# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 10:18:58 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 2,2'-[pyrimidine-4,6-diylbis(iminomethanediyl)]diphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccccc1CNc2cc(NCc3ccccc3O)ncn2
#
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
 2J7  2J7  2,2'-[pyrimidine-4,6-diylbis(iminomethanediyl)]diphenol  ligand  42  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2J7
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
 2J7  C7   C  CH2   0  -0.363  -2.5647   0.4299  -0.5920
 2J7  N8   N  NH1   0  -0.703  -2.3865  -0.9822  -0.2943
 2J7  C9   C  CR6   0   0.533  -1.1544  -1.5601  -0.1941
 2J7  C2   C  CR16  0  -0.254  -6.6724   1.6246  -0.2525
 2J7  C10  C  CR16  0  -0.487   0.0170  -0.8224  -0.0376
 2J7  C4   C  CR6   0   0.321  -4.7391   0.5353   0.6829
 2J7  C6   C  CR16  0  -0.303  -4.6500   1.4799  -1.5246
 2J7  C1   C  CR16  0  -0.269  -5.9703   1.8936  -1.4196
 2J7  C3   C  CR16  0  -0.333  -6.0655   0.9436   0.7916
 2J7  C5   C  CR6   0  -0.025  -4.0146   0.8114  -0.4846
 2J7  C11  C  CR6   0   0.533   1.1973  -1.5519   0.0865
 2J7  N12  N  N     0  -0.470   1.2047  -2.8917   0.0644
 2J7  C13  C  CR16  0   0.058   0.0331  -3.4757  -0.0951
 2J7  N14  N  N     0  -0.470  -1.1453  -2.8996  -0.2300
 2J7  N15  N  NH1   0  -0.702   2.4222  -0.9636   0.2101
 2J7  C16  C  CH2   0  -0.364   2.5835   0.4369   0.5650
 2J7  C17  C  CR6   0  -0.025   4.0283   0.8400   0.4737
 2J7  C18  C  CR16  0  -0.303   4.6586   1.4637   1.5440
 2J7  C19  C  CR16  0  -0.269   5.9726   1.9010   1.4555
 2J7  C20  C  CR16  0  -0.254   6.6726   1.7028   0.2730
 2J7  C21  C  CR16  0  -0.333   6.0712   1.0658  -0.8017
 2J7  C22  C  CR6   0   0.321   4.7522   0.6308  -0.7080
 2J7  O23  O  OH1   0  -0.636   4.2064   0.0308  -1.7863
 2J7  H1   H  HCH2  0   0.272  -1.9833   1.0121   0.1282
 2J7  H2   H  HCH2  0   0.271  -2.1832   0.6838  -1.5860
 2J7  H3   H  HNH1  0   0.396  -3.0786  -1.5979  -0.7000
 2J7  H4   H  HCR6  0   0.257  -7.7037   1.9376  -0.1518
 2J7  H5   H  HCR6  0   0.285   0.0102   0.2561  -0.0141
 2J7  H6   H  HCR6  0   0.257  -4.0917   1.6863  -2.4303
 2J7  H7   H  HCR6  0   0.253  -6.4436   2.4173  -2.2389
 2J7  H8   H  HCR6  0   0.262  -6.6157   0.7228   1.6980
 2J7  H9   H  HCR6  0   0.255   0.0397  -4.5611  -0.1183
 2J7  H10  H  HNH1  0   0.396   3.1230  -1.5873   0.5879
 2J7  H11  H  HCH2  0   0.272   1.9952   1.0405  -0.1315
 2J7  H12  H  HCH2  0   0.271   2.1999   0.6471   1.5684
 2J7  H13  H  HCR6  0   0.257   4.1008   1.6145   2.4610
 2J7  H14  H  HCR6  0   0.253   6.4423   2.3886   2.2989
 2J7  H15  H  HCR6  0   0.257   7.6981   2.0372   0.1837
 2J7  H16  H  HCR6  0   0.262   6.6203   0.9011  -1.7207
