# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 12:43:38 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 2-({2-[(4-carboxyphenyl)amino]pyrimidin-4-yl}amino)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2nccc(Nc3ccccc3C(O)=O)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
 0C9  0C9  '2-({2-[(4-carboxyphenyl)amino]pyrimidin-4-yl}amino)benzoic acid'  ligand  38  26  .  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_0C9
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
 0C9  N01  N  NH1    0  -0.768   1.6257   0.8531   0.5016
 0C9  N02  N  N      0  -0.531  -0.6196   0.9865   0.3081
 0C9  N03  N  N      0  -0.494   0.5737  -0.6150  -0.9734
 0C9  C05  C  CR16   0  -0.281   4.8432  -0.6192  -0.6371
 0C9  C06  C  CR6    0  -0.117   5.7439   0.0114   0.2142
 0C9  C07  C  CR16   0  -0.281   5.2211   0.9069   1.1458
 0C9  C08  C  CR16   0  -0.348   3.8646   1.1568   1.2200
 0C9  C09  C  CR6    0   0.354   2.9645   0.5179   0.3560
 0C9  C10  C  CR16   0  -0.306   3.4767  -0.3828  -0.5821
 0C9  C12  C  CR6    0   0.593   0.4936   0.3729  -0.0933
 0C9  C13  C  CR6    0   0.523  -1.7729   0.5774  -0.2093
 0C9  C14  C  CR16   0  -0.430  -1.8059  -0.4601  -1.1639
 0C9  C15  C  CR16   0  -0.016  -0.5939  -1.0048  -1.4933
 0C9  C16  C  CR6    0   0.276  -4.2075   0.9179  -0.0869
 0C9  C17  C  CR16   0  -0.296  -5.0271   1.9188  -0.6056
 0C9  C18  C  CR16   0  -0.270  -6.3587   1.6663  -0.8925
 0C9  C19  C  CR16   0  -0.250  -6.8685   0.3886  -0.7058
 0C9  C20  C  CR16   0  -0.298  -6.0443  -0.6107  -0.2116
 0C9  C21  C  CR6    0  -0.083  -4.7177  -0.3653   0.1414
 0C9  C22  C  C      0   0.391  -3.9382  -1.4856   0.8268
 0C9  O23  O  OC    -1  -0.594  -4.1457  -2.6349   0.3964
 0C9  O24  O  O      0  -0.583  -3.2085  -1.1549   1.7770
 0C9  O25  O  O      0  -0.599   7.6085  -1.0944  -0.7171
 0C9  O26  O  OC    -1  -0.599   7.9647   0.3722   0.9217
 0C9  H1   H  HNH1   0   0.402   1.4369   1.5757   1.1797
 0C9  H2   H  HNH1   0   0.392  -2.6972   2.0589   0.7706
 0C9  H3   H  HCR6   0   0.239   5.2179  -1.3192  -1.3730
 0C9  H4   H  HCR6   0   0.241   5.8882   1.4174   1.8278
 0C9  H5   H  HCR6   0   0.257   3.4881   1.8572   1.9578
 0C9  H6   H  HCR6   0   0.274   2.8136  -0.8936  -1.2605
 0C9  H7   H  HCR6   0   0.277  -2.7188  -0.8087  -1.6209
 0C9  H8   H  HCR6   0   0.262  -0.5441  -1.8038  -2.2249
 0C9  H9   H  HCR6   0   0.261  -4.6090   2.9016  -0.7881
 0C9  H10  H  HCR6   0   0.255  -6.9861   2.4590  -1.2793
 0C9  H11  H  HCR6   0   0.251  -7.9016   0.1715  -0.9448
 0C9  H12  H  HCR6   0   0.249  -6.4425  -1.6066  -0.0659
