# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 14:53:11 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-{[4-(2,6-difluoro-4-methoxybenzene-1-carbonyl)pyrimidin-2-yl]amino}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(F)c(c(F)c1)C(=O)c2ccnc(Nc3ccc(cc3)C#N)n2
#
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
 IB1  IB1  4-{[4-(2,6-difluoro-4-methoxybenzene-1-carbonyl)pyrimidin-2-yl]amino}benzonitrile  ligand  39  27  .  2021-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IB1
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
 IB1  C01  C  CR16  0  -0.354   0.2597   3.3453   0.2373
 IB1  C02  C  CR6   0   0.180   0.8527   2.1471  -0.1349
 IB1  N03  N  N     0  -0.462   0.1735   1.0234  -0.2541
 IB1  C04  C  CR6   0   0.614  -1.1339   1.0783   0.0019
 IB1  N05  N  N     0  -0.451  -1.7999   2.1627   0.3791
 IB1  C06  C  CR16  0   0.017  -1.0984   3.2805   0.4942
 IB1  C07  C  C     0   0.385   2.3143   2.0948  -0.4809
 IB1  O08  O  O     0  -0.348   2.8714   3.0941  -0.8684
 IB1  C09  C  CR6   0  -0.467   3.0037   0.7900  -0.3815
 IB1  C10  C  CR6   0   0.581   3.8726   0.3403  -1.3771
 IB1  C11  C  CR16  0  -0.518   4.5412  -0.8556  -1.3141
 IB1  C12  C  CR6   0   0.435   4.3714  -1.6636  -0.1850
 IB1  C13  C  CR16  0  -0.557   3.5326  -1.2517   0.8510
 IB1  C14  C  CR6   0   0.634   2.8758  -0.0478   0.7183
 IB1  F15  F  F     0  -0.293   2.1094   0.3570   1.7324
 IB1  O16  O  O2    0  -0.454   5.0513  -2.8073  -0.1782
 IB1  N17  N  NH1   0  -0.772  -1.7792  -0.1152  -0.1488
 IB1  C18  C  CR6   0   0.391  -3.1038  -0.4704   0.0016
 IB1  C19  C  CR16  0  -0.302  -4.1418   0.4133   0.3223
 IB1  C20  C  CR16  0  -0.229  -5.4356  -0.0568   0.4413
 IB1  C21  C  CR6   0  -0.019  -5.7294  -1.4054   0.2470
 IB1  C22  C  CR16  0  -0.229  -4.6973  -2.2910  -0.0736
 IB1  C23  C  CR16  0  -0.346  -3.4077  -1.8275  -0.1939
 IB1  C24  C  CSP   0   0.048  -7.0665  -1.8746   0.3747
 IB1  N25  N  NS    0  -0.262  -8.1513  -2.2524   0.4795
 IB1  F26  F  F     0  -0.289   4.0282   1.0907  -2.4675
 IB1  C27  C  CH3   0  -0.446   4.9173  -3.6831   0.9309
 IB1  H1   H  HCR6  0   0.289   0.8149   4.2655   0.3346
 IB1  H2   H  HCR6  0   0.287  -1.6448   4.1627   0.8058
 IB1  H3   H  HCR6  0   0.300   5.1850  -1.1693  -2.1254
 IB1  H4   H  HCR6  0   0.313   3.3921  -1.8328   1.7516
 IB1  H5   H  HNH1  0   0.419  -1.1565  -0.8654  -0.4121
 IB1  H6   H  HCR6  0   0.300  -3.9437   1.4599   0.4786
 IB1  H7   H  HCR6  0   0.281  -6.2271   0.6381   0.6879
 IB1  H8   H  HCR6  0   0.282  -4.9058  -3.3411  -0.2267
 IB1  H9   H  HCR6  0   0.285  -2.6162  -2.5242  -0.4413
