# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 20:21:26 2021
#   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  37  24  .  2021-08-03  2022-11-17
;
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  -0.769  -10.0658  10.6998  13.5140
 0BY  N02  N   N     0  -0.522  -11.8140   9.1891  13.2392
 0BY  N03  N   N     0  -0.485  -11.3802  10.2670  15.3051
 0BY  N04  N   NH1   0  -0.752  -13.5043   7.7133  12.9256
 0BY  C05  C   CR16  0  -0.246   -9.2155  10.0423   9.9679
 0BY  C06  C   CR6   0  -0.104   -8.1425  10.9136   9.7976
 0BY  C07  C   CR16  0  -0.249   -7.7455  11.6931  10.8867
 0BY  C08  C   CR16  0  -0.344   -8.4031  11.5962  12.0928
 0BY  C09  C   CR6   0   0.379   -9.4853  10.7184  12.2630
 0BY  C10  C   CR16  0  -0.302   -9.8861   9.9369  11.1722
 0BY  C12  C   CR6   0   0.605  -11.1343  10.0109  14.0195
 0BY  C13  C   CR6   0   0.544  -12.8510   8.5449  13.7752
 0BY  C14  C   CR16  0  -0.437  -13.1927   8.7209  15.1228
 0BY  C15  C   CR16  0  -0.026  -12.4052   9.6050  15.8271
 0BY  C16  C   CR6   0   0.400  -14.6847   7.0114  13.1753
 0BY  C17  C   CR16  0  -0.299  -15.7970   7.6307  13.7434
 0BY  C18  C   CR16  0  -0.248  -16.9652   6.9224  13.9697
 0BY  C19  C   CR16  0  -0.267  -17.0556   5.5875  13.5999
 0BY  C20  C   CR16  0  -0.215  -15.9701   4.9613  13.0076
 0BY  C21  C   CR6   0  -0.110  -14.7950   5.6685  12.8091
 0BY  O25  O   O     0  -0.449   -7.7850  10.2983   7.5317
 0BY  O26  O   OH1   0  -0.598   -6.4834  11.8606   8.4458
 0BY  CL2  CL  CL    0  -0.108  -13.4390   4.8692  12.0887
 0BY  H1   H   HNH1  0   0.412   -9.6422  11.3124  14.1959
 0BY  H2   H   HNH1  0   0.403  -13.0553   7.5756  12.0314
 0BY  H3   H   HCR6  0   0.263   -9.5431   9.4257   9.1412
 0BY  H4   H   HCR6  0   0.268   -6.9177  12.3838  10.8053
 0BY  H5   H   HCR6  0   0.275   -8.0791  12.2104  12.9241
 0BY  H6   H   HCR6  0   0.293  -10.7133   9.2540  11.2632
 0BY  H7   H   HCR6  0   0.289  -14.0041   8.1963  15.6017
 0BY  H8   H   HCR6  0   0.274  -12.6108   9.7877  16.8759
 0BY  H9   H   HCR6  0   0.291  -15.7456   8.6811  13.9979
 0BY  H10  H   HCR6  0   0.270  -17.8132   7.4224  14.4172
 0BY  H11  H   HCR6  0   0.271  -17.9688   5.0321  13.7650
 0BY  H12  H   HCR6  0   0.284  -16.0307   3.9237  12.7087
 0BY  H13  H   HOH1  0   0.485   -6.0780  11.8620   7.5663
 0BY  C11  C   C     0   0.524   -7.4740  10.9760   8.4847

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  double    1.210  0.020  1.210
 0BY  O26  C11  single    1.329  0.020  1.329
 0BY  C11  C06  single    1.475  0.020  1.475
 0BY  C06  C05  aromatic  1.393  0.020  1.393
 0BY  C06  C07  aromatic  1.397  0.020  1.397
 0BY  C05  C10  aromatic  1.382  0.020  1.382
 0BY  C07  C08  aromatic  1.377  0.020  1.377
 0BY  C10  C09  aromatic  1.400  0.020  1.400
 0BY  C08  C09  aromatic  1.404  0.020  1.404
 0BY  CL2  C21  single    1.731  0.020  1.731
 0BY  C09  N01  single    1.379  0.020  1.379
 0BY  N04  C16  single    1.396  0.020  1.396
 0BY  N04  C13  single    1.356  0.020  1.356
 0BY  C21  C16  aromatic  1.396  0.020  1.396
 0BY  C21  C20  aromatic  1.386  0.020  1.386
 0BY  C16  C17  aromatic  1.394  0.020  1.394
 0BY  C20  C19  aromatic  1.386  0.020  1.386
 0BY  N02  C13  aromatic  1.333  0.020  1.333
 0BY  N02  C12  aromatic  1.321  0.020  1.321
