# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:24:45 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 4-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-2-methoxyphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(ccc1O)c2ccc3c([nH]nc3c4[nH]c5ccccc5n4)c2
#
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
 ABO  ABO  4-[3-(1H-benzimidazol-2-yl)-1H-indazol-6-yl]-2-methoxyphenol  ligand  43  27  .  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_ABO
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
 ABO  C18   C  CH3   0  -0.434  -5.4199   3.0821  -1.1427
 ABO  O17   O  O2    0  -0.489  -6.1088   1.9864  -0.5736
 ABO  C12   C  CR6   0   0.322  -5.3955   0.9245  -0.1429
 ABO  C11   C  CR16  0  -0.451  -4.0194   0.8009  -0.2180
 ABO  C13   C  CR6   0   0.274  -6.1657  -0.1144   0.4082
 ABO  O16   O  OH1   0  -0.628  -7.5066  -0.0243   0.4935
 ABO  C14   C  CR16  0  -0.331  -5.5291  -1.2520   0.8717
 ABO  C15   C  CR16  0  -0.326  -4.1473  -1.3704   0.7928
 ABO  C10   C  CR6   0   0.089  -3.3749  -0.3519   0.2475
 ABO  C8    C  CR6   0   0.078  -1.9073  -0.4776   0.1526
 ABO  C9    C  CR16  0  -0.373  -1.3339  -1.7017  -0.1399
 ABO  C7    C  CR16  0  -0.316  -1.0827   0.6577   0.3671
 ABO  C6    C  CR16  0  -0.321   0.2877   0.5925   0.2972
 ABO  C5    C  CR56  0  -0.106   0.8783  -0.6433   0.0043
 ABO  C4    C  CR56  0   0.459   0.0591  -1.7635  -0.2047
 ABO  N3    N  NR15  0  -0.544   0.8982  -2.7953  -0.4695
 ABO  N1    N  N     0  -0.250   2.1723  -2.4334  -0.4422
 ABO  C2    C  CR5   0   0.153   2.1984  -1.1483  -0.1617
 ABO  C19   C  CR5   0   0.444   3.4513  -0.4351  -0.0586
 ABO  N21   N  NR15  0  -0.709   4.6506  -1.0442  -0.2540
 ABO  C22   C  CR56  0   0.337   5.6191  -0.0941  -0.0851
 ABO  C27   C  CR16  0  -0.313   7.0063  -0.1370  -0.1628
 ABO  C26   C  CR16  0  -0.278   7.6783   1.0495   0.0751
 ABO  C25   C  CR16  0  -0.270   6.9916   2.2354   0.3796
 ABO  C24   C  CR16  0  -0.344   5.6110   2.2703   0.4541
 ABO  C23   C  CR56  0   0.152   4.9141   1.0852   0.2168
 ABO  N20   N  N     0  -0.488   3.5641   0.8365   0.2246
 ABO  H181  H  HCH3  0   0.264  -6.1747   3.8169  -1.4102
 ABO  H182  H  HCH3  0   0.232  -4.7214   3.5331  -0.4331
 ABO  H183  H  HCH3  0   0.232  -4.8726   2.7924  -2.0434
 ABO  H11   H  HCR6  0   0.282  -3.4316   1.5911  -0.6665
 ABO  H16   H  HOH1  0   0.473  -7.8084   0.8195   0.1355
 ABO  H14   H  HCR6  0   0.267  -6.1195  -2.0488   1.3066
 ABO  H15   H  HCR6  0   0.254  -3.6752  -2.2616   1.1847
 ABO  H9    H  HCR6  0   0.271  -1.9403  -2.5772  -0.3324
 ABO  H7    H  HCR6  0   0.255  -1.5486   1.6018   0.6184