 IB1  H10  H  HCH3  0   0.241   5.2521  -3.2130   1.8576
 IB1  H11  H  HCH3  0   0.241   3.8868  -4.0234   1.0511
 IB1  H12  H  HCH3  0   0.272   5.5501  -4.5400   0.7188

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
 IB1  C27  O16  single    1.420  0.020  1.420
 IB1  O16  C12  single    1.330  0.020  1.330
 IB1  C12  C11  aromatic  1.399  0.020  1.399
 IB1  C12  C13  aromatic  1.395  0.020  1.395
 IB1  C11  C10  aromatic  1.372  0.020  1.372
 IB1  C13  C14  aromatic  1.378  0.020  1.378
 IB1  C10  F26  single    1.333  0.020  1.333
 IB1  C10  C09  aromatic  1.396  0.020  1.396
 IB1  N25  C24  triple    1.153  0.020  1.153
 IB1  C24  C21  single    1.423  0.020  1.423
 IB1  C14  C09  aromatic  1.389  0.020  1.389
 IB1  C14  F15  single    1.334  0.020  1.334
 IB1  C09  C07  single    1.479  0.020  1.479
 IB1  C22  C21  aromatic  1.397  0.020  1.397
 IB1  C22  C23  aromatic  1.376  0.020  1.376
 IB1  C21  C20  aromatic  1.394  0.020  1.394
 IB1  O08  C07  double    1.208  0.020  1.208
 IB1  C07  C02  single    1.503  0.020  1.503
 IB1  C23  C18  aromatic  1.404  0.020  1.404
 IB1  C20  C19  aromatic  1.382  0.020  1.382
 IB1  N03  C02  aromatic  1.318  0.020  1.318
 IB1  N03  C04  aromatic  1.333  0.020  1.333
 IB1  C02  C01  aromatic  1.388  0.020  1.388
 IB1  C18  C19  aromatic  1.400  0.020  1.400
 IB1  C18  N17  single    1.380  0.020  1.380
 IB1  N17  C04  single    1.365  0.020  1.365
 IB1  C04  N05  aromatic  1.327  0.020  1.327
 IB1  C01  C06  aromatic  1.384  0.020  1.384
 IB1  N05  C06  aromatic  1.325  0.020  1.325
 IB1  C01  H1   single    0.930  0.020  1.080
 IB1  C06  H2   single    0.930  0.020  1.080
 IB1  C11  H3   single    0.930  0.020  1.080
 IB1  C13  H4   single    0.930  0.020  1.080
 IB1  N17  H5   single    0.860  0.020  1.020
 IB1  C19  H6   single    0.930  0.020  1.080
 IB1  C20  H7   single    0.930  0.020  1.080
 IB1  C22  H8   single    0.930  0.020  1.080
 IB1  C23  H9   single    0.930  0.020  1.080
 IB1  C27  H10  single    0.970  0.020  1.090
 IB1  C27  H11  single    0.970  0.020  1.090
 IB1  C27  H12  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
 IB1  H1   C01  C06  121.88  3.000
 IB1  H1   C01  C02  122.73  3.000
 IB1  C06  C01  C02  115.39  3.000
 IB1  C07  C02  N03  116.77  3.000
 IB1  N03  C02  C01  122.69  3.000
 IB1  C07  C02  C01  120.49  3.000
 IB1  C04  N03  C02  116.92  3.000
 IB1  N17  C04  N05  120.56  3.000
 IB1  N05  C04  N03  125.46  3.000
 IB1  N17  C04  N03  113.98  3.000
 IB1  C06  N05  C04  116.64  3.000
 IB1  H2   C06  N05  116.42  3.000
 IB1  H2   C06  C01  120.68  3.000
 IB1  N05  C06  C01  122.90  3.000
 IB1  C09  C07  O08  122.44  3.000
