# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 14:19:58 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: ~{N}-[2-methoxy-5-(oxidanylcarbamoyl)phenyl]dibenzofuran-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1NC(=O)c2cccc3c2oc4ccccc34)C(=O)NO
#
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
 5IB  5IB  "~{N}-[2-methoxy-5-(oxidanylcarbamoyl)phenyl]dibenzofuran-4-carboxamide"  ligand  44  28  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5IB
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
 5IB  N    N  NH1   0  -0.384  81.7841  36.4542  71.9563
 5IB  C    C  CH3   0  -0.439  77.8026  30.6828  72.7358
 5IB  C1   C  CR6   0   0.379  79.2628  32.0979  71.5198
 5IB  C10  C  CR16  0  -0.296  78.3077  29.8710  67.1935
 5IB  C11  C  CR16  0  -0.250  77.9159  29.2099  66.0299
 5IB  C12  C  CR16  0  -0.365  78.7838  28.3564  65.3689
 5IB  C13  C  CR56  0   0.077  80.0544  28.1675  65.8993
 5IB  C14  C  CR56  0   0.079  81.2152  27.4022  65.5122
 5IB  C15  C  CR16  0  -0.363  81.5290  26.5477  64.4602
 5IB  C16  C  CR16  0  -0.255  82.7948  25.9849  64.4286
 5IB  C17  C  CR16  0  -0.265  83.7338  26.2664  65.4258
 5IB  C18  C  CR16  0  -0.341  83.4388  27.1166  66.4826
 5IB  C19  C  CR56  0   0.349  82.1719  27.6675  66.4922
 5IB  C2   C  CR16  0  -0.381  79.5689  32.8701  72.6376
 5IB  C20  C  CR56  0   0.354  80.4200  28.8222  67.0785
 5IB  C3   C  CR16  0  -0.269  80.4298  33.9517  72.5270
 5IB  C4   C  CR6   0  -0.079  81.0075  34.2866  71.3081
 5IB  C5   C  C     0   0.496  81.9724  35.4077  71.1306
 5IB  C6   C  CR16  0  -0.300  80.7311  33.4853  70.2014
 5IB  C7   C  CR6   0   0.260  79.8690  32.4122  70.2911
 5IB  C9   C  CR6   0  -0.155  79.5737  29.6953  67.7493
 5IB  N1   N  NH1   0  -0.739  79.5798  31.6409  69.1472
 5IB  O1   O  O     0  -0.464  82.8459  35.3826  70.2793
 5IB  O2   O  OH1   0  -0.535  82.7028  37.4551  72.0103
 5IB  O3   O  O     0  -0.445  80.6497  29.7792  69.8623
 5IB  O4   O  O     0  -0.469  81.6915  28.5239  67.4345
 5IB  H1   H  HNH1  0   0.420  81.0358  36.5216  72.6298
 5IB  H2   H  HCH3  0   0.264  77.1778  29.8244  72.5048
 5IB  H3   H  HCH3  0   0.235  78.5401  30.3927  73.4877
 5IB  H4   H  HCH3  0   0.234  77.1749  31.4797  73.1413
 5IB  H6   H  HCR6  0   0.266  76.9179  29.3681  65.6445
 5IB  H7   H  HCR6  0   0.264  78.4796  27.8497  64.4622
 5IB  H8   H  HCR6  0   0.259  80.8037  26.3283  63.6874
 5IB  H9   H  HCR6  0   0.260  83.0638  25.3166  63.6215
 5IB  H10  H  HCR6  0   0.265  84.7140  25.8112  65.3747
 5IB  H11  H  HCR6  0   0.273  84.1640  27.3355  67.2550
 5IB  H12  H  HCR6  0   0.290  79.1420  32.6445  73.6048
 5IB  H13  H  HCR6  0   0.266  80.6542  34.5116  73.4260
 5IB  H14  H  HCR6  0   0.269  81.1919  33.7016  69.2459