 ABO  H6    H  HCR6  0   0.258   0.8966   1.4681   0.4744
 ABO  H3    H  HNR5  0   0.424   0.6569  -3.7548  -0.6602
 ABO  H21   H  HNR5  0   0.420   4.7885  -2.0181  -0.4751
 ABO  H27   H  HCR6  0   0.266   7.5377  -1.0498  -0.3979
 ABO  H26   H  HCR6  0   0.256   8.7591   1.0638   0.0257
 ABO  H25   H  HCR6  0   0.253   7.5585   3.1391   0.5613
 ABO  H24   H  HCR6  0   0.254   5.0843   3.1858   0.6914

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
 ABO  C18  O17   single    1.414  0.020  1.414
 ABO  C18  H181  single    0.970  0.020  1.090
 ABO  C18  H182  single    0.970  0.020  1.090
 ABO  C18  H183  single    0.970  0.020  1.090
 ABO  O17  C12   single    1.350  0.020  1.350
 ABO  C12  C11   aromatic  1.384  0.020  1.384
 ABO  C12  C13   aromatic  1.406  0.020  1.406
 ABO  C11  C10   aromatic  1.400  0.020  1.400
 ABO  C11  H11   single    0.930  0.020  1.080
 ABO  C13  O16   single    1.347  0.020  1.347
 ABO  C13  C14   aromatic  1.384  0.020  1.384
 ABO  O16  H16   single    0.850  0.020  0.980
 ABO  C14  C15   aromatic  1.389  0.020  1.389
 ABO  C14  H14   single    0.930  0.020  1.080
 ABO  C15  C10   aromatic  1.390  0.020  1.390
 ABO  C15  H15   single    0.930  0.020  1.080
 ABO  C10  C8    single    1.476  0.020  1.476
 ABO  C8   C9    aromatic  1.383  0.020  1.383
 ABO  C8   C7    aromatic  1.419  0.020  1.419
 ABO  C9   C4    aromatic  1.396  0.020  1.396
 ABO  C9   H9    single    0.930  0.020  1.080
 ABO  C7   C6    aromatic  1.374  0.020  1.374
 ABO  C7   H7    single    0.930  0.020  1.080
 ABO  C6   C5    aromatic  1.401  0.020  1.401
 ABO  C6   H6    single    0.930  0.020  1.080
 ABO  C5   C4    aromatic  1.403  0.020  1.403
 ABO  C5   C2    aromatic  1.423  0.020  1.423
 ABO  C4   N3    aromatic  1.356  0.020  1.356
 ABO  N3   N1    aromatic  1.325  0.020  1.325
 ABO  N3   H3    single    0.860  0.020  1.020
 ABO  N1   C2    aromatic  1.316  0.020  1.316
 ABO  C2   C19   single    1.445  0.020  1.445
 ABO  C19  N21   aromatic  1.359  0.020  1.359
 ABO  C19  N20   aromatic  1.308  0.020  1.308
 ABO  N21  C22   aromatic  1.367  0.020  1.367
 ABO  N21  H21   single    0.860  0.020  1.020
 ABO  C22  C27   aromatic  1.390  0.020  1.390
 ABO  C22  C23   aromatic  1.407  0.020  1.407
 ABO  C27  C26   aromatic  1.384  0.020  1.384
 ABO  C27  H27   single    0.930  0.020  1.080
 ABO  C26  C25   aromatic  1.404  0.020  1.404
 ABO  C26  H26   single    0.930  0.020  1.080
 ABO  C25  C24   aromatic  1.383  0.020  1.383
 ABO  C25  H25   single    0.930  0.020  1.080
 ABO  C24  C23   aromatic  1.395  0.020  1.395
 ABO  C24  H24   single    0.930  0.020  1.080
