# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 19:41:57 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: N,N'-bis(4-fluoro-3-methylbenzyl)pyrimidine-4,6-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(CNC(=O)c2cc(ncn2)C(=O)NCc3ccc(F)c(C)c3)ccc1F
#
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
 PB4  PB4  N,N'-bis(4-fluoro-3-methylbenzyl)pyrimidine-4,6-dicarboxamide  ligand  50  30  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PB4
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
 PB4  C1    C  CR6   0   0.167   1.7689   0.5851  -1.1573
 PB4  C2    C  CR16  0  -0.289   1.6894  -0.0793   0.0549
 PB4  C3    C  CR6   0   0.163   1.7132   0.7170   1.1876
 PB4  C7    C  CH3   0  -0.717  -1.9304  -2.8890   6.1639
 PB4  C8    C  CH3   0  -0.717  -2.6186  -2.3618  -5.3888
 PB4  C9    C  C     0   0.559   1.6301   0.0833   2.5532
 PB4  C10   C  CH2   0  -0.393   1.5917   0.5230   4.9506
 PB4  C11   C  CR6   0   0.127   0.1778   0.1887   5.3562
 PB4  C12   C  C     0   0.556   1.7459  -0.1996  -2.4454
 PB4  C13   C  CH2   0  -0.402   1.8166  -0.0017  -4.8867
 PB4  C14   C  CR6   0   0.132   0.4155  -0.0448  -5.4429
 PB4  C15   C  CR16  0  -0.326  -0.4149  -1.1352  -5.1942
 PB4  C16   C  CR6   0   0.505  -2.1719  -0.0967  -6.3900
 PB4  C19   C  CR16  0  -0.295  -0.7622   1.2015   5.5149
 PB4  C20   C  CR16  0  -0.393  -2.0667   0.9009   5.8757
 PB4  C21   C  CR6   0   0.502  -2.4102  -0.4214   6.0759
 PB4  C22   C  CR16  0  -0.323  -0.2128  -1.1289   5.5648
 PB4  N1    N  N     0  -0.421   1.8064   2.0378   1.1170
 PB4  C5    C  CR16  0   0.072   1.8765   2.5743  -0.0895
 PB4  N2    N  N     0  -0.421   1.8620   1.9060  -1.2302
 PB4  N3    N  NH1   0  -0.633   1.6916   0.9434   3.5690
 PB4  N4    N  NH1   0  -0.627   1.8592   0.5436  -3.5453
 PB4  C6    C  CR6   0  -0.078  -1.7248  -1.1892  -5.6594
 PB4  C17   C  CR16  0  -0.393  -1.3828   1.0007  -6.6640
 PB4  C18   C  CR16  0  -0.299  -0.0805   1.0206  -6.1840
 PB4  C4    C  CR6   0  -0.080  -1.5122  -1.4681   5.9329
 PB4  O1    O  O     0  -0.472   1.6397  -1.4164  -2.4218
 PB4  O2    O  O     0  -0.464   1.5267  -1.1277   2.6687
 PB4  F1    F  F     0  -0.314  -3.6759  -0.7118   6.4299
 PB4  F2    F  F     0  -0.313  -3.4347  -0.1146  -6.8543
 PB4  H2    H  HCR6  0   0.291   1.6140  -1.1543   0.1144
 PB4  H71   H  HCH3  0   0.251  -2.2813  -3.0446   7.1849
 PB4  H72   H  HCH3  0   0.251  -2.7394  -3.1863   5.4953
 PB4  H73   H  HCH3  0   0.249  -1.0956  -3.5663   5.9945
 PB4  H81   H  HCH3  0   0.251  -2.9866  -2.8118  -6.3115
 PB4  H82   H  HCH3  0   0.250  -2.0839  -3.1303  -4.8340
 PB4  H83   H  HCH3  0   0.252  -3.4904  -2.0732  -4.7999
