# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:35:02 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4,4'-(pyrimidine-2,4-diyldiimino)dibenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(Nc2ccnc(Nc3ccc(cc3)C(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
 NHI  NHI  '4,4'-(pyrimidine-2,4-diyldiimino)dibenzoic acid'  ligand  38  26  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NHI
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
 NHI  C01   C  C      0   0.333   6.4381  -2.1269   0.2587
 NHI  O01   O  O      0  -0.365   7.6287  -1.8030   0.0786
 NHI  N02   N  N      0  -0.493   0.5313   1.1420  -0.0138
 NHI  O02   O  OC    -1  -0.676   6.0099  -3.2694   0.5165
 NHI  N03   N  N      0  -0.431  -1.4517   2.4440  -0.1292
 NHI  C05   C  CR16   0  -0.363  -5.1910   0.3458   0.0147
 NHI  C06   C  CR6    0   0.107  -5.5423  -0.9986   0.0683
 NHI  C07   C  CR16   0  -0.385  -4.5046  -1.9276   0.1163
 NHI  C08   C  CR16   0  -0.187  -3.1815  -1.5291   0.1104
 NHI  C09   C  CR6    0   0.197  -2.8379  -0.1718   0.0580
 NHI  C10   C  CR16   0  -0.169  -3.8691   0.7700   0.0093
 NHI  C12   C  CR6    0   0.564  -0.7978   1.2977  -0.0298
 NHI  C13   C  CR6    0   0.430   1.2743   2.2293  -0.1161
 NHI  C14   C  CR16   0  -0.338   0.6812   3.5064  -0.2319
 NHI  C15   C  CR16   0  -0.020  -0.6840   3.5335  -0.2293
 NHI  C16   C  CR6    0   0.280   3.4865   1.0463  -0.0220
 NHI  C17   C  CR16   0  -0.268   4.8508   1.3123  -0.1893
 NHI  C18   C  CR16   0  -0.316   5.7864   0.2996  -0.1024
 NHI  C19   C  CR6    0  -0.144   5.4077  -1.0159   0.1585
 NHI  C20   C  CR16   0  -0.310   4.0506  -1.2689   0.3231
 NHI  C21   C  CR16   0  -0.295   3.0924  -0.2686   0.2356
 NHI  O25   O  O      0  -0.546  -7.8550  -0.5371   0.0301
 NHI  O26   O  OC    -1  -0.729  -7.2050  -2.6661   0.1583
 NHI  HN01  H  HNH1   0   0.392  -0.8685  -0.6791   0.1268
 NHI  HN04  H  HNH1   0   0.337   3.0996   3.0225  -0.2441
 NHI  H05   H  HCR6   0   0.214  -5.9736   1.0926  -0.0233
 NHI  H07   H  HCR6   0   0.212  -4.7360  -2.9840   0.1601
 NHI  H08   H  HCR6   0   0.272  -2.3977  -2.2778   0.1463
 NHI  H10   H  HCR6   0   0.275  -3.6423   1.8221  -0.0324
 NHI  H14   H  HCR6   0   0.271   1.2690   4.4089  -0.3196
 NHI  H15   H  HCR6   0   0.289  -1.2076   4.4790  -0.3143
 NHI  H17   H  HCR6   0   0.263   5.1772   2.3255  -0.3940
 NHI  H18   H  HCR6   0   0.225   6.8331   0.5376  -0.2395
 NHI  H20   H  HCR6   0   0.226   3.7235  -2.2799   0.5286
 NHI  H21   H  HCR6   0   0.263   2.0516  -0.5094   0.3720
 NHI  N04   N  NH1    0  -0.666   2.6282   2.1401  -0.1164