 2J7  H17  H  HOH1  0   0.478   3.4152  -0.4642  -1.5186
 2J7  H18  H  HOH1  0   0.478  -3.3869  -0.5731   1.4474
 2J7  O24  O  OH1   0  -0.636  -4.1877  -0.1052   1.7344

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
 2J7  C1   C6   aromatic  1.388  0.020  1.388
 2J7  C1   C2   aromatic  1.388  0.020  1.388
 2J7  C6   C5   aromatic  1.390  0.020  1.390
 2J7  N8   C7   single    1.454  0.020  1.454
 2J7  N8   C9   single    1.365  0.020  1.365
 2J7  C2   C3   aromatic  1.386  0.020  1.386
 2J7  C5   C7   single    1.503  0.020  1.503
 2J7  C5   C4   aromatic  1.402  0.020  1.402
 2J7  C10  C9   aromatic  1.393  0.020  1.393
 2J7  C10  C11  aromatic  1.393  0.020  1.393
 2J7  N15  C11  single    1.365  0.020  1.365
 2J7  N15  C16  single    1.454  0.020  1.454
 2J7  C9   N14  aromatic  1.340  0.020  1.340
 2J7  C3   C4   aromatic  1.392  0.020  1.392
 2J7  C11  N12  aromatic  1.340  0.020  1.340
 2J7  C18  C19  aromatic  1.388  0.020  1.388
 2J7  C18  C17  aromatic  1.390  0.020  1.390
 2J7  C4   O24  single    1.349  0.020  1.349
 2J7  C16  C17  single    1.503  0.020  1.503
 2J7  C19  C20  aromatic  1.388  0.020  1.388
 2J7  C17  C22  aromatic  1.402  0.020  1.402
 2J7  N14  C13  aromatic  1.319  0.020  1.319
 2J7  N12  C13  aromatic  1.319  0.020  1.319
 2J7  C20  C21  aromatic  1.387  0.020  1.387
 2J7  C22  C21  aromatic  1.392  0.020  1.392
 2J7  C22  O23  single    1.349  0.020  1.349
 2J7  C7   H1   single    0.970  0.020  1.090
 2J7  C7   H2   single    0.970  0.020  1.090
 2J7  N8   H3   single    0.890  0.020  1.040
 2J7  C2   H4   single    0.930  0.020  1.080
 2J7  C10  H5   single    0.930  0.020  1.080
 2J7  C6   H6   single    0.930  0.020  1.080
 2J7  C1   H7   single    0.930  0.020  1.080
 2J7  C3   H8   single    0.930  0.020  1.080
 2J7  C13  H9   single    0.930  0.020  1.080
 2J7  N15  H10  single    0.890  0.020  1.040
 2J7  C16  H11  single    0.970  0.020  1.090
 2J7  C16  H12  single    0.970  0.020  1.090
 2J7  C18  H13  single    0.930  0.020  1.080
 2J7  C19  H14  single    0.930  0.020  1.080
 2J7  C20  H15  single    0.930  0.020  1.080
 2J7  C21  H16  single    0.930  0.020  1.080
 2J7  O23  H17  single    0.850  0.020  0.980
 2J7  O24  H18  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
 2J7  H2   C7   H1   106.82  3.000
 2J7  H2   C7   C5   110.02  3.000
 2J7  H1   C7   C5   109.31  3.000
 2J7  H2   C7   N8   111.62  3.000
 2J7  H1   C7   N8   108.48  3.000
 2J7  C5   C7   N8   110.49  3.000
 2J7  H3   N8   C9   112.92  3.000
 2J7  H3   N8   C7   115.17  3.000
 2J7  C9   N8   C7   122.48  3.000
 2J7  N14  C9   C10  121.78  3.000
 2J7  N14  C9   N8   115.31  3.000
 2J7  C10  C9   N8   122.90  3.000
 2J7  H4   C2   C3   119.28  3.000
 2J7  H4   C2   C1   120.26  3.000