 5IB  H15  H  HNH1  0   0.415  79.2052  32.1180  68.3409
 5IB  H16  H  HOH1  0   0.475  82.4275  38.1167  71.3607
 5IB  O    O  O2    0  -0.449  78.4174  31.0662  71.5188
 5IB  C8   C  C     0   0.520  79.9910  30.3561  69.0186
 5IB  H5   H  HCR6  0   0.273  77.5964  30.5197  67.6889

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
 5IB  C15  C16  aromatic  1.386  0.020  1.386
 5IB  C15  C14  aromatic  1.391  0.020  1.391
 5IB  C16  C17  aromatic  1.398  0.020  1.398
 5IB  C12  C11  aromatic  1.385  0.020  1.385
 5IB  C12  C13  aromatic  1.390  0.020  1.390
 5IB  C14  C13  aromatic  1.443  0.020  1.443
 5IB  C14  C19  aromatic  1.395  0.020  1.395
 5IB  C17  C18  aromatic  1.388  0.020  1.388
 5IB  C11  C10  aromatic  1.395  0.020  1.395
 5IB  C13  C20  aromatic  1.397  0.020  1.397
 5IB  C19  C18  aromatic  1.381  0.020  1.381
 5IB  C19  O4   aromatic  1.361  0.020  1.361
 5IB  C10  C9   aromatic  1.394  0.020  1.394
 5IB  C20  O4   aromatic  1.354  0.020  1.354
 5IB  C20  C9   aromatic  1.389  0.020  1.389
 5IB  C9   C8   single    1.491  0.020  1.491
 5IB  C8   N1   single    1.355  0.020  1.355
 5IB  C8   O3   double    1.216  0.020  1.216
 5IB  N1   C7   single    1.410  0.020  1.410
 5IB  O1   C5   double    1.220  0.020  1.220
 5IB  C6   C7   aromatic  1.379  0.020  1.379
 5IB  C6   C4   aromatic  1.394  0.020  1.394
 5IB  C7   C1   aromatic  1.406  0.020  1.406
 5IB  C5   C4   single    1.490  0.020  1.490
 5IB  C5   N    single    1.346  0.020  1.346
 5IB  C4   C3   aromatic  1.390  0.020  1.390
 5IB  O2   N    single    1.360  0.020  1.360
 5IB  C1   O    single    1.334  0.020  1.334
 5IB  C1   C2   aromatic  1.393  0.020  1.393
 5IB  O    C    single    1.416  0.020  1.416
 5IB  C3   C2   aromatic  1.387  0.020  1.387
 5IB  N    H1   single    0.860  0.020  1.020
 5IB  C    H2   single    0.970  0.020  1.090
 5IB  C    H3   single    0.970  0.020  1.090
 5IB  C    H4   single    0.970  0.020  1.090
 5IB  C10  H5   single    0.930  0.020  1.080
 5IB  C11  H6   single    0.930  0.020  1.080
 5IB  C12  H7   single    0.930  0.020  1.080
 5IB  C15  H8   single    0.930  0.020  1.080
 5IB  C16  H9   single    0.930  0.020  1.080
 5IB  C17  H10  single    0.930  0.020  1.080
 5IB  C18  H11  single    0.930  0.020  1.080
 5IB  C2   H12  single    0.930  0.020  1.080
 5IB  C3   H13  single    0.930  0.020  1.080
 5IB  C6   H14  single    0.930  0.020  1.080
 5IB  N1   H15  single    0.860  0.020  1.020
 5IB  O2   H16  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
 5IB  H1   N    O2   115.18  3.000
 5IB  H1   N    C5   124.41  3.000
 5IB  O2   N    C5   120.14  3.000
 5IB  H4   C    H3   109.03  3.000
 5IB  H4   C    H2   108.95  3.000
 5IB  H3   C    H2   108.95  3.000
 5IB  H4   C    O    111.77  3.000
 5IB  H3   C    O    111.73  3.000