 NHI  N01   N  NH1    0  -0.786  -1.4788   0.1211   0.0630
 NHI  C11   C  C      0   0.334  -6.9964  -1.4396   0.0807

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
 NHI  O01  C01   deloc     1.247  0.020  1.247
 NHI  O02  C01   deloc     1.247  0.020  1.247
 NHI  C01  C19   single    1.519  0.020  1.519
 NHI  C09  N01   single    1.390  0.020  1.390
 NHI  N01  C12   single    1.363  0.020  1.363
 NHI  N01  HN01  single    0.860  0.020  1.020
 NHI  N02  C13   aromatic  1.321  0.020  1.321
 NHI  N02  C12   aromatic  1.338  0.020  1.338
 NHI  C12  N03   aromatic  1.323  0.020  1.323
 NHI  N03  C15   aromatic  1.337  0.020  1.337
 NHI  C16  N04   single    1.393  0.020  1.393
 NHI  N04  C13   single    1.357  0.020  1.357
 NHI  N04  HN04  single    0.860  0.020  1.020
 NHI  C06  C05   aromatic  1.391  0.020  1.391
 NHI  C05  C10   aromatic  1.388  0.020  1.388
 NHI  C05  H05   single    0.930  0.020  1.080
 NHI  C11  C06   single    1.520  0.020  1.520
 NHI  C06  C07   aromatic  1.394  0.020  1.394
 NHI  C07  C08   aromatic  1.382  0.020  1.382
 NHI  C07  H07   single    0.930  0.020  1.080
 NHI  C08  C09   aromatic  1.401  0.020  1.401
 NHI  C08  H08   single    0.930  0.020  1.080
 NHI  C10  C09   aromatic  1.397  0.020  1.397
 NHI  C10  H10   single    0.930  0.020  1.080
 NHI  O25  C11   deloc     1.247  0.020  1.247
 NHI  O26  C11   deloc     1.247  0.020  1.247
 NHI  C13  C14   aromatic  1.413  0.020  1.413
 NHI  C14  C15   aromatic  1.365  0.020  1.365
 NHI  C14  H14   single    0.930  0.020  1.080
 NHI  C15  H15   single    0.930  0.020  1.080
 NHI  C21  C16   aromatic  1.397  0.020  1.397
 NHI  C17  C16   aromatic  1.400  0.020  1.400
 NHI  C18  C17   aromatic  1.381  0.020  1.381
 NHI  C17  H17   single    0.930  0.020  1.080
 NHI  C19  C18   aromatic  1.394  0.020  1.394
 NHI  C18  H18   single    0.930  0.020  1.080
 NHI  C19  C20   aromatic  1.390  0.020  1.390
 NHI  C20  C21   aromatic  1.388  0.020  1.388
 NHI  C20  H20   single    0.930  0.020  1.080
 NHI  C21  H21   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
 NHI  C19   C01  O02  116.81  3.000
 NHI  C19   C01  O01  116.64  3.000
 NHI  O02   C01  O01  126.56  3.000
 NHI  C13   N02  C12  117.51  3.000
 NHI  C15   N03  C12  115.33  3.000
 NHI  H05   C05  C10  118.52  3.000
 NHI  H05   C05  C06  119.06  3.000
 NHI  C10   C05  C06  122.42  3.000
 NHI  C11   C06  C07  121.25  3.000
 NHI  C07   C06  C05  117.24  3.000
 NHI  C11   C06  C05  121.51  3.000
 NHI  H07   C07  C08  119.11  3.000
 NHI  H07   C07  C06  119.53  3.000
 NHI  C08   C07  C06  121.37  3.000
 NHI  H08   C08  C09  119.53  3.000
 NHI  H08   C08  C07  119.52  3.000