 PB4  H101  H  HCH2  0   0.281   1.9733   1.3431   5.5581
 PB4  H102  H  HCH2  0   0.268   2.2468  -0.3325   5.1192
 PB4  H131  H  HCH2  0   0.270   2.2578  -0.9976  -4.8724
 PB4  H132  H  HCH2  0   0.280   2.4514   0.6243  -5.5131
 PB4  H15   H  HCR6  0   0.255  -0.0347  -1.9728  -4.6213
 PB4  H19   H  HCR6  0   0.262  -0.4794   2.2359   5.3617
 PB4  H20   H  HCR6  0   0.275  -2.8050   1.6815   6.0050
 PB4  H22   H  HCR6  0   0.253   0.5152  -1.9219   5.4415
 PB4  H5    H  HCR6  0   0.281   1.9524   3.6530  -0.1486
 PB4  HN3   H  HNH1  0   0.414   1.7587   1.9271   3.3557
 PB4  HN4   H  HNH1  0   0.414   1.8968   1.5461  -3.4316
 PB4  H17   H  HCR6  0   0.276  -1.7763   1.8256  -7.2437
 PB4  H18   H  HCR6  0   0.262   0.5498   1.8757  -6.3965

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
 PB4  C1   C2    aromatic  1.385  0.020  1.385
 PB4  C1   C12   single    1.508  0.020  1.508
 PB4  C1   N2    aromatic  1.326  0.020  1.326
 PB4  C2   C3    aromatic  1.385  0.020  1.385
 PB4  C2   H2    single    0.930  0.020  1.080
 PB4  C3   C9    single    1.508  0.020  1.508
 PB4  C3   N1    aromatic  1.326  0.020  1.326
 PB4  C7   C4    single    1.499  0.020  1.499
 PB4  C7   H71   single    0.970  0.020  1.090
 PB4  C7   H72   single    0.970  0.020  1.090
 PB4  C7   H73   single    0.970  0.020  1.090
 PB4  C8   C6    single    1.499  0.020  1.499
 PB4  C8   H81   single    0.970  0.020  1.090
 PB4  C8   H82   single    0.970  0.020  1.090
 PB4  C8   H83   single    0.970  0.020  1.090
 PB4  C9   N3    single    1.333  0.020  1.333
 PB4  C9   O2    double    1.221  0.020  1.221
 PB4  C10  C11   single    1.508  0.020  1.508
 PB4  C10  N3    single    1.448  0.020  1.448
 PB4  C10  H101  single    0.970  0.020  1.090
 PB4  C10  H102  single    0.970  0.020  1.090
 PB4  C11  C19   aromatic  1.391  0.020  1.391
 PB4  C11  C22   aromatic  1.390  0.020  1.390
 PB4  C12  N4    single    1.332  0.020  1.332
 PB4  C12  O1    double    1.222  0.020  1.222
 PB4  C13  C14   single    1.508  0.020  1.508
 PB4  C13  N4    single    1.449  0.020  1.449
 PB4  C13  H131  single    0.970  0.020  1.090
 PB4  C13  H132  single    0.970  0.020  1.090
 PB4  C14  C15   aromatic  1.393  0.020  1.393
 PB4  C14  C18   aromatic  1.389  0.020  1.389
 PB4  C15  C6    aromatic  1.391  0.020  1.391
 PB4  C15  H15   single    0.930  0.020  1.080
 PB4  C16  C6    aromatic  1.388  0.020  1.388
 PB4  C16  C17   aromatic  1.379  0.020  1.379
 PB4  C16  F2    single    1.346  0.020  1.346
 PB4  C19  C20   aromatic  1.387  0.020  1.387
 PB4  C19  H19   single    0.930  0.020  1.080
 PB4  C20  C21   aromatic  1.381  0.020  1.381
 PB4  C20  H20   single    0.930  0.020  1.080