 2J7  C3   C2   C1   120.45  3.000
 2J7  H5   C10  C11  121.80  3.000
 2J7  H5   C10  C9   121.77  3.000
 2J7  C11  C10  C9   116.43  3.000
 2J7  O24  C4   C5   122.11  3.000
 2J7  O24  C4   C3   117.90  3.000
 2J7  C5   C4   C3   119.99  3.000
 2J7  H6   C6   C5   118.77  3.000
 2J7  H6   C6   C1   119.78  3.000
 2J7  C5   C6   C1   121.45  3.000
 2J7  H7   C1   C6   120.23  3.000
 2J7  H7   C1   C2   120.62  3.000
 2J7  C6   C1   C2   119.15  3.000
 2J7  H8   C3   C4   119.31  3.000
 2J7  H8   C3   C2   120.53  3.000
 2J7  C4   C3   C2   120.16  3.000
 2J7  C6   C5   C4   118.80  3.000
 2J7  C4   C5   C7   120.54  3.000
 2J7  C6   C5   C7   120.63  3.000
 2J7  N15  C11  N12  115.32  3.000
 2J7  N12  C11  C10  121.79  3.000
 2J7  N15  C11  C10  122.88  3.000
 2J7  C13  N12  C11  116.09  3.000
 2J7  H9   C13  N14  116.11  3.000
 2J7  H9   C13  N12  116.10  3.000
 2J7  N14  C13  N12  127.80  3.000
 2J7  C13  N14  C9   116.11  3.000
 2J7  H10  N15  C16  115.22  3.000
 2J7  H10  N15  C11  112.95  3.000
 2J7  C16  N15  C11  122.48  3.000
 2J7  H12  C16  H11  106.82  3.000
 2J7  H12  C16  C17  109.95  3.000
 2J7  H11  C16  C17  109.30  3.000
 2J7  H12  C16  N15  111.71  3.000
 2J7  H11  C16  N15  108.46  3.000
 2J7  C17  C16  N15  110.50  3.000
 2J7  C22  C17  C18  118.82  3.000
 2J7  C22  C17  C16  120.51  3.000
 2J7  C18  C17  C16  120.63  3.000
 2J7  H13  C18  C19  119.83  3.000
 2J7  H13  C18  C17  118.72  3.000
 2J7  C19  C18  C17  121.45  3.000
 2J7  H14  C19  C20  120.63  3.000
 2J7  H14  C19  C18  120.24  3.000
 2J7  C20  C19  C18  119.13  3.000
 2J7  H15  C20  C21  119.27  3.000
 2J7  H15  C20  C19  120.26  3.000
 2J7  C21  C20  C19  120.47  3.000
 2J7  H16  C21  C22  119.34  3.000
 2J7  H16  C21  C20  120.50  3.000
 2J7  C22  C21  C20  120.16  3.000
 2J7  O23  C22  C21  117.94  3.000
 2J7  O23  C22  C17  122.09  3.000
 2J7  C21  C22  C17  119.97  3.000
 2J7  H17  O23  C22  109.63  3.000
 2J7  H18  O24  C4   109.61  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
 2J7  CONST_01  N12  C11  C10  C9      0.00   0.0  0
 2J7  CONST_02  N12  C13  N14  C9      0.00   0.0  0
 2J7  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 2J7  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 2J7  CONST_05  C13  N14  C9   C10     0.00   0.0  0
 2J7  CONST_06  C13  N12  C11  C10     0.00   0.0  0
 2J7  CONST_07  C1   C6   C5   C4      0.00   0.0  0
 2J7  CONST_08  C1   C2   C3   C4      0.00   0.0  0
 2J7  CONST_09  C3   C2   C1   C6      0.00   0.0  0
 2J7  CONST_10  C3   C4   C5   C6      0.00   0.0  0
 2J7  CONST_11  N14  C9   C10  C11     0.00   0.0  0
 2J7  CONST_12  N14  C13  N12  C11     0.00   0.0  0
 2J7  CONST_13  C20  C19  C18  C17     0.00   0.0  0
 2J7  CONST_14  C20  C21  C22  C17     0.00   0.0  0