 NHI  C09   C08  C07  120.95  3.000
 NHI  C10   C09  C08  118.24  3.000
 NHI  C10   C09  N01  125.42  3.000
 NHI  C08   C09  N01  116.33  3.000
 NHI  H10   C10  C09  120.28  3.000
 NHI  H10   C10  C05  119.94  3.000
 NHI  C09   C10  C05  119.78  3.000
 NHI  N03   C12  N02  126.33  3.000
 NHI  N03   C12  N01  120.40  3.000
 NHI  N02   C12  N01  113.27  3.000
 NHI  C14   C13  N04  118.58  3.000
 NHI  C14   C13  N02  120.95  3.000
 NHI  N04   C13  N02  120.47  3.000
 NHI  H14   C14  C15  121.83  3.000
 NHI  H14   C14  C13  122.22  3.000
 NHI  C15   C14  C13  115.95  3.000
 NHI  H15   C15  C14  120.01  3.000
 NHI  H15   C15  N03  116.06  3.000
 NHI  C14   C15  N03  123.93  3.000
 NHI  C21   C16  C17  118.41  3.000
 NHI  C17   C16  N04  116.30  3.000
 NHI  C21   C16  N04  125.29  3.000
 NHI  H17   C17  C18  119.55  3.000
 NHI  H17   C17  C16  119.57  3.000
 NHI  C18   C17  C16  120.88  3.000
 NHI  H18   C18  C19  119.61  3.000
 NHI  H18   C18  C17  119.08  3.000
 NHI  C19   C18  C17  121.31  3.000
 NHI  C20   C19  C18  117.34  3.000
 NHI  C20   C19  C01  121.43  3.000
 NHI  C18   C19  C01  121.24  3.000
 NHI  H20   C20  C21  118.46  3.000
 NHI  H20   C20  C19  119.18  3.000
 NHI  C21   C20  C19  122.36  3.000
 NHI  H21   C21  C20  119.87  3.000
 NHI  H21   C21  C16  120.44  3.000
 NHI  C20   C21  C16  119.69  3.000
 NHI  HN04  N04  C16  114.05  3.000
 NHI  HN04  N04  C13  114.13  3.000
 NHI  C16   N04  C13  131.77  3.000
 NHI  HN01  N01  C12  112.77  3.000
 NHI  HN01  N01  C09  115.13  3.000
 NHI  C12   N01  C09  132.08  3.000
 NHI  O26   C11  O25  126.84  3.000
 NHI  O26   C11  C06  116.50  3.000
 NHI  O25   C11  C06  116.66  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
 NHI  CONST_01  C15  C14  C13  N02     0.00   0.0  0
 NHI  CONST_02  C15  N03  C12  N02     0.00   0.0  0
 NHI  CONST_03  C13  N02  C12  N03     0.00   0.0  0
 NHI  CONST_04  C13  C14  C15  N03     0.00   0.0  0
 NHI  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 NHI  CONST_06  C08  C09  C10  C05     0.00   0.0  0
 NHI  CONST_07  C09  C10  C05  C06     0.00   0.0  0
 NHI  CONST_08  C09  C08  C07  C06     0.00   0.0  0
 NHI  CONST_09  C10  C05  C06  C07     0.00   0.0  0
 NHI  CONST_10  C10  C09  C08  C07     0.00   0.0  0
 NHI  CONST_11  C14  C13  N02  C12     0.00   0.0  0
 NHI  CONST_12  C14  C15  N03  C12     0.00   0.0  0
 NHI  CONST_13  C19  C20  C21  C16     0.00   0.0  0
 NHI  CONST_14  C19  C18  C17  C16     0.00   0.0  0
 NHI  CONST_15  C20  C21  C16  C17     0.00   0.0  0
 NHI  CONST_16  C20  C19  C18  C17     0.00   0.0  0
 NHI  CONST_17  C21  C16  C17  C18     0.00   0.0  0