 PB4  C21  C4    aromatic  1.386  0.020  1.386
 PB4  C21  F1    single    1.346  0.020  1.346
 PB4  C22  C4    aromatic  1.392  0.020  1.392
 PB4  C22  H22   single    0.930  0.020  1.080
 PB4  N1   C5    aromatic  1.322  0.020  1.322
 PB4  C5   N2    aromatic  1.322  0.020  1.322
 PB4  C5   H5    single    0.930  0.020  1.080
 PB4  N3   HN3   single    0.860  0.020  1.020
 PB4  N4   HN4   single    0.860  0.020  1.020
 PB4  C17  C18   aromatic  1.388  0.020  1.388
 PB4  C17  H17   single    0.930  0.020  1.080
 PB4  C18  H18   single    0.930  0.020  1.080

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
 PB4  N2    C1   C12   118.18  3.000
 PB4  N2    C1   C2    122.01  3.000
 PB4  C12   C1   C2    119.81  3.000
 PB4  H2    C2   C3    121.93  3.000
 PB4  H2    C2   C1    122.02  3.000
 PB4  C3    C2   C1    116.06  3.000
 PB4  N1    C3   C9    118.09  3.000
 PB4  N1    C3   C2    122.03  3.000
 PB4  C9    C3   C2    119.88  3.000
 PB4  H73   C7   H72   107.69  3.000
 PB4  H73   C7   H71   107.68  3.000
 PB4  H72   C7   H71   107.23  3.000
 PB4  H73   C7   C4    110.61  3.000
 PB4  H72   C7   C4    111.77  3.000
 PB4  H71   C7   C4    111.67  3.000
 PB4  H83   C8   H82   107.72  3.000
 PB4  H83   C8   H81   107.23  3.000
 PB4  H82   C8   H81   107.80  3.000
 PB4  H83   C8   C6    111.53  3.000
 PB4  H82   C8   C6    110.58  3.000
 PB4  H81   C8   C6    111.79  3.000
 PB4  O2    C9   N3    124.89  3.000
 PB4  O2    C9   C3    120.48  3.000
 PB4  N3    C9   C3    114.62  3.000
 PB4  H102  C10  H101  107.09  3.000
 PB4  H102  C10  N3    109.51  3.000
 PB4  H101  C10  N3    106.82  3.000
 PB4  H102  C10  C11   110.34  3.000
 PB4  H101  C10  C11   110.19  3.000
 PB4  N3    C10  C11   112.68  3.000
 PB4  C22   C11  C19   118.90  3.000
 PB4  C22   C11  C10   120.92  3.000
 PB4  C19   C11  C10   120.18  3.000
 PB4  O1    C12  N4    125.37  3.000
 PB4  O1    C12  C1    120.20  3.000
 PB4  N4    C12  C1    114.42  3.000
 PB4  H132  C13  H131  107.27  3.000
 PB4  H132  C13  N4    107.40  3.000
 PB4  H131  C13  N4    108.67  3.000
 PB4  H132  C13  C14   110.22  3.000
 PB4  H131  C13  C14   110.79  3.000
 PB4  N4    C13  C14   112.31  3.000
 PB4  C18   C14  C15   118.86  3.000
 PB4  C18   C14  C13   120.43  3.000
 PB4  C15   C14  C13   120.69  3.000
 PB4  H15   C15  C6    118.50  3.000
 PB4  H15   C15  C14   119.36  3.000
 PB4  C6    C15  C14   122.14  3.000
 PB4  F2    C16  C17   118.62  3.000
 PB4  F2    C16  C6    118.25  3.000
 PB4  C17   C16  C6    123.13  3.000
 PB4  H19   C19  C20   119.30  3.000
 PB4  H19   C19  C11   120.19  3.000
 PB4  C20   C19  C11   120.51  3.000
 PB4  H20   C20  C21   120.25  3.000