 IB1  O08  C07  C02  119.57  3.000
 IB1  C09  C07  C02  117.94  3.000
 IB1  C14  C09  C10  115.34  3.000
 IB1  C14  C09  C07  122.86  3.000
 IB1  C10  C09  C07  121.76  3.000
 IB1  F26  C10  C11  118.14  3.000
 IB1  F26  C10  C09  118.35  3.000
 IB1  C11  C10  C09  123.47  3.000
 IB1  H3   C11  C12  120.66  3.000
 IB1  H3   C11  C10  120.55  3.000
 IB1  C12  C11  C10  118.79  3.000
 IB1  O16  C12  C13  123.86  3.000
 IB1  C13  C12  C11  120.12  3.000
 IB1  O16  C12  C11  116.02  3.000
 IB1  H4   C13  C14  119.20  3.000
 IB1  H4   C13  C12  122.56  3.000
 IB1  C14  C13  C12  118.23  3.000
 IB1  F15  C14  C13  117.77  3.000
 IB1  F15  C14  C09  118.16  3.000
 IB1  C13  C14  C09  124.03  3.000
 IB1  C27  O16  C12  119.08  3.000
 IB1  H5   N17  C18  115.41  3.000
 IB1  H5   N17  C04  112.75  3.000
 IB1  C18  N17  C04  131.83  3.000
 IB1  C23  C18  C19  118.76  3.000
 IB1  C19  C18  N17  125.04  3.000
 IB1  C23  C18  N17  116.19  3.000
 IB1  H6   C19  C20  119.38  3.000
 IB1  H6   C19  C18  120.68  3.000
 IB1  C20  C19  C18  119.94  3.000
 IB1  H7   C20  C21  119.94  3.000
 IB1  H7   C20  C19  119.09  3.000
 IB1  C21  C20  C19  120.97  3.000
 IB1  C24  C21  C22  120.38  3.000
 IB1  C22  C21  C20  119.31  3.000
 IB1  C24  C21  C20  120.31  3.000
 IB1  H8   C22  C23  119.70  3.000
 IB1  H8   C22  C21  120.37  3.000
 IB1  C23  C22  C21  119.93  3.000
 IB1  H9   C23  C22  119.23  3.000
 IB1  H9   C23  C18  119.69  3.000
 IB1  C22  C23  C18  121.08  3.000
 IB1  N25  C24  C21  180.00  3.000
 IB1  H12  C27  H11  109.00  3.000
 IB1  H12  C27  H10  109.07  3.000
 IB1  H11  C27  H10  109.28  3.000
 IB1  H12  C27  O16  106.22  3.000
 IB1  H11  C27  O16  111.56  3.000
 IB1  H10  C27  O16  111.62  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
 IB1  CONST_01  C04  N03  C02  C01     0.00   0.0  0
 IB1  CONST_02  C04  N05  C06  C01     0.00   0.0  0
 IB1  CONST_03  N05  C04  N03  C02     0.00   0.0  0
 IB1  CONST_04  N05  C06  C01  C02     0.00   0.0  0
 IB1  CONST_05  C06  C01  C02  N03     0.00   0.0  0
 IB1  CONST_06  C06  N05  C04  N03     0.00   0.0  0
 IB1  CONST_07  C12  C11  C10  C09     0.00   0.0  0
 IB1  CONST_08  C12  C13  C14  C09     0.00   0.0  0
 IB1  CONST_09  C13  C12  C11  C10     0.00   0.0  0
 IB1  CONST_10  C13  C14  C09  C10     0.00   0.0  0
 IB1  CONST_11  C14  C13  C12  C11     0.00   0.0  0
 IB1  CONST_12  C14  C09  C10  C11     0.00   0.0  0
 IB1  CONST_13  C21  C22  C23  C18     0.00   0.0  0
 IB1  CONST_14  C21  C20  C19  C18     0.00   0.0  0
 IB1  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 IB1  CONST_16  C22  C23  C18  C19     0.00   0.0  0
