# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 18:07:04 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-({4-[(2-chlorophenyl)amino]pyrimidin-2-yl}amino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2nccc(Nc3ccccc3Cl)n2)cc1
#
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
 0BY  0BY  '4-({4-[(2-chlorophenyl)amino]pyrimidin-2-yl}amino)benzoic acid'  ligand  36  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0BY
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
 0BY  N01  N   NH1    0  -0.768  -1.2019   0.2080  -0.0525
 0BY  N02  N   N      0  -0.521   0.9687  -0.3790  -0.2172
 0BY  N03  N   N      0  -0.491  -0.7107  -2.0524  -0.3486
 0BY  C05  C   CR16   0  -0.282  -4.7899  -0.7657  -0.0283
 0BY  C06  C   CR6    0  -0.116  -5.3978   0.4594   0.2231
 0BY  C07  C   CR16   0  -0.280  -4.5652   1.5673   0.3721
 0BY  C08  C   CR16   0  -0.348  -3.1921   1.4521   0.2760
 0BY  C09  C   CR6    0   0.354  -2.5890   0.2124   0.0263
 0BY  C10  C   CR16   0  -0.304  -3.4125  -0.9057  -0.1277
 0BY  C12  C   CR6    0   0.610  -0.3006  -0.8000  -0.2147
 0BY  C13  C   CR6    0   0.562   1.9123  -1.2883  -0.3678
 0BY  C14  C   CR16   0  -0.460   1.5945  -2.6536  -0.5132
 0BY  C15  C   CR16   0   0.004   0.2592  -2.9590  -0.4928
 0BY  C16  C   CR6    0   0.430   3.7584   0.3660  -0.2535
 0BY  C17  C   CR16   0  -0.293   3.1374   1.5087  -0.7641
 0BY  C18  C   CR16   0  -0.246   3.7364   2.7521  -0.6499
 0BY  C19  C   CR16   0  -0.277   4.9764   2.8901  -0.0427
 0BY  C20  C   CR16   0  -0.211   5.6185   1.7673   0.4537
 0BY  C21  C   CR6    0  -0.138   5.0098   0.5275   0.3535
 0BY  O25  O   O      0  -0.598  -7.5722  -0.4541   0.1725
 0BY  O26  O   OC    -1  -0.599  -7.3554   1.7268   0.5743
 0BY  CL2  CL  CL     0  -0.116   5.8326  -0.8562   1.0044
 0BY  H1   H   HNH1   0   0.405  -0.7640   1.1107   0.0528
 0BY  H2   H   HNH1   0   0.407   3.8825  -1.6715  -0.3712
 0BY  H3   H   HCR6   0   0.241  -5.4087  -1.6452  -0.1523
 0BY  H4   H   HCR6   0   0.242  -4.9988   2.5386   0.5701
 0BY  H5   H   HCR6   0   0.259  -2.5706   2.3325   0.3986
 0BY  H6   H   HCR6   0   0.276  -2.9825  -1.8743  -0.3235
 0BY  H7   H   HCR6   0   0.280   2.3527  -3.4141  -0.6312
 0BY  H8   H   HCR6   0   0.270  -0.0631  -3.9887  -0.5998
 0BY  H9   H   HCR6   0   0.281   2.1810   1.4199  -1.2539
 0BY  H10  H   HCR6   0   0.265   3.2289   3.6191  -1.0513
 0BY  H11  H   HCR6   0   0.266   5.4455   3.8605   0.0445
 0BY  H12  H   HCR6   0   0.281   6.5865   1.8519   0.9284
 0BY  C11  C   C      0   0.390  -6.9066   0.5884   0.3327
 0BY  N04  N   NH1    0  -0.774   3.2199  -0.9115  -0.3701

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
 0BY  O25  C11  deloc     1.247  0.020  1.247
 0BY  O26  C11  deloc     1.247  0.020  1.247
 0BY  C11  C06  single    1.518  0.020  1.518
 0BY  C06  C05  aromatic  1.391  0.020  1.391
 0BY  C06  C07  aromatic  1.394  0.020  1.394
 0BY  C05  C10  aromatic  1.388  0.020  1.388
 0BY  C07  C08  aromatic  1.381  0.020  1.381
 0BY  C10  C09  aromatic  1.397  0.020  1.397
 0BY  C08  C09  aromatic  1.401  0.020  1.401
 0BY  CL2  C21  single    1.736  0.020  1.736
 0BY  C09  N01  single    1.389  0.020  1.389
 0BY  N04  C16  single    1.391  0.020  1.391
 0BY  N04  C13  single    1.361  0.020  1.361
 0BY  C21  C16  aromatic  1.400  0.020  1.400