 PB4  H20   C20  C19   121.10  3.000
 PB4  C21   C20  C19   118.65  3.000
 PB4  F1    C21  C4    118.25  3.000
 PB4  F1    C21  C20   118.60  3.000
 PB4  C4    C21  C20   123.15  3.000
 PB4  H22   C22  C4    118.61  3.000
 PB4  H22   C22  C11   119.20  3.000
 PB4  C4    C22  C11   122.19  3.000
 PB4  C5    N1   C3    117.16  3.000
 PB4  H5    C5   N2    117.20  3.000
 PB4  H5    C5   N1    117.24  3.000
 PB4  N2    C5   N1    125.56  3.000
 PB4  C5    N2   C1    117.18  3.000
 PB4  HN3   N3   C10   119.32  3.000
 PB4  HN3   N3   C9    118.12  3.000
 PB4  C10   N3   C9    122.48  3.000
 PB4  HN4   N4   C13   118.63  3.000
 PB4  HN4   N4   C12   117.65  3.000
 PB4  C13   N4   C12   123.50  3.000
 PB4  C16   C6   C15   116.66  3.000
 PB4  C16   C6   C8    121.24  3.000
 PB4  C15   C6   C8    122.10  3.000
 PB4  H17   C17  C18   121.02  3.000
 PB4  H17   C17  C16   120.32  3.000
 PB4  C18   C17  C16   118.65  3.000
 PB4  H18   C18  C17   119.30  3.000
 PB4  H18   C18  C14   120.15  3.000
 PB4  C17   C18  C14   120.55  3.000
 PB4  C22   C4   C21   116.60  3.000
 PB4  C22   C4   C7    122.13  3.000
 PB4  C21   C4   C7    121.26  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
 PB4  CONST_01  N1   C3   C2   C1      0.00   0.0  0
 PB4  CONST_02  N1   C5   N2   C1      0.00   0.0  0
 PB4  CONST_03  C5   N2   C1   C2      0.00   0.0  0
 PB4  CONST_04  C5   N1   C3   C2      0.00   0.0  0
 PB4  CONST_05  N2   C1   C2   C3      0.00   0.0  0
 PB4  CONST_06  N2   C5   N1   C3      0.00   0.0  0
 PB4  CONST_07  C21  C20  C19  C11     0.00   0.0  0
 PB4  CONST_08  C21  C4   C22  C11     0.00   0.0  0
 PB4  CONST_09  C16  C6   C15  C14     0.00   0.0  0
 PB4  CONST_10  C16  C17  C18  C14     0.00   0.0  0
 PB4  CONST_11  C17  C18  C14  C15     0.00   0.0  0
 PB4  CONST_12  C17  C16  C6   C15     0.00   0.0  0
 PB4  CONST_13  C4   C22  C11  C19     0.00   0.0  0
 PB4  CONST_14  C4   C21  C20  C19     0.00   0.0  0
 PB4  CONST_15  C22  C11  C19  C20     0.00   0.0  0
 PB4  CONST_16  C22  C4   C21  C20     0.00   0.0  0
 PB4  CONST_17  C18  C14  C15  C6      0.00   0.0  0
 PB4  CONST_18  C18  C17  C16  C6      0.00   0.0  0
 PB4  CONST_19  C9   C3   C2   C1    180.00   0.0  0
 PB4  CONST_20  C12  C1   C2   C3    180.00   0.0  0
 PB4  CONST_21  C20  C21  C4   C7    180.00   0.0  0
 PB4  CONST_22  C11  C22  C4   C7    180.00   0.0  0
 PB4  CONST_23  C14  C15  C6   C8    180.00   0.0  0
 PB4  CONST_24  C17  C16  C6   C8    180.00   0.0  0
 PB4  CONST_25  C5   N1   C3   C9    180.00   0.0  0
 PB4  CONST_26  C20  C19  C11  C10   180.00   0.0  0
 PB4  CONST_27  C4   C22  C11  C10   180.00   0.0  0
 PB4  CONST_28  C5   N2   C1   C12   180.00   0.0  0
