# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 02:41:14 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  40  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   0.526   6.3878  -2.0952   0.2431
 NHI  O01   O  O     0  -0.447   7.5785  -1.8911   0.1788
 NHI  N02   N  N     0  -0.532   0.5293   1.1539  -0.0345
 NHI  O02   O  OH1   0  -0.597   5.8722  -3.3084   0.4038
 NHI  N03   N  N     0  -0.489  -1.4424   2.4667  -0.1651
 NHI  C05   C  CR16  0  -0.246  -5.1800   0.4228   0.0471
 NHI  C06   C  CR6   0  -0.103  -5.5372  -0.9212   0.1239
 NHI  C07   C  CR16  0  -0.248  -4.5173  -1.8738   0.1808
 NHI  C08   C  CR16  0  -0.346  -3.1957  -1.4860   0.1605
 NHI  C09   C  CR6   0   0.381  -2.8381  -0.1311   0.0806
 NHI  C10   C  CR16  0  -0.300  -3.8580   0.8263   0.0241
 NHI  C12   C  CR6   0   0.630  -0.7960   1.3204  -0.0495
 NHI  C13   C  CR6   0   0.583   1.2792   2.2339  -0.1503
 NHI  C14   C  CR16  0  -0.461   0.6990   3.5114  -0.2819
 NHI  C15   C  CR16  0   0.008  -0.6697   3.5507  -0.2805
 NHI  C16   C  CR6   0   0.377   3.4772   1.0379  -0.0424
 NHI  C17   C  CR16  0  -0.350   4.8516   1.2991  -0.1482
 NHI  C18   C  CR16  0  -0.244   5.7739   0.2818  -0.0525
 NHI  C19   C  CR6   0  -0.101   5.3633  -1.0368   0.1505
 NHI  C20   C  CR16  0  -0.249   3.9988  -1.2947   0.2579
 NHI  C21   C  CR16  0  -0.298   3.0606  -0.2813   0.1651
 NHI  O25   O  O     0  -0.449  -7.8686  -0.4706   0.1056
 NHI  O26   O  OH1   0  -0.598  -7.1797  -2.5881   0.2069
 NHI  HN01  H  HNH1  0   0.415  -0.8805  -0.6583   0.1387
 NHI  HO02  H  HOH1  0   0.486   6.5838  -3.9630   0.4601
 NHI  HN04  H  HNH1  0   0.423   3.1159   3.0128  -0.2671
 NHI  H05   H  HCR6  0   0.264  -5.9507   1.1807   0.0045
 NHI  H07   H  HCR6  0   0.267  -4.7424  -2.9296   0.2412
 NHI  H08   H  HCR6  0   0.276  -2.4214  -2.2423   0.2042
 NHI  H10   H  HCR6  0   0.291  -3.6192   1.8745  -0.0384
 NHI  H14   H  HCR6  0   0.286   1.2941   4.4081  -0.3795
 NHI  H15   H  HCR6  0   0.275  -1.1869   4.4982  -0.3780
 NHI  H17   H  HCR6  0   0.277   5.1937   2.3142  -0.3116
 NHI  H18   H  HCR6  0   0.267   6.8261   0.5158  -0.1420
 NHI  H20   H  HCR6  0   0.267   3.6400  -2.3017   0.4211
 NHI  H21   H  HCR6  0   0.297   2.0141  -0.5160   0.2554
 NHI  HO26  H  HOH1  0   0.485  -8.1318  -2.7656   0.2160
 NHI  N04   N  NH1   0  -0.778   2.6368   2.1327  -0.1495
 NHI  N01   N  NH1   0  -0.771  -1.4864   0.1455   0.0676
 NHI  C11   C  C     0   0.524  -6.9679  -1.2780   0.1433

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   double    1.210  0.020  1.210
 NHI  O02  C01   single    1.328  0.020  1.328
 NHI  C01  C19   single    1.476  0.020  1.476
 NHI  C09  N01   single    1.380  0.020  1.380
 NHI  N01  C12   single    1.368  0.020  1.368
 NHI  N01  HN01  single    0.860  0.020  1.020
 NHI  N02  C13   aromatic  1.320  0.020  1.320
 NHI  N02  C12   aromatic  1.336  0.020  1.336
 NHI  O02  HO02  single    0.850  0.020  0.980
 NHI  C12  N03   aromatic  1.321  0.020  1.321
 NHI  N03  C15   aromatic  1.336  0.020  1.336
 NHI  C16  N04   single    1.384  0.020  1.384
 NHI  N04  C13   single    1.361  0.020  1.361
 NHI  N04  HN04  single    0.860  0.020  1.020
 NHI  C06  C05   aromatic  1.393  0.020  1.393
 NHI  C05  C10   aromatic  1.382  0.020  1.382
 NHI  C05  H05   single    0.930  0.020  1.080
 NHI  C11  C06   single    1.475  0.020  1.475
 NHI  C06  C07   aromatic  1.397  0.020  1.397
 NHI  C07  C08   aromatic  1.378  0.020  1.378
 NHI  C07  H07   single    0.930  0.020  1.080
 NHI  C08  C09   aromatic  1.404  0.020  1.404
 NHI  C08  H08   single    0.930  0.020  1.080
 NHI  C10  C09   aromatic  1.400  0.020  1.400
 NHI  C10  H10   single    0.930  0.020  1.080
 NHI  O25  C11   double    1.210  0.020  1.210
 NHI  O26  C11   single    1.329  0.020  1.329