 5IB  H2   C    O    106.31  3.000
 5IB  C7   C1   C2   118.87  3.000
 5IB  C2   C1   O    124.67  3.000
 5IB  C7   C1   O    116.46  3.000
 5IB  H5   C10  C9   119.34  3.000
 5IB  H5   C10  C11  118.76  3.000
 5IB  C9   C10  C11  121.89  3.000
 5IB  H6   C11  C12  119.89  3.000
 5IB  H6   C11  C10  119.17  3.000
 5IB  C12  C11  C10  120.95  3.000
 5IB  H7   C12  C13  120.87  3.000
 5IB  H7   C12  C11  120.81  3.000
 5IB  C13  C12  C11  118.32  3.000
 5IB  C20  C13  C14  105.32  3.000
 5IB  C20  C13  C12  119.84  3.000
 5IB  C14  C13  C12  134.83  3.000
 5IB  C19  C14  C15  119.56  3.000
 5IB  C19  C14  C13  105.21  3.000
 5IB  C15  C14  C13  135.23  3.000
 5IB  H8   C15  C16  120.90  3.000
 5IB  H8   C15  C14  120.88  3.000
 5IB  C16  C15  C14  118.21  3.000
 5IB  H9   C16  C17  119.31  3.000
 5IB  H9   C16  C15  119.67  3.000
 5IB  C17  C16  C15  121.02  3.000
 5IB  H10  C17  C18  119.09  3.000
 5IB  H10  C17  C16  119.34  3.000
 5IB  C18  C17  C16  121.57  3.000
 5IB  H11  C18  C19  121.95  3.000
 5IB  H11  C18  C17  121.67  3.000
 5IB  C19  C18  C17  116.39  3.000
 5IB  O4   C19  C18  125.41  3.000
 5IB  O4   C19  C14  111.34  3.000
 5IB  C18  C19  C14  123.24  3.000
 5IB  H12  C2   C3   118.64  3.000
 5IB  H12  C2   C1   121.04  3.000
 5IB  C3   C2   C1   120.33  3.000
 5IB  O4   C20  C9   125.73  3.000
 5IB  C9   C20  C13  122.87  3.000
 5IB  O4   C20  C13  111.37  3.000
 5IB  H13  C3   C4   121.16  3.000
 5IB  H13  C3   C2   117.76  3.000
 5IB  C4   C3   C2   121.06  3.000
 5IB  C6   C4   C5   117.80  3.000
 5IB  C5   C4   C3   123.72  3.000
 5IB  C6   C4   C3   118.38  3.000
 5IB  O1   C5   C4   122.11  3.000
 5IB  C4   C5   N    114.91  3.000
 5IB  O1   C5   N    122.96  3.000
 5IB  H14  C6   C7   118.61  3.000
 5IB  H14  C6   C4   120.09  3.000
 5IB  C7   C6   C4   121.30  3.000
 5IB  N1   C7   C6   120.07  3.000
 5IB  C6   C7   C1   120.02  3.000
 5IB  N1   C7   C1   119.90  3.000
 5IB  C8   C9   C20  121.30  3.000
 5IB  C8   C9   C10  122.54  3.000
 5IB  C20  C9   C10  116.12  3.000
 5IB  H15  N1   C8   119.02  3.000
 5IB  H15  N1   C7   117.77  3.000
 5IB  C8   N1   C7   122.25  3.000
 5IB  H16  O2   N    106.53  3.000
 5IB  C20  O4   C19  106.75  3.000
 5IB  C1   O    C    118.94  3.000
 5IB  O3   C8   N1   123.26  3.000
 5IB  O3   C8   C9   122.15  3.000
 5IB  N1   C8   C9   114.59  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
 5IB  CONST_01  C4   C6   C7   C1      0.00   0.0  0
 5IB  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5IB  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 5IB  CONST_04  C13  C20  C9   C10     0.00   0.0  0
 5IB  CONST_05  O4   C20  C9   C10   180.00   0.0  0
 5IB  CONST_06  C14  C13  C12  C11   180.00   0.0  0
 5IB  CONST_07  C20  C13  C12  C11     0.00   0.0  0