 ABO  C23  N20   aromatic  1.373  0.020  1.373

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
 ABO  H183  C18  H182  108.92  3.000
 ABO  H183  C18  H181  108.92  3.000
 ABO  H182  C18  H181  108.95  3.000
 ABO  H183  C18  O17   111.73  3.000
 ABO  H182  C18  O17   111.70  3.000
 ABO  H181  C18  O17   106.54  3.000
 ABO  C12   O17  C18   118.73  3.000
 ABO  C13   C12  C11   120.01  3.000
 ABO  C13   C12  O17   114.64  3.000
 ABO  C11   C12  O17   125.35  3.000
 ABO  H11   C11  C10   119.27  3.000
 ABO  H11   C11  C12   119.83  3.000
 ABO  C10   C11  C12   120.88  3.000
 ABO  C14   C13  O16   119.47  3.000
 ABO  C14   C13  C12   119.13  3.000
 ABO  O16   C13  C12   121.40  3.000
 ABO  H16   O16  C13   110.26  3.000
 ABO  H14   C14  C15   120.16  3.000
 ABO  H14   C14  C13   119.26  3.000
 ABO  C15   C14  C13   120.59  3.000
 ABO  H15   C15  C10   120.21  3.000
 ABO  H15   C15  C14   118.93  3.000
 ABO  C10   C15  C14   120.84  3.000
 ABO  C8    C10  C15   121.03  3.000
 ABO  C8    C10  C11   120.42  3.000
 ABO  C15   C10  C11   118.55  3.000
 ABO  C7    C8   C9    119.93  3.000
 ABO  C7    C8   C10   119.99  3.000
 ABO  C9    C8   C10   120.08  3.000
 ABO  H9    C9   C4    121.01  3.000
 ABO  H9    C9   C8    121.42  3.000
 ABO  C4    C9   C8    117.56  3.000
 ABO  H7    C7   C6    118.86  3.000
 ABO  H7    C7   C8    118.86  3.000
 ABO  C6    C7   C8    122.27  3.000
 ABO  H6    C6   C5    120.76  3.000
 ABO  H6    C6   C7    121.00  3.000
 ABO  C5    C6   C7    118.24  3.000
 ABO  C2    C5   C4    103.94  3.000
 ABO  C2    C5   C6    136.77  3.000
 ABO  C4    C5   C6    119.29  3.000
 ABO  N3    C4   C5    105.97  3.000
 ABO  N3    C4   C9    131.32  3.000
 ABO  C5    C4   C9    122.70  3.000
 ABO  H3    N3   N1    119.63  3.000
 ABO  H3    N3   C4    127.83  3.000
 ABO  N1    N3   C4    112.53  3.000
 ABO  C2    N1   N3    106.88  3.000
 ABO  C19   C2   N1    120.96  3.000
 ABO  C19   C2   C5    128.36  3.000
 ABO  N1    C2   C5    110.68  3.000
 ABO  N20   C19  N21   113.01  3.000
 ABO  N20   C19  C2    124.76  3.000
 ABO  N21   C19  C2    122.23  3.000
 ABO  H21   N21  C22   126.97  3.000
 ABO  H21   N21  C19   125.82  3.000
 ABO  C22   N21  C19   107.21  3.000
 ABO  C23   C22  C27   122.55  3.000
 ABO  C23   C22  N21   104.72  3.000
 ABO  C27   C22  N21   132.73  3.000
 ABO  H27   C27  C26   121.47  3.000
 ABO  H27   C27  C22   121.89  3.000
 ABO  C26   C27  C22   116.64  3.000
 ABO  H26   C26  C25   119.17  3.000
 ABO  H26   C26  C27   119.24  3.000
 ABO  C25   C26  C27   121.60  3.000
 ABO  H25   C25  C24   119.52  3.000
 ABO  H25   C25  C26   119.05  3.000
 ABO  C24   C25  C26   121.42  3.000