 0BY  C21  C20  aromatic  1.385  0.020  1.385
 0BY  C16  C17  aromatic  1.397  0.020  1.397
 0BY  C20  C19  aromatic  1.385  0.020  1.385
 0BY  N02  C13  aromatic  1.319  0.020  1.319
 0BY  N02  C12  aromatic  1.337  0.020  1.337
 0BY  C13  C14  aromatic  1.409  0.020  1.409
 0BY  C17  C18  aromatic  1.385  0.020  1.385
 0BY  N01  C12  single    1.362  0.020  1.362
 0BY  C19  C18  aromatic  1.388  0.020  1.388
 0BY  C12  N03  aromatic  1.325  0.020  1.325
 0BY  C14  C15  aromatic  1.370  0.020  1.370
 0BY  N03  C15  aromatic  1.335  0.020  1.335
 0BY  N01  H1   single    0.860  0.020  1.020
 0BY  N04  H2   single    0.860  0.020  1.020
 0BY  C05  H3   single    0.930  0.020  1.080
 0BY  C07  H4   single    0.930  0.020  1.080
 0BY  C08  H5   single    0.930  0.020  1.080
 0BY  C10  H6   single    0.930  0.020  1.080
 0BY  C14  H7   single    0.930  0.020  1.080
 0BY  C15  H8   single    0.930  0.020  1.080
 0BY  C17  H9   single    0.930  0.020  1.080
 0BY  C18  H10  single    0.930  0.020  1.080
 0BY  C19  H11  single    0.930  0.020  1.080
 0BY  C20  H12  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
 0BY  H1   N01  C12  112.79  3.000
 0BY  H1   N01  C09  115.13  3.000
 0BY  C12  N01  C09  132.05  3.000
 0BY  C13  N02  C12  117.53  3.000
 0BY  C15  N03  C12  115.33  3.000
 0BY  H3   C05  C10  118.49  3.000
 0BY  H3   C05  C06  119.12  3.000
 0BY  C10  C05  C06  122.38  3.000
 0BY  C11  C06  C07  121.23  3.000
 0BY  C07  C06  C05  117.29  3.000
 0BY  C11  C06  C05  121.48  3.000
 0BY  H4   C07  C08  119.07  3.000
 0BY  H4   C07  C06  119.58  3.000
 0BY  C08  C07  C06  121.34  3.000
 0BY  H5   C08  C09  119.45  3.000
 0BY  H5   C08  C07  119.62  3.000
 0BY  C09  C08  C07  120.93  3.000
 0BY  C10  C09  C08  118.30  3.000
 0BY  C08  C09  N01  116.27  3.000
 0BY  C10  C09  N01  125.43  3.000
 0BY  H6   C10  C09  120.27  3.000
 0BY  H6   C10  C05  119.98  3.000
 0BY  C09  C10  C05  119.75  3.000
 0BY  N03  C12  N02  126.25  3.000
 0BY  N03  C12  N01  120.46  3.000
 0BY  N02  C12  N01  113.29  3.000
 0BY  C14  C13  N04  119.00  3.000
 0BY  C14  C13  N02  121.22  3.000
 0BY  N04  C13  N02  119.78  3.000
 0BY  H7   C14  C15  121.92  3.000
 0BY  H7   C14  C13  122.35  3.000
 0BY  C15  C14  C13  115.74  3.000
 0BY  H8   C15  C14  120.00  3.000
 0BY  H8   C15  N03  116.07  3.000
 0BY  C14  C15  N03  123.93  3.000
 0BY  C21  C16  C17  117.47  3.000
 0BY  C17  C16  N04  123.25  3.000
 0BY  C21  C16  N04  119.22  3.000
 0BY  H9   C17  C18  119.67  3.000
 0BY  H9   C17  C16  119.54  3.000
 0BY  C18  C17  C16  120.80  3.000
 0BY  H10  C18  C19  120.12  3.000
 0BY  H10  C18  C17  119.09  3.000
 0BY  C19  C18  C17  120.79  3.000
 0BY  H11  C19  C20  119.82  3.000
 0BY  H11  C19  C18  120.81  3.000
 0BY  C20  C19  C18  119.36  3.000
 0BY  H12  C20  C21  119.68  3.000
 0BY  H12  C20  C19  120.58  3.000
 0BY  C21  C20  C19  119.73  3.000
 0BY  CL2  C21  C20  118.56  3.000
 0BY  C20  C21  C16  121.83  3.000
 0BY  CL2  C21  C16  119.61  3.000
 0BY  O26  C11  O25  126.57  3.000
 0BY  O26  C11  C06  116.68  3.000
 0BY  O25  C11  C06  116.75  3.000
 0BY  H2   N04  C16  115.96  3.000
 0BY  H2   N04  C13  115.01  3.000
 0BY  C16  N04  C13  128.76  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
 0BY  CONST_01  C15  C14  C13  N02     0.00   0.0  0