 2J7  CONST_15  C21  C20  C19  C18     0.00   0.0  0
 2J7  CONST_16  C21  C22  C17  C18     0.00   0.0  0
 2J7  CONST_17  C22  C17  C18  C19     0.00   0.0  0
 2J7  CONST_18  C22  C21  C20  C19     0.00   0.0  0
 2J7  CONST_19  C1   C6   C5   C7    180.00   0.0  0
 2J7  CONST_20  C3   C4   C5   C7    180.00   0.0  0
 2J7  CONST_21  C11  C10  C9   N8    180.00   0.0  0
 2J7  CONST_22  C13  N14  C9   N8    180.00   0.0  0
 2J7  CONST_23  N15  C11  C10  C9    180.00   0.0  0
 2J7  CONST_24  O24  C4   C3   C2    180.00   0.0  0
 2J7  CONST_25  O24  C4   C5   C6    180.00   0.0  0
 2J7  CONST_26  N15  C11  N12  C13   180.00   0.0  0
 2J7  CONST_27  C19  C18  C17  C16   180.00   0.0  0
 2J7  CONST_28  C21  C22  C17  C16   180.00   0.0  0
 2J7  CONST_29  O23  C22  C17  C18   180.00   0.0  0
 2J7  CONST_30  O23  C22  C21  C20   180.00   0.0  0
 2J7  CONST_31  H9   C13  N14  C9    180.00   0.0  0
 2J7  CONST_32  H6   C6   C1   C2    180.00   0.0  0
 2J7  CONST_33  H4   C2   C3   C4    180.00   0.0  0
 2J7  CONST_34  H8   C3   C2   C1    180.00   0.0  0
 2J7  CONST_35  H7   C1   C2   C3    180.00   0.0  0
 2J7  CONST_36  H5   C10  C11  N12   180.00   0.0  0
 2J7  CONST_37  H14  C19  C18  C17   180.00   0.0  0
 2J7  CONST_38  H16  C21  C22  C17   180.00   0.0  0
 2J7  CONST_39  H15  C20  C19  C18   180.00   0.0  0
 2J7  CONST_40  H13  C18  C19  C20   180.00   0.0  0
 2J7  CONST_44  C16  N15  C11  N12   180.00   0.0  0
 2J7  Var_01    C6   C5   C7   N8   -128.15  30.0  2
 2J7  Var_02    C5   C7   N8   C9   -173.55  30.0  3
 2J7  Var_03    C17  C16  N15  C11  -173.57  30.0  3
 2J7  Var_04    C18  C17  C16  N15  -127.64  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
 2J7  plan-1  N8   0.020
 2J7  plan-1  C9   0.020
 2J7  plan-1  C10  0.020
 2J7  plan-1  C11  0.020
 2J7  plan-1  N12  0.020
 2J7  plan-1  C13  0.020
 2J7  plan-1  N14  0.020
 2J7  plan-1  N15  0.020
 2J7  plan-1  H5   0.020
 2J7  plan-1  H9   0.020
 2J7  plan-2  C7   0.020
 2J7  plan-2  C2   0.020
 2J7  plan-2  C4   0.020
 2J7  plan-2  C6   0.020
 2J7  plan-2  C1   0.020
 2J7  plan-2  C3   0.020
 2J7  plan-2  C5   0.020
 2J7  plan-2  H4   0.020
 2J7  plan-2  H6   0.020
 2J7  plan-2  H7   0.020
 2J7  plan-2  H8   0.020
 2J7  plan-2  O24  0.020
 2J7  plan-3  C16  0.020
 2J7  plan-3  C17  0.020
 2J7  plan-3  C18  0.020
 2J7  plan-3  C19  0.020
 2J7  plan-3  C20  0.020
 2J7  plan-3  C21  0.020
 2J7  plan-3  C22  0.020
 2J7  plan-3  O23  0.020
 2J7  plan-3  H13  0.020
 2J7  plan-3  H14  0.020
 2J7  plan-3  H15  0.020
 2J7  plan-3  H16  0.020
 2J7  plan-4  C7   0.020
 2J7  plan-4  N8   0.020
 2J7  plan-4  C9   0.020
 2J7  plan-4  H3   0.020
 2J7  plan-5  C11  0.020
 2J7  plan-5  N15  0.020
 2J7  plan-5  C16  0.020
 2J7  plan-5  H10  0.020