 IB1  CONST_17  C23  C22  C21  C20     0.00   0.0  0
 IB1  CONST_18  C23  C18  C19  C20     0.00   0.0  0
 IB1  CONST_19  N17  C04  N03  C02   180.00   0.0  0
 IB1  CONST_20  C07  C02  N03  C04   180.00   0.0  0
 IB1  CONST_21  C07  C02  C01  C06   180.00   0.0  0
 IB1  CONST_22  N17  C04  N05  C06   180.00   0.0  0
 IB1  CONST_23  C11  C10  C09  C07   180.00   0.0  0
 IB1  CONST_24  C13  C14  C09  C07   180.00   0.0  0
 IB1  CONST_25  O16  C12  C11  C10   180.00   0.0  0
 IB1  CONST_26  F15  C14  C09  C10   180.00   0.0  0
 IB1  CONST_27  F26  C10  C11  C12   180.00   0.0  0
 IB1  CONST_28  F15  C14  C13  C12   180.00   0.0  0
 IB1  CONST_29  O16  C12  C13  C14   180.00   0.0  0
 IB1  CONST_30  F26  C10  C09  C14   180.00   0.0  0
 IB1  CONST_31  C22  C23  C18  N17   180.00   0.0  0
 IB1  CONST_32  C20  C19  C18  N17   180.00   0.0  0
 IB1  CONST_33  C24  C21  C20  C19   180.00   0.0  0
 IB1  CONST_34  C24  C21  C22  C23   180.00   0.0  0
 IB1  CONST_35  H2   C06  C01  C02   180.00   0.0  0
 IB1  CONST_36  H1   C01  C02  N03   180.00   0.0  0
 IB1  CONST_37  H3   C11  C10  C09   180.00   0.0  0
 IB1  CONST_38  H4   C13  C14  C09   180.00   0.0  0
 IB1  CONST_39  H8   C22  C23  C18   180.00   0.0  0
 IB1  CONST_40  H7   C20  C19  C18   180.00   0.0  0
 IB1  CONST_41  H9   C23  C18  C19   180.00   0.0  0
 IB1  CONST_42  H6   C19  C20  C21   180.00   0.0  0
 IB1  Var_01    C09  C07  C02  C01   157.85  30.0  2
 IB1  Var_02    C10  C09  C07  C02   135.33  30.0  2
 IB1  Var_03    C18  N17  C04  N03  -179.16  30.0  1
 IB1  Var_04    C23  C18  N17  C04  -177.81  30.0  2
 IB1  Var_05    H10  C27  O16  C12   -61.45  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
 IB1  plan-1  C01  0.020
 IB1  plan-1  C02  0.020
 IB1  plan-1  N03  0.020
 IB1  plan-1  C04  0.020
 IB1  plan-1  N05  0.020
 IB1  plan-1  C06  0.020
 IB1  plan-1  C07  0.020
 IB1  plan-1  N17  0.020
 IB1  plan-1  H1   0.020
 IB1  plan-1  H2   0.020
 IB1  plan-2  C07  0.020
 IB1  plan-2  C09  0.020
 IB1  plan-2  C10  0.020
 IB1  plan-2  C11  0.020
 IB1  plan-2  C12  0.020
 IB1  plan-2  C13  0.020
 IB1  plan-2  C14  0.020
 IB1  plan-2  F15  0.020
 IB1  plan-2  O16  0.020
 IB1  plan-2  F26  0.020
 IB1  plan-2  H3   0.020
 IB1  plan-2  H4   0.020
 IB1  plan-3  N17  0.020
 IB1  plan-3  C18  0.020
 IB1  plan-3  C19  0.020
 IB1  plan-3  C20  0.020
 IB1  plan-3  C21  0.020
 IB1  plan-3  C22  0.020
 IB1  plan-3  C23  0.020
 IB1  plan-3  C24  0.020
 IB1  plan-3  N25  0.020
 IB1  plan-3  H6   0.020
 IB1  plan-3  H7   0.020
 IB1  plan-3  H8   0.020
 IB1  plan-3  H9   0.020
 IB1  plan-4  C02  0.020
 IB1  plan-4  C07  0.020
 IB1  plan-4  O08  0.020
 IB1  plan-4  C09  0.020