 0BY  CONST_02  C15  N03  C12  N02     0.00   0.0  0
 0BY  CONST_03  C13  N02  C12  N03     0.00   0.0  0
 0BY  CONST_04  C13  C14  C15  N03     0.00   0.0  0
 0BY  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 0BY  CONST_06  C08  C09  C10  C05     0.00   0.0  0
 0BY  CONST_07  C09  C10  C05  C06     0.00   0.0  0
 0BY  CONST_08  C09  C08  C07  C06     0.00   0.0  0
 0BY  CONST_09  C10  C05  C06  C07     0.00   0.0  0
 0BY  CONST_10  C10  C09  C08  C07     0.00   0.0  0
 0BY  CONST_11  C14  C13  N02  C12     0.00   0.0  0
 0BY  CONST_12  C14  C15  N03  C12     0.00   0.0  0
 0BY  CONST_13  C19  C20  C21  C16     0.00   0.0  0
 0BY  CONST_14  C19  C18  C17  C16     0.00   0.0  0
 0BY  CONST_15  C20  C21  C16  C17     0.00   0.0  0
 0BY  CONST_16  C20  C19  C18  C17     0.00   0.0  0
 0BY  CONST_17  C21  C16  C17  C18     0.00   0.0  0
 0BY  CONST_18  C21  C20  C19  C18     0.00   0.0  0
 0BY  CONST_19  C05  C10  C09  N01   180.00   0.0  0
 0BY  CONST_20  C07  C08  C09  N01   180.00   0.0  0
 0BY  CONST_21  C13  N02  C12  N01   180.00   0.0  0
 0BY  CONST_22  C15  N03  C12  N01   180.00   0.0  0
 0BY  CONST_23  C20  C21  C16  N04   180.00   0.0  0
 0BY  CONST_24  C18  C17  C16  N04   180.00   0.0  0
 0BY  CONST_25  C12  N02  C13  N04   180.00   0.0  0
 0BY  CONST_26  C15  C14  C13  N04   180.00   0.0  0
 0BY  CONST_27  C11  C06  C07  C08   180.00   0.0  0
 0BY  CONST_28  C11  C06  C05  C10   180.00   0.0  0
 0BY  CONST_29  CL2  C21  C16  C17   180.00   0.0  0
 0BY  CONST_30  CL2  C21  C20  C19   180.00   0.0  0
 0BY  CONST_31  H7   C14  C13  N02   180.00   0.0  0
 0BY  CONST_32  H4   C07  C06  C05   180.00   0.0  0
 0BY  CONST_33  H6   C10  C05  C06   180.00   0.0  0
 0BY  CONST_34  H5   C08  C07  C06   180.00   0.0  0
 0BY  CONST_35  H3   C05  C06  C07   180.00   0.0  0
 0BY  CONST_36  H8   C15  N03  C12   180.00   0.0  0
 0BY  CONST_37  H12  C20  C21  C16   180.00   0.0  0
 0BY  CONST_38  H10  C18  C17  C16   180.00   0.0  0
 0BY  CONST_39  H11  C19  C18  C17   180.00   0.0  0
 0BY  CONST_40  H9   C17  C18  C19   180.00   0.0  0
 0BY  Var_01    C16  N04  C13  N02    -1.26  30.0  3
 0BY  Var_02    C09  N01  C12  N02  -178.95  30.0  2
 0BY  Var_03    C12  N01  C09  C08   176.43  30.0  2
 0BY  Var_04    C21  C16  N04  C13   149.17  30.0  2
 0BY  Var_05    O25  C11  C06  C05    -0.72  30.0  2

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
 0BY  plan-1  N01  0.020
 0BY  plan-1  N02  0.020
 0BY  plan-1  N03  0.020
 0BY  plan-1  C12  0.020
 0BY  plan-1  C13  0.020
 0BY  plan-1  C14  0.020
 0BY  plan-1  C15  0.020
 0BY  plan-1  H7   0.020
 0BY  plan-1  H8   0.020
 0BY  plan-1  N04  0.020
 0BY  plan-2  N01  0.020
 0BY  plan-2  C05  0.020
 0BY  plan-2  C06  0.020
 0BY  plan-2  C07  0.020
 0BY  plan-2  C08  0.020
 0BY  plan-2  C09  0.020
 0BY  plan-2  C10  0.020
 0BY  plan-2  H3   0.020
 0BY  plan-2  H4   0.020
 0BY  plan-2  H5   0.020
 0BY  plan-2  H6   0.020
 0BY  plan-2  C11  0.020
 0BY  plan-3  C16  0.020
 0BY  plan-3  C17  0.020
 0BY  plan-3  C18  0.020
 0BY  plan-3  C19  0.020
 0BY  plan-3  C20  0.020
 0BY  plan-3  C21  0.020
 0BY  plan-3  CL2  0.020
 0BY  plan-3  H9   0.020
 0BY  plan-3  H10  0.020
 0BY  plan-3  H11  0.020
 0BY  plan-3  H12  0.020
 0BY  plan-3  N04  0.020
 0BY  plan-4  C06  0.020
 0BY  plan-4  O25  0.020
 0BY  plan-4  O26  0.020
 0BY  plan-4  C11  0.020