 PB4  CONST_29  C6   C15  C14  C13   180.00   0.0  0
 PB4  CONST_30  C17  C18  C14  C13   180.00   0.0  0
 PB4  CONST_31  F2   C16  C6   C15   180.00   0.0  0
 PB4  CONST_32  F1   C21  C20  C19   180.00   0.0  0
 PB4  CONST_33  F1   C21  C4   C22   180.00   0.0  0
 PB4  CONST_34  F2   C16  C17  C18   180.00   0.0  0
 PB4  CONST_35  H5   C5   N2   C1    180.00   0.0  0
 PB4  CONST_36  H20  C20  C19  C11   180.00   0.0  0
 PB4  CONST_37  H17  C17  C18  C14   180.00   0.0  0
 PB4  CONST_38  H18  C18  C14  C15   180.00   0.0  0
 PB4  CONST_39  H15  C15  C6   C16   180.00   0.0  0
 PB4  CONST_40  H22  C22  C11  C19   180.00   0.0  0
 PB4  CONST_41  H19  C19  C20  C21   180.00   0.0  0
 PB4  CONST_42  H2   C2   C3   N1    180.00   0.0  0
 PB4  CONST_43  C13  N4   C12  C1    180.00   0.0  0
 PB4  CONST_44  C10  N3   C9   C3    180.00   0.0  0
 PB4  CONST_45  HN4  N4   C12  C1      0.00   0.0  0
 PB4  CONST_46  HN3  N3   C9   C3      0.00   0.0  0
 PB4  CONST_47  O2   C9   N3   C10     0.00   0.0  0
 PB4  CONST_48  O1   C12  N4   C13     0.00   0.0  0
 PB4  Var_01    N4   C12  C1   C2   -178.54  30.0  2
 PB4  Var_02    N3   C9   C3   C2    178.59  30.0  2
 PB4  Var_03    N4   C13  C14  C15   -86.63  30.0  2
 PB4  Var_04    N3   C10  C11  C19   -71.74  30.0  3
 PB4  Var_05    H81  C8   C6   C15  -122.23  30.0  2
 PB4  Var_06    H71  C7   C4   C21   -60.70  30.0  2
 PB4  Var_07    C11  C10  N3   C9    -75.99  30.0  2
 PB4  Var_08    C14  C13  N4   C12    90.00  30.0  1

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
 PB4  plan-1  C1   0.020
 PB4  plan-1  C2   0.020
 PB4  plan-1  C3   0.020
 PB4  plan-1  C9   0.020
 PB4  plan-1  C12  0.020
 PB4  plan-1  N1   0.020
 PB4  plan-1  C5   0.020
 PB4  plan-1  N2   0.020
 PB4  plan-1  H2   0.020
 PB4  plan-1  H5   0.020
 PB4  plan-2  C7   0.020
 PB4  plan-2  C10  0.020
 PB4  plan-2  C11  0.020
 PB4  plan-2  C19  0.020
 PB4  plan-2  C20  0.020
 PB4  plan-2  C21  0.020
 PB4  plan-2  C22  0.020
 PB4  plan-2  C4   0.020
 PB4  plan-2  F1   0.020
 PB4  plan-2  H19  0.020
 PB4  plan-2  H20  0.020
 PB4  plan-2  H22  0.020
 PB4  plan-3  C8   0.020
 PB4  plan-3  C13  0.020
 PB4  plan-3  C14  0.020
 PB4  plan-3  C15  0.020
 PB4  plan-3  C16  0.020
 PB4  plan-3  C6   0.020
 PB4  plan-3  C17  0.020
 PB4  plan-3  C18  0.020
 PB4  plan-3  F2   0.020
 PB4  plan-3  H15  0.020
 PB4  plan-3  H17  0.020
 PB4  plan-3  H18  0.020
 PB4  plan-4  C3   0.020
 PB4  plan-4  C9   0.020
 PB4  plan-4  C10  0.020
 PB4  plan-4  N3   0.020
 PB4  plan-4  O2   0.020
 PB4  plan-4  HN3  0.020
 PB4  plan-5  C1   0.020
 PB4  plan-5  C12  0.020
 PB4  plan-5  C13  0.020
 PB4  plan-5  N4   0.020
 PB4  plan-5  O1   0.020
 PB4  plan-5  HN4  0.020