 5IB  CONST_08  C20  C9   C10  C11     0.00   0.0  0
 5IB  CONST_09  C9   C10  C11  C12     0.00   0.0  0
 5IB  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 5IB  CONST_11  C19  C14  C13  C12   180.00   0.0  0
 5IB  CONST_12  O4   C20  C13  C12   180.00   0.0  0
 5IB  CONST_13  C9   C20  C13  C12     0.00   0.0  0
 5IB  CONST_14  C16  C15  C14  C13   180.00   0.0  0
 5IB  CONST_15  C18  C19  C14  C13   180.00   0.0  0
 5IB  CONST_16  O4   C19  C14  C13     0.00   0.0  0
 5IB  CONST_17  C19  O4   C20  C13     0.00   0.0  0
 5IB  CONST_18  C17  C16  C15  C14     0.00   0.0  0
 5IB  CONST_19  O4   C20  C13  C14     0.00   0.0  0
 5IB  CONST_20  C9   C20  C13  C14   180.00   0.0  0
 5IB  CONST_21  C17  C18  C19  C14     0.00   0.0  0
 5IB  CONST_22  C20  O4   C19  C14     0.00   0.0  0
 5IB  CONST_23  C18  C17  C16  C15     0.00   0.0  0
 5IB  CONST_24  C20  C13  C14  C15   180.00   0.0  0
 5IB  CONST_25  C18  C19  C14  C15     0.00   0.0  0
 5IB  CONST_26  O4   C19  C14  C15   180.00   0.0  0
 5IB  CONST_27  C19  C14  C15  C16     0.00   0.0  0
 5IB  CONST_28  C19  C18  C17  C16     0.00   0.0  0
 5IB  CONST_29  O4   C19  C18  C17   180.00   0.0  0
 5IB  CONST_30  C20  O4   C19  C18   180.00   0.0  0
 5IB  CONST_31  C20  C13  C14  C19     0.00   0.0  0
 5IB  CONST_32  C9   C20  O4   C19   180.00   0.0  0
 5IB  CONST_33  C6   C7   C1   C2      0.00   0.0  0
 5IB  CONST_34  C6   C4   C3   C2      0.00   0.0  0
 5IB  CONST_35  C7   C6   C4   C3      0.00   0.0  0
 5IB  CONST_36  C7   C1   C2   C3      0.00   0.0  0
 5IB  CONST_37  C6   C7   C1   O     180.00   0.0  0
 5IB  CONST_38  C3   C2   C1   O     180.00   0.0  0
 5IB  CONST_39  C8   C9   C10  C11   180.00   0.0  0
 5IB  CONST_40  C8   C9   C20  C13   180.00   0.0  0
 5IB  CONST_41  N1   C7   C1   C2    180.00   0.0  0
 5IB  CONST_42  C5   C4   C3   C2    180.00   0.0  0
 5IB  CONST_43  N1   C7   C6   C4    180.00   0.0  0
 5IB  CONST_44  C7   C6   C4   C5    180.00   0.0  0
 5IB  CONST_45  O4   C20  C9   C8      0.00   0.0  0
 5IB  CONST_46  H14  C6   C7   C1    180.00   0.0  0
 5IB  CONST_47  H13  C3   C2   C1    180.00   0.0  0
 5IB  CONST_48  H7   C12  C11  C10   180.00   0.0  0
 5IB  CONST_49  H5   C10  C11  C12   180.00   0.0  0
 5IB  CONST_50  H6   C11  C12  C13   180.00   0.0  0
 5IB  CONST_51  H8   C15  C14  C13     0.00   0.0  0
 5IB  CONST_52  H9   C16  C15  C14   180.00   0.0  0
 5IB  CONST_53  H7   C12  C13  C14     0.00   0.0  0
 5IB  CONST_54  H11  C18  C19  C14   180.00   0.0  0
 5IB  CONST_55  H10  C17  C16  C15   180.00   0.0  0
 5IB  CONST_56  H11  C18  C17  C16   180.00   0.0  0
 5IB  CONST_57  H8   C15  C16  C17   180.00   0.0  0
 5IB  CONST_58  H9   C16  C17  C18   180.00   0.0  0
 5IB  CONST_59  H8   C15  C14  C19   180.00   0.0  0