 ABO  H24   C24  C23   120.84  3.000
 ABO  H24   C24  C25   121.25  3.000
 ABO  C23   C24  C25   117.90  3.000
 ABO  N20   C23  C24   130.10  3.000
 ABO  N20   C23  C22   110.01  3.000
 ABO  C24   C23  C22   119.88  3.000
 ABO  C23   N20  C19   105.06  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
 ABO  CONST_01  C15   C10  C11  C12     0.00   0.0  0
 ABO  CONST_02  C8    C10  C11  C12   180.00   0.0  0
 ABO  CONST_03  C15   C14  C13  C12     0.00   0.0  0
 ABO  CONST_04  C14   C13  C12  C11     0.00   0.0  0
 ABO  CONST_05  C14   C15  C10  C11     0.00   0.0  0
 ABO  CONST_08  C10   C11  C12  C13     0.00   0.0  0
 ABO  CONST_09  C10   C15  C14  C13     0.00   0.0  0
 ABO  CONST_10  C8    C10  C15  C14   180.00   0.0  0
 ABO  CONST_13  C4    C9   C8   C10   180.00   0.0  0
 ABO  CONST_14  C6    C7   C8   C10   180.00   0.0  0
 ABO  CONST_15  C5    C4   C9   C8      0.00   0.0  0
 ABO  CONST_16  N3    C4   C9   C8    180.00   0.0  0
 ABO  CONST_17  C5    C6   C7   C8      0.00   0.0  0
 ABO  CONST_18  C6    C7   C8   C9      0.00   0.0  0
 ABO  CONST_19  C6    C5   C4   C9      0.00   0.0  0
 ABO  CONST_20  C2    C5   C4   C9    180.00   0.0  0
 ABO  CONST_21  N1    N3   C4   C9    180.00   0.0  0
 ABO  CONST_22  C4    C9   C8   C7      0.00   0.0  0
 ABO  CONST_23  C4    C5   C6   C7      0.00   0.0  0
 ABO  CONST_24  C2    C5   C6   C7    180.00   0.0  0
 ABO  CONST_25  N3    C4   C5   C6    180.00   0.0  0
 ABO  CONST_26  N1    C2   C5   C6    180.00   0.0  0
 ABO  CONST_27  C19   C2   C5   C6      0.00   0.0  0
 ABO  CONST_28  N1    N3   C4   C5      0.00   0.0  0
 ABO  CONST_29  N3    N1   C2   C5      0.00   0.0  0
 ABO  CONST_30  N21   C19  C2   C5    180.00   0.0  0
 ABO  CONST_31  N20   C19  C2   C5      0.00   0.0  0
 ABO  CONST_32  N1    C2   C5   C4      0.00   0.0  0
 ABO  CONST_33  C19   C2   C5   C4    180.00   0.0  0
 ABO  CONST_34  C2    N1   N3   C4      0.00   0.0  0
 ABO  CONST_35  C2    C5   C4   N3      0.00   0.0  0
 ABO  CONST_36  C19   C2   N1   N3    180.00   0.0  0
 ABO  CONST_37  N21   C19  C2   N1      0.00   0.0  0
 ABO  CONST_38  N20   C19  C2   N1    180.00   0.0  0
 ABO  CONST_39  C22   N21  C19  C2    180.00   0.0  0
 ABO  CONST_40  C23   N20  C19  C2    180.00   0.0  0
 ABO  CONST_41  C27   C22  N21  C19   180.00   0.0  0
 ABO  CONST_42  C23   C22  N21  C19     0.00   0.0  0
 ABO  CONST_43  C22   C23  N20  C19     0.00   0.0  0
 ABO  CONST_44  C24   C23  N20  C19   180.00   0.0  0
 ABO  CONST_45  C23   N20  C19  N21     0.00   0.0  0
 ABO  CONST_46  C26   C27  C22  N21   180.00   0.0  0
 ABO  CONST_47  C24   C23  C22  N21   180.00   0.0  0