 0C9  C11  C  C      0   0.389   7.2348  -0.2608   0.1325
 0C9  N04  N  NH1    0  -0.740  -2.8697   1.2550   0.1860

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
 0C9  O25  C11  deloc     1.248  0.020  1.248
 0C9  O26  C11  deloc     1.247  0.020  1.247
 0C9  C11  C06  single    1.518  0.020  1.518
 0C9  C19  C18  aromatic  1.388  0.020  1.388
 0C9  C19  C20  aromatic  1.386  0.020  1.386
 0C9  C18  C17  aromatic  1.385  0.020  1.385
 0C9  C06  C05  aromatic  1.391  0.020  1.391
 0C9  C06  C07  aromatic  1.394  0.020  1.394
 0C9  C05  C10  aromatic  1.388  0.020  1.388
 0C9  C20  C21  aromatic  1.395  0.020  1.395
 0C9  C07  C08  aromatic  1.381  0.020  1.381
 0C9  C17  C16  aromatic  1.394  0.020  1.394
 0C9  C10  C09  aromatic  1.398  0.020  1.398
 0C9  C21  C16  aromatic  1.400  0.020  1.400
 0C9  C21  C22  single    1.527  0.020  1.527
 0C9  C16  N04  single    1.406  0.020  1.406
 0C9  C08  C09  aromatic  1.402  0.020  1.402
 0C9  C22  O24  deloc     1.243  0.020  1.243
 0C9  C22  O23  deloc     1.245  0.020  1.245
 0C9  C09  N01  single    1.388  0.020  1.388
 0C9  N04  C13  single    1.348  0.020  1.348
 0C9  N02  C13  aromatic  1.329  0.020  1.329
 0C9  N02  C12  aromatic  1.333  0.020  1.333
 0C9  N01  C12  single    1.366  0.020  1.366
 0C9  C13  C14  aromatic  1.410  0.020  1.410
 0C9  C12  N03  aromatic  1.326  0.020  1.326
 0C9  C14  C15  aromatic  1.369  0.020  1.369
 0C9  N03  C15  aromatic  1.336  0.020  1.336
 0C9  N01  H1   single    0.860  0.020  1.020
 0C9  N04  H2   single    0.860  0.020  1.020
 0C9  C05  H3   single    0.930  0.020  1.080
 0C9  C07  H4   single    0.930  0.020  1.080
 0C9  C08  H5   single    0.930  0.020  1.080
 0C9  C10  H6   single    0.930  0.020  1.080
 0C9  C14  H7   single    0.930  0.020  1.080
 0C9  C15  H8   single    0.930  0.020  1.080
 0C9  C17  H9   single    0.930  0.020  1.080
 0C9  C18  H10  single    0.930  0.020  1.080
 0C9  C19  H11  single    0.930  0.020  1.080
 0C9  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
 0C9  H1   N01  C12  112.93  3.000
 0C9  H1   N01  C09  115.09  3.000
 0C9  C12  N01  C09  131.98  3.000
 0C9  C13  N02  C12  117.77  3.000
 0C9  C15  N03  C12  115.02  3.000
 0C9  H3   C05  C10  118.55  3.000
 0C9  H3   C05  C06  119.03  3.000
 0C9  C10  C05  C06  122.42  3.000
 0C9  C11  C06  C07  121.30  3.000
 0C9  C07  C06  C05  117.23  3.000
 0C9  C11  C06  C05  121.47  3.000
 0C9  H4   C07  C08  119.09  3.000
 0C9  H4   C07  C06  119.55  3.000
 0C9  C08  C07  C06  121.36  3.000
 0C9  H5   C08  C09  119.39  3.000
 0C9  H5   C08  C07  119.62  3.000