 NHI  CONST_18  C21  C20  C19  C18     0.00   0.0  0
 NHI  CONST_19  C17  C18  C19  C01   180.00   0.0  0
 NHI  CONST_20  C21  C20  C19  C01   180.00   0.0  0
 NHI  CONST_21  C07  C08  C09  N01   180.00   0.0  0
 NHI  CONST_22  C05  C10  C09  N01   180.00   0.0  0
 NHI  CONST_23  C13  N02  C12  N01   180.00   0.0  0
 NHI  CONST_24  C15  N03  C12  N01   180.00   0.0  0
 NHI  CONST_25  C20  C21  C16  N04   180.00   0.0  0
 NHI  CONST_26  C18  C17  C16  N04   180.00   0.0  0
 NHI  CONST_27  C12  N02  C13  N04   180.00   0.0  0
 NHI  CONST_28  C15  C14  C13  N04   180.00   0.0  0
 NHI  CONST_29  C11  C06  C07  C08   180.00   0.0  0
 NHI  CONST_30  C11  C06  C05  C10   180.00   0.0  0
 NHI  CONST_31  H14  C14  C13  N02   180.00   0.0  0
 NHI  CONST_32  H07  C07  C06  C05   180.00   0.0  0
 NHI  CONST_33  H10  C10  C05  C06   180.00   0.0  0
 NHI  CONST_34  H08  C08  C07  C06   180.00   0.0  0
 NHI  CONST_35  H05  C05  C06  C07   180.00   0.0  0
 NHI  CONST_36  H15  C15  N03  C12   180.00   0.0  0
 NHI  CONST_37  H20  C20  C21  C16   180.00   0.0  0
 NHI  CONST_38  H18  C18  C17  C16   180.00   0.0  0
 NHI  CONST_39  H21  C21  C16  C17   180.00   0.0  0
 NHI  CONST_40  H17  C17  C18  C19   180.00   0.0  0
 NHI  Var_01    C16  N04  C13  N02    -0.08  30.0  2
 NHI  Var_02    C09  N01  C12  N02  -178.62  30.0  2
 NHI  Var_03    C12  N01  C09  C08   177.04  30.0  2
 NHI  Var_04    C21  C16  N04  C13    -6.78  30.0  2
 NHI  Var_05    C18  C19  C01  O01    -0.91  30.0  2
 NHI  Var_06    O25  C11  C06  C05     0.53  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
 NHI  plan-1  N02  0.020
 NHI  plan-1  N03  0.020
 NHI  plan-1  C12  0.020
 NHI  plan-1  C13  0.020
 NHI  plan-1  C14  0.020
 NHI  plan-1  C15  0.020
 NHI  plan-1  H14  0.020
 NHI  plan-1  H15  0.020
 NHI  plan-1  N04  0.020
 NHI  plan-1  N01  0.020
 NHI  plan-2  C05  0.020
 NHI  plan-2  C06  0.020
 NHI  plan-2  C07  0.020
 NHI  plan-2  C08  0.020
 NHI  plan-2  C09  0.020
 NHI  plan-2  C10  0.020
 NHI  plan-2  H05  0.020
 NHI  plan-2  H07  0.020
 NHI  plan-2  H08  0.020
 NHI  plan-2  H10  0.020
 NHI  plan-2  N01  0.020
 NHI  plan-2  C11  0.020
 NHI  plan-3  C01  0.020
 NHI  plan-3  C16  0.020
 NHI  plan-3  C17  0.020
 NHI  plan-3  C18  0.020
 NHI  plan-3  C19  0.020
 NHI  plan-3  C20  0.020
 NHI  plan-3  C21  0.020
 NHI  plan-3  H17  0.020
 NHI  plan-3  H18  0.020
 NHI  plan-3  H20  0.020
 NHI  plan-3  H21  0.020
 NHI  plan-3  N04  0.020
 NHI  plan-4  C01  0.020
 NHI  plan-4  O01  0.020
 NHI  plan-4  O02  0.020
 NHI  plan-4  C19  0.020
 NHI  plan-5  C06  0.020
 NHI  plan-5  O25  0.020
 NHI  plan-5  O26  0.020
 NHI  plan-5  C11  0.020

