C13  C12  C11    0.00   0.0  0
 IBB  CONST_22  C15  N5   C12  C11    0.00   0.0  0
 IBB  CONST_23  C14  C22  C23  C11    0.00   0.0  0
 IBB  CONST_24  C16  C15  N6   C11  180.00   0.0  0
 IBB  CONST_25  N5   C15  N6   C11    0.00   0.0  0
 IBB  CONST_26  C22  C23  C11  C12    0.00   0.0  0
 IBB  CONST_27  C15  N6   C11  C12    0.00   0.0  0
 IBB  CONST_28  C22  C14  C13  C12    0.00   0.0  0
 IBB  CONST_29  C16  C15  N5   C12  180.00   0.0  0
 IBB  CONST_30  N6   C15  N5   C12    0.00   0.0  0
 IBB  CONST_31  C23  C11  C12  C13    0.00   0.0  0
 IBB  CONST_32  N6   C11  C12  C13  180.00   0.0  0
 IBB  CONST_33  C15  N5   C12  C13  180.00   0.0  0
 IBB  CONST_34  C23  C22  C14  C13    0.00   0.0  0
 IBB  CONST_35  N5   C12  C13  C14  180.00   0.0  0
 IBB  CONST_36  N3   C10  C22  C14    0.00   0.0  0
 IBB  CONST_37  N4   C10  C22  C14  180.00   0.0  0
 IBB  CONST_38  C18  C17  C16  C15  180.00   0.0  0
 IBB  CONST_39  C20  C21  C16  C15  180.00   0.0  0
 IBB  CONST_40  C23  C11  N6   C15  180.00   0.0  0
 IBB  CONST_41  C19  C18  C17  C16    0.00   0.0  0
 IBB  CONST_42  C19  C20  C21  C16    0.00   0.0  0
 IBB  CONST_43  N5   C15  C16  C17    0.00   0.0  0
 IBB  CONST_44  N6   C15  C16  C17  180.00   0.0  0
 IBB  CONST_45  C20  C21  C16  C17    0.00   0.0  0
 IBB  CONST_46  C20  C19  C18  C17    0.00   0.0  0
 IBB  CONST_47  C21  C16  C17  C18    0.00   0.0  0
 IBB  CONST_48  C21  C20  C19  C18    0.00   0.0  0
 IBB  CONST_49  N5   C15  C16  C21  180.00   0.0  0
 IBB  CONST_50  N6   C15  C16  C21    0.00   0.0  0
 IBB  CONST_51  N6   C11  C23  C22  180.00   0.0  0
 IBB  CONST_52  N5   C12  C11  C23  180.00   0.0  0
 IBB  CONST_53  N3   C10  C22  C23  180.00   0.0  0
 IBB  CONST_54  N4   C10  C22  C23    0.00   0.0  0
 IBB  CONST_55  N4   C7   C8   N3     0.00   0.0  0
 IBB  CONST_56  N6   C11  C12  N5     0.00   0.0  0
 IBB  CONST_57  C6   C5   C4   C1   180.00   0.0  0
 IBB  CONST_58  C8   C9   C4   C1   180.00   0.0  0
 IBB  CONST_59  O1   C19  C18  C17  180.00   0.0  0
 IBB  CONST_60  O1   C19  C20  C21  180.00   0.0  0
 IBB  CONST_61  H5   C5   C4   C1     0.00   0.0  0
 IBB  CONST_62  H9   C9   C4   C1     0.00   0.0  0
 IBB  CONST_63  H6   C6   C5   C4   180.00   0.0  0
 IBB  CONST_64  HN3  N3   C8   C7   180.00   0.0  0
 IBB  CONST_65  H14  C14  C22  C10    0.00   0.0  0
 IBB  CONST_66  H23  C23  C22  C10    0.00   0.0  0
 IBB  CONST_67  H13  C13  C12  C11  180.00   0.0  0
 IBB  CONST_68  HN6  N6   C11  C12  180.00   0.0  0
 IBB  CONST_69  H17  C17  C16  C15    0.00   0.0  0
 IBB  CONST_70  H21  C21  C16  C15    0.00   0.0  0
 IBB  CONST_71  H18  C18  C17  C16  180.00   0.0  0
 IBB  CONST_72  H20  C20  C21  C16  180.00   0.0  0
 IBB  Var_01    C3   C2   N1   C1   -36.60  30.0  1
 IBB  Var_02    C2   C3   N2   C1    -8.85  30.0  1
 IBB  Var_03    N2   C3   C2   N1    28.08  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 IBB  chir_01  C1  C4  N1  N2  negativ

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
 IBB  plan-1  C15  0.020
 IBB  plan-1  C16  0.020
 IBB  plan-1  C17  0.020
 IBB  plan-1  C18  0.020
 IBB  plan-1  C19  0.020
 IBB  plan-1  C20  0.020
 IBB  plan-1  C21  0.020
 IBB  plan-1  O1   0.020
 IBB  plan-1  H17  0.020
 IBB  plan-1  H18  0.020
 IBB  plan-1  H20  0.020
 IBB  plan-1  H21  0.020
 IBB  plan-2  C1   0.020
 IBB  plan-2  C4   0.020
 IBB  plan-2  C5   0.020
 IBB  plan-2  C6   0.020
 IBB  plan-2  C7   0.020
 IBB  plan-2  C8   0.020
 IBB  plan-2  C9   0.020
 IBB  plan-2  C10  0.020
 IBB  plan-2  C22  0.020
 IBB  plan-2  N3   0.020
 IBB  plan-2  N4   0.020
 IBB  plan-2  H5   0.020
 IBB  plan-2  H6   0.020
 IBB  plan-2  H9   0.020
 IBB  plan-2  HN3  0.020
 IBB  plan-3  C10  0.020
 IBB  plan-3  C11  0.020
 IBB  plan-3  C12  0.020
 IBB  plan-3  C13  0.020
 IBB  plan-3  C14  0.020
 IBB  plan-3  C15  0.020
 IBB  plan-3  C16  0.020
 IBB  plan-3  C22  0.020
 IBB  plan-3  C23  0.020
 IBB  plan-3  N5   0.020
 IBB  plan-3  N6   0.020
 IBB  plan-3  H13  0.020
 IBB  plan-3  H14  0.020
 IBB  plan-3  H23  0.020
 IBB  plan-3  HN6  0.020