 0C9  C09  C08  C07  121.00  3.000
 0C9  C10  C09  C08  118.17  3.000
 0C9  C08  C09  N01  116.40  3.000
 0C9  C10  C09  N01  125.42  3.000
 0C9  H6   C10  C09  120.17  3.000
 0C9  H6   C10  C05  120.01  3.000
 0C9  C09  C10  C05  119.82  3.000
 0C9  N03  C12  N02  126.41  3.000
 0C9  N03  C12  N01  120.07  3.000
 0C9  N02  C12  N01  113.52  3.000
 0C9  C14  C13  N04  123.30  3.000
 0C9  C14  C13  N02  120.70  3.000
 0C9  N04  C13  N02  115.92  3.000
 0C9  H7   C14  C15  121.25  3.000
 0C9  H7   C14  C13  122.98  3.000
 0C9  C15  C14  C13  115.77  3.000
 0C9  H8   C15  C14  119.74  3.000
 0C9  H8   C15  N03  115.93  3.000
 0C9  C14  C15  N03  124.33  3.000
 0C9  C21  C16  C17  120.31  3.000
 0C9  C21  C16  N04  122.34  3.000
 0C9  C17  C16  N04  117.35  3.000
 0C9  H9   C17  C18  120.09  3.000
 0C9  H9   C17  C16  119.16  3.000
 0C9  C18  C17  C16  120.76  3.000
 0C9  H10  C18  C19  120.62  3.000
 0C9  H10  C18  C17  119.84  3.000
 0C9  C19  C18  C17  119.53  3.000
 0C9  H11  C19  C20  120.11  3.000
 0C9  H11  C19  C18  120.35  3.000
 0C9  C20  C19  C18  119.54  3.000
 0C9  H12  C20  C21  118.55  3.000
 0C9  H12  C20  C19  119.50  3.000
 0C9  C21  C20  C19  121.93  3.000
 0C9  C22  C21  C20  118.04  3.000
 0C9  C22  C21  C16  124.03  3.000
 0C9  C20  C21  C16  117.83  3.000
 0C9  O24  C22  O23  127.44  3.000
 0C9  O23  C22  C21  115.91  3.000
 0C9  O24  C22  C21  116.59  3.000
 0C9  O26  C11  O25  126.49  3.000
 0C9  O26  C11  C06  116.72  3.000
 0C9  O25  C11  C06  116.79  3.000
 0C9  H2   N04  C16  117.78  3.000
 0C9  H2   N04  C13  115.55  3.000
 0C9  C16  N04  C13  126.61  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
 0C9  CONST_01  C15  C14  C13  N02     0.00   0.0  0
 0C9  CONST_02  C15  N03  C12  N02     0.00   0.0  0
 0C9  CONST_03  C13  N02  C12  N03     0.00   0.0  0
 0C9  CONST_04  C13  C14  C15  N03     0.00   0.0  0
 0C9  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 0C9  CONST_06  C08  C09  C10  C05     0.00   0.0  0
 0C9  CONST_07  C09  C10  C05  C06     0.00   0.0  0
 0C9  CONST_08  C09  C08  C07  C06     0.00   0.0  0
 0C9  CONST_09  C10  C05  C06  C07     0.00   0.0  0
 0C9  CONST_10  C10  C09  C08  C07     0.00   0.0  0
 0C9  CONST_11  C14  C13  N02  C12     0.00   0.0  0
 0C9  CONST_12  C14  C15  N03  C12     0.00   0.0  0
 0C9  CONST_13  C19  C18  C17  C16     0.00   0.0  0
 0C9  CONST_14  C19  C20  C21  C16     0.00   0.0  0
 0C9  CONST_15  C20  C19  C18  C17     0.00   0.0  0
 0C9  CONST_16  C20  C21  C16  C17     0.00   0.0  0
 0C9  CONST_17  C21  C20  C19  C18     0.00   0.0  0
 0C9  CONST_18  C21  C16  C17  C18     0.00   0.0  0