 0BY  C13  C14  aromatic  1.401  0.020  1.401
 0BY  C17  C18  aromatic  1.385  0.020  1.385
 0BY  N01  C12  single    1.368  0.020  1.368
 0BY  C19  C18  aromatic  1.388  0.020  1.388
 0BY  C12  N03  aromatic  1.334  0.020  1.334
 0BY  C14  C15  aromatic  1.378  0.020  1.378
 0BY  N03  C15  aromatic  1.327  0.020  1.327
 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
 0BY  O26  H13  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
 0BY  H1   N01  C12  112.55  3.000
 0BY  H1   N01  C09  115.33  3.000
 0BY  C12  N01  C09  132.11  3.000
 0BY  C13  N02  C12  117.59  3.000
 0BY  C15  N03  C12  115.19  3.000
 0BY  H2   N04  C16  117.76  3.000
 0BY  H2   N04  C13  115.09  3.000
 0BY  C16  N04  C13  127.11  3.000
 0BY  H3   C05  C10  118.38  3.000
 0BY  H3   C05  C06  119.76  3.000
 0BY  C10  C05  C06  121.87  3.000
 0BY  C11  C06  C07  122.80  3.000
 0BY  C07  C06  C05  118.21  3.000
 0BY  C11  C06  C05  118.99  3.000
 0BY  H4   C07  C08  118.46  3.000
 0BY  H4   C07  C06  121.02  3.000
 0BY  C08  C07  C06  120.52  3.000
 0BY  H5   C08  C09  119.48  3.000
 0BY  H5   C08  C07  119.30  3.000
 0BY  C09  C08  C07  121.22  3.000
 0BY  C10  C09  C08  118.37  3.000
 0BY  C08  C09  N01  116.28  3.000
 0BY  C10  C09  N01  125.35  3.000
 0BY  H6   C10  C09  120.54  3.000
 0BY  H6   C10  C05  119.65  3.000
 0BY  C09  C10  C05  119.81  3.000
 0BY  N03  C12  N02  126.43  3.000
 0BY  N03  C12  N01  113.79  3.000
 0BY  N02  C12  N01  119.78  3.000
 0BY  C14  C13  N04  124.19  3.000
 0BY  C14  C13  N02  121.03  3.000
 0BY  N04  C13  N02  114.77  3.000
 0BY  H7   C14  C15  121.01  3.000
 0BY  H7   C14  C13  123.33  3.000
 0BY  C15  C14  C13  115.65  3.000
 0BY  H8   C15  C14  119.62  3.000
 0BY  H8   C15  N03  116.28  3.000
 0BY  C14  C15  N03  124.09  3.000
 0BY  C21  C16  C17  118.10  3.000
 0BY  C17  C16  N04  121.62  3.000
 0BY  C21  C16  N04  120.23  3.000
 0BY  H9   C17  C18  119.88  3.000
 0BY  H9   C17  C16  119.29  3.000
 0BY  C18  C17  C16  120.83  3.000
 0BY  H10  C18  C19  120.25  3.000
 0BY  H10  C18  C17  119.52  3.000
 0BY  C19  C18  C17  120.22  3.000
 0BY  H11  C19  C20  119.64  3.000
 0BY  H11  C19  C18  120.54  3.000
 0BY  C20  C19  C18  119.82  3.000
 0BY  H12  C20  C21  119.84  3.000
 0BY  H12  C20  C19  120.51  3.000
 0BY  C21  C20  C19  119.65  3.000
 0BY  CL2  C21  C20  119.22  3.000
 0BY  C20  C21  C16  121.35  3.000
 0BY  CL2  C21  C16  119.43  3.000
 0BY  H13  O26  C11  109.86  3.000
 0BY  O26  C11  O25  122.78  3.000
 0BY  O26  C11  C06  113.10  3.000
 0BY  O25  C11  C06  124.12  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  CONST_41  H13  O26  C11  C06   180.00   0.0  0
 0BY  Var_01    C16  N04  C13  N02  -173.79  30.0  2
 0BY  Var_02    C09  N01  C12  N02    -0.66  30.0  2
 0BY  Var_03    C12  N01  C09  C08   178.11  30.0  2
 0BY  Var_04    C21  C16  N04  C13  -135.11  30.0  2
 0BY  Var_05    O25  C11  C06  C05    -1.08  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
 0BY  plan-1  N01  0.020
 0BY  plan-1  N02  0.020
 0BY  plan-1  N03  0.020
 0BY  plan-1  N04  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-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  N04  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-4  C06  0.020
 0BY  plan-4  O25  0.020
 0BY  plan-4  O26  0.020
 0BY  plan-4  H13  0.020
 0BY  plan-4  C11  0.020