 ABO  CONST_48  N20   C23  C22  N21     0.00   0.0  0
 ABO  CONST_49  N20   C19  N21  C22     0.00   0.0  0
 ABO  CONST_50  C25   C26  C27  C22     0.00   0.0  0
 ABO  CONST_51  C25   C24  C23  C22     0.00   0.0  0
 ABO  CONST_52  C24   C23  C22  C27     0.00   0.0  0
 ABO  CONST_53  N20   C23  C22  C27   180.00   0.0  0
 ABO  CONST_54  C24   C25  C26  C27     0.00   0.0  0
 ABO  CONST_55  C23   C22  C27  C26     0.00   0.0  0
 ABO  CONST_56  C23   C24  C25  C26     0.00   0.0  0
 ABO  CONST_57  N20   C23  C24  C25   180.00   0.0  0
 ABO  CONST_58  C10   C11  C12  O17   180.00   0.0  0
 ABO  CONST_59  C14   C13  C12  O17   180.00   0.0  0
 ABO  CONST_60  O16   C13  C12  C11   180.00   0.0  0
 ABO  CONST_61  C15   C14  C13  O16   180.00   0.0  0
 ABO  CONST_62  H14   C14  C13  C12   180.00   0.0  0
 ABO  CONST_63  H15   C15  C10  C11   180.00   0.0  0
 ABO  CONST_64  H11   C11  C12  C13   180.00   0.0  0
 ABO  CONST_65  H9    C9   C8   C10     0.00   0.0  0
 ABO  CONST_66  H7    C7   C8   C10     0.00   0.0  0
 ABO  CONST_67  H6    C6   C7   C8    180.00   0.0  0
 ABO  CONST_68  H3    N3   C4   C9      0.00   0.0  0
 ABO  CONST_69  H21   N21  C19  C2      0.00   0.0  0
 ABO  CONST_70  H27   C27  C22  N21     0.00   0.0  0
 ABO  CONST_71  H26   C26  C27  C22   180.00   0.0  0
 ABO  CONST_72  H24   C24  C23  C22   180.00   0.0  0
 ABO  CONST_73  H25   C25  C26  C27   180.00   0.0  0
 ABO  Var_01    C11   C12  O17  C18    -0.56  30.0  2
 ABO  Var_02    H181  C18  O17  C12  -179.62  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
 ABO  plan-1  O17  0.020
 ABO  plan-1  C12  0.020
 ABO  plan-1  C11  0.020
 ABO  plan-1  C13  0.020
 ABO  plan-1  O16  0.020
 ABO  plan-1  C14  0.020
 ABO  plan-1  C15  0.020
 ABO  plan-1  C10  0.020
 ABO  plan-1  C8   0.020
 ABO  plan-1  H11  0.020
 ABO  plan-1  H14  0.020
 ABO  plan-1  H15  0.020
 ABO  plan-2  C10  0.020
 ABO  plan-2  C8   0.020
 ABO  plan-2  C9   0.020
 ABO  plan-2  C7   0.020
 ABO  plan-2  C6   0.020
 ABO  plan-2  C5   0.020
 ABO  plan-2  C4   0.020
 ABO  plan-2  N3   0.020
 ABO  plan-2  N1   0.020
 ABO  plan-2  C2   0.020
 ABO  plan-2  C19  0.020
 ABO  plan-2  H9   0.020
 ABO  plan-2  H7   0.020
 ABO  plan-2  H6   0.020
 ABO  plan-2  H3   0.020
 ABO  plan-3  C2   0.020
 ABO  plan-3  C19  0.020
 ABO  plan-3  N21  0.020
 ABO  plan-3  C22  0.020
 ABO  plan-3  C27  0.020
 ABO  plan-3  C26  0.020
 ABO  plan-3  C25  0.020
 ABO  plan-3  C24  0.020
 ABO  plan-3  C23  0.020
 ABO  plan-3  N20  0.020
 ABO  plan-3  H21  0.020
 ABO  plan-3  H27  0.020
 ABO  plan-3  H26  0.020
 ABO  plan-3  H25  0.020
 ABO  plan-3  H24  0.020