 0C9  CONST_19  C05  C10  C09  N01   180.00   0.0  0
 0C9  CONST_20  C07  C08  C09  N01   180.00   0.0  0
 0C9  CONST_21  C13  N02  C12  N01   180.00   0.0  0
 0C9  CONST_22  C15  N03  C12  N01   180.00   0.0  0
 0C9  CONST_23  C18  C17  C16  N04   180.00   0.0  0
 0C9  CONST_24  C20  C21  C16  N04   180.00   0.0  0
 0C9  CONST_25  C12  N02  C13  N04   180.00   0.0  0
 0C9  CONST_26  C15  C14  C13  N04   180.00   0.0  0
 0C9  CONST_27  C11  C06  C07  C08   180.00   0.0  0
 0C9  CONST_28  C11  C06  C05  C10   180.00   0.0  0
 0C9  CONST_29  C22  C21  C16  C17   180.00   0.0  0
 0C9  CONST_30  C22  C21  C20  C19   180.00   0.0  0
 0C9  CONST_31  H7   C14  C13  N02   180.00   0.0  0
 0C9  CONST_32  H4   C07  C06  C05   180.00   0.0  0
 0C9  CONST_33  H6   C10  C05  C06   180.00   0.0  0
 0C9  CONST_34  H5   C08  C07  C06   180.00   0.0  0
 0C9  CONST_35  H3   C05  C06  C07   180.00   0.0  0
 0C9  CONST_36  H8   C15  N03  C12   180.00   0.0  0
 0C9  CONST_37  H10  C18  C17  C16   180.00   0.0  0
 0C9  CONST_38  H12  C20  C21  C16   180.00   0.0  0
 0C9  CONST_39  H11  C19  C18  C17   180.00   0.0  0
 0C9  CONST_40  H9   C17  C18  C19   180.00   0.0  0
 0C9  Var_01    C16  N04  C13  N02  -171.72  30.0  2
 0C9  Var_02    C09  N01  C12  N02  -178.83  30.0  2
 0C9  Var_03    C12  N01  C09  C08  -175.05  30.0  2
 0C9  Var_04    C17  C16  N04  C13  -129.77  30.0  2
 0C9  Var_05    O25  C11  C06  C05    -1.28  30.0  2
 0C9  Var_06    O24  C22  C21  C16    38.02  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
 0C9  plan-1  N01  0.020
 0C9  plan-1  N02  0.020
 0C9  plan-1  N03  0.020
 0C9  plan-1  C12  0.020
 0C9  plan-1  C13  0.020
 0C9  plan-1  C14  0.020
 0C9  plan-1  C15  0.020
 0C9  plan-1  H7   0.020
 0C9  plan-1  H8   0.020
 0C9  plan-1  N04  0.020
 0C9  plan-2  N01  0.020
 0C9  plan-2  C05  0.020
 0C9  plan-2  C06  0.020
 0C9  plan-2  C07  0.020
 0C9  plan-2  C08  0.020
 0C9  plan-2  C09  0.020
 0C9  plan-2  C10  0.020
 0C9  plan-2  H3   0.020
 0C9  plan-2  H4   0.020
 0C9  plan-2  H5   0.020
 0C9  plan-2  H6   0.020
 0C9  plan-2  C11  0.020
 0C9  plan-3  C16  0.020
 0C9  plan-3  C17  0.020
 0C9  plan-3  C18  0.020
 0C9  plan-3  C19  0.020
 0C9  plan-3  C20  0.020
 0C9  plan-3  C21  0.020
 0C9  plan-3  C22  0.020
 0C9  plan-3  H9   0.020
 0C9  plan-3  H10  0.020
 0C9  plan-3  H11  0.020
 0C9  plan-3  H12  0.020
 0C9  plan-3  N04  0.020
 0C9  plan-4  C21  0.020
 0C9  plan-4  C22  0.020
 0C9  plan-4  O23  0.020
 0C9  plan-4  O24  0.020
 0C9  plan-5  C06  0.020
 0C9  plan-5  O25  0.020
 0C9  plan-5  O26  0.020
 0C9  plan-5  C11  0.020