 NHI  C13  C14   aromatic  1.409  0.020  1.409
 NHI  C14  C15   aromatic  1.369  0.020  1.369
 NHI  C14  H14   single    0.930  0.020  1.080
 NHI  C15  H15   single    0.930  0.020  1.080
 NHI  C21  C16   aromatic  1.399  0.020  1.399
 NHI  C17  C16   aromatic  1.403  0.020  1.403
 NHI  C18  C17   aromatic  1.376  0.020  1.376
 NHI  C17  H17   single    0.930  0.020  1.080
 NHI  C19  C18   aromatic  1.396  0.020  1.396
 NHI  C18  H18   single    0.930  0.020  1.080
 NHI  C19  C20   aromatic  1.393  0.020  1.393
 NHI  C20  C21   aromatic  1.384  0.020  1.384
 NHI  C20  H20   single    0.930  0.020  1.080
 NHI  C21  H21   single    0.930  0.020  1.080
 NHI  O26  HO26  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
 NHI  C19   C01  O02  113.16  3.000
 NHI  C19   C01  O01  123.98  3.000
 NHI  O02   C01  O01  122.86  3.000
 NHI  C13   N02  C12  117.43  3.000
 NHI  HO02  O02  C01  109.83  3.000
 NHI  C15   N03  C12  115.38  3.000
 NHI  H05   C05  C10  118.44  3.000
 NHI  H05   C05  C06  119.70  3.000
 NHI  C10   C05  C06  121.86  3.000
 NHI  C11   C06  C07  122.88  3.000
 NHI  C07   C06  C05  118.24  3.000
 NHI  C11   C06  C05  118.89  3.000
 NHI  H07   C07  C08  118.39  3.000
 NHI  H07   C07  C06  121.08  3.000
 NHI  C08   C07  C06  120.53  3.000
 NHI  H08   C08  C09  119.61  3.000
 NHI  H08   C08  C07  119.25  3.000
 NHI  C09   C08  C07  121.14  3.000
 NHI  C10   C09  C08  118.47  3.000
 NHI  C10   C09  N01  125.19  3.000
 NHI  C08   C09  N01  116.34  3.000
 NHI  H10   C10  C09  120.43  3.000
 NHI  H10   C10  C05  119.81  3.000
 NHI  C09   C10  C05  119.76  3.000
 NHI  N03   C12  N02  126.48  3.000
 NHI  N03   C12  N01  120.39  3.000
 NHI  N02   C12  N01  113.12  3.000
 NHI  C14   C13  N04  118.56  3.000
 NHI  C14   C13  N02  121.07  3.000
 NHI  N04   C13  N02  120.37  3.000
 NHI  H14   C14  C15  121.79  3.000
 NHI  H14   C14  C13  122.27  3.000
 NHI  C15   C14  C13  115.94  3.000
 NHI  H15   C15  C14  120.14  3.000
 NHI  H15   C15  N03  116.17  3.000
 NHI  C14   C15  N03  123.70  3.000
 NHI  C21   C16  C17  118.58  3.000
 NHI  C17   C16  N04  116.21  3.000
 NHI  C21   C16  N04  125.21  3.000
 NHI  H17   C17  C18  119.42  3.000
 NHI  H17   C17  C16  119.67  3.000
 NHI  C18   C17  C16  120.90  3.000
 NHI  H18   C18  C19  120.17  3.000
 NHI  H18   C18  C17  119.09  3.000
 NHI  C19   C18  C17  120.74  3.000
 NHI  C20   C19  C18  118.32  3.000
 NHI  C20   C19  C01  122.85  3.000
 NHI  C18   C19  C01  118.84  3.000
 NHI  H20   C20  C21  117.84  3.000
 NHI  H20   C20  C19  120.61  3.000
 NHI  C21   C20  C19  121.55  3.000
 NHI  H21   C21  C20  119.59  3.000
 NHI  H21   C21  C16  120.50  3.000
 NHI  C20   C21  C16  119.91  3.000
 NHI  HO26  O26  C11  109.74  3.000
 NHI  HN04  N04  C16  114.25  3.000
 NHI  HN04  N04  C13  114.11  3.000
 NHI  C16   N04  C13  131.63  3.000
 NHI  HN01  N01  C12  112.78  3.000
 NHI  HN01  N01  C09  115.33  3.000
 NHI  C12   N01  C09  131.87  3.000
 NHI  O26   C11  O25  122.73  3.000
 NHI  O26   C11  C06  113.20  3.000
 NHI  O25   C11  C06  124.07  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  CONST_41  HO26  O26  C11  C06   180.00   0.0  0
 NHI  CONST_42  HO02  O02  C01  C19   180.00   0.0  0
 NHI  Var_01    C16   N04  C13  N02    -0.05  30.0  2
 NHI  Var_02    C09   N01  C12  N02  -179.12  30.0  2
 NHI  Var_03    C12   N01  C09  C08   177.26  30.0  2
 NHI  Var_04    C21   C16  N04  C13    -3.41  30.0  2
 NHI  Var_05    C18   C19  C01  O01     1.46  30.0  2
 NHI  Var_06    O25   C11  C06  C05    -0.54  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
 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-4  HO02  0.020
 NHI  plan-5  C06   0.020
 NHI  plan-5  O25   0.020
 NHI  plan-5  O26   0.020
 NHI  plan-5  HO26  0.020
 NHI  plan-5  C11   0.020