 5IB  CONST_60  H10  C17  C18  C19   180.00   0.0  0
 5IB  CONST_61  H7   C12  C13  C20   180.00   0.0  0
 5IB  CONST_62  H5   C10  C9   C20   180.00   0.0  0
 5IB  CONST_63  H14  C6   C4   C3    180.00   0.0  0
 5IB  CONST_64  H12  C2   C3   C4    180.00   0.0  0
 5IB  CONST_65  H13  C3   C4   C6    180.00   0.0  0
 5IB  CONST_66  H12  C2   C1   C7    180.00   0.0  0
 5IB  CONST_67  H6   C11  C10  C9    180.00   0.0  0
 5IB  CONST_68  H11  C18  C19  O4      0.00   0.0  0
 5IB  CONST_69  C9   C8   N1   C7    180.00   0.0  0
 5IB  CONST_74  O2   N    C5   C4    180.00   0.0  0
 5IB  CONST_75  O3   C8   N1   C7      0.00   0.0  0
 5IB  CONST_76  H1   N    C5   C4      0.00   0.0  0
 5IB  CONST_77  H15  N1   C8   C9      0.00   0.0  0
 5IB  CONST_78  O2   N    C5   O1      0.00   0.0  0
 5IB  CONST_79  H1   N    C5   O1    180.00   0.0  0
 5IB  CONST_80  H15  N1   C8   O3    180.00   0.0  0
 5IB  Var_01    C6   C4   C5   N     152.18  30.0  2
 5IB  Var_02    C3   C4   C5   N     -31.60  30.0  2
 5IB  Var_03    C7   C1   O    C     178.44  30.0  1
 5IB  Var_04    C2   C1   O    C      -1.93  30.0  1
 5IB  Var_05    N1   C8   C9   C10   -40.69  30.0  2
 5IB  Var_06    O3   C8   C9   C10   139.45  30.0  2
 5IB  Var_07    N1   C8   C9   C20   141.81  30.0  2
 5IB  Var_08    O3   C8   C9   C20   -38.05  30.0  2
 5IB  Var_09    O1   C5   C4   C3    149.91  30.0  2
 5IB  Var_10    O1   C5   C4   C6    -26.31  30.0  2
 5IB  Var_11    H2   C    O    C1   -179.10  30.0  3
 5IB  Var_12    H3   C    O    C1    -60.35  30.0  3
 5IB  Var_13    H4   C    O    C1     62.14  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
 5IB  plan-1  C1   0.020
 5IB  plan-1  C2   0.020
 5IB  plan-1  C3   0.020
 5IB  plan-1  C4   0.020
 5IB  plan-1  C5   0.020
 5IB  plan-1  C6   0.020
 5IB  plan-1  C7   0.020
 5IB  plan-1  N1   0.020
 5IB  plan-1  H12  0.020
 5IB  plan-1  H13  0.020
 5IB  plan-1  H14  0.020
 5IB  plan-1  O    0.020
 5IB  plan-2  C10  0.020
 5IB  plan-2  C11  0.020
 5IB  plan-2  C12  0.020
 5IB  plan-2  C13  0.020
 5IB  plan-2  C14  0.020
 5IB  plan-2  C15  0.020
 5IB  plan-2  C16  0.020
 5IB  plan-2  C17  0.020
 5IB  plan-2  C18  0.020
 5IB  plan-2  C19  0.020
 5IB  plan-2  C20  0.020
 5IB  plan-2  C9   0.020
 5IB  plan-2  O4   0.020
 5IB  plan-2  H6   0.020
 5IB  plan-2  H7   0.020
 5IB  plan-2  H8   0.020
 5IB  plan-2  H9   0.020
 5IB  plan-2  H10  0.020
 5IB  plan-2  H11  0.020
 5IB  plan-2  C8   0.020
 5IB  plan-2  H5   0.020
 5IB  plan-3  N    0.020
 5IB  plan-3  C4   0.020
 5IB  plan-3  C5   0.020
 5IB  plan-3  O1   0.020
 5IB  plan-3  O2   0.020
 5IB  plan-3  H1   0.020
 5IB  plan-4  C7   0.020
 5IB  plan-4  C9   0.020
 5IB  plan-4  N1   0.020
 5IB  plan-4  O3   0.020
 5IB  plan-4  H15  0.020
 5IB  plan-4  C8   0.020

