# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 22:54:13 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: 2,6-bis[(4,6-dimethoxypyrimidin-2-yl)oxy]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)nc(Oc2cccc(Oc3nc(OC)cc(OC)n3)c2C(O)=O)n1
#
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
 6QL  6QL  '2,6-bis[(4,6-dimethoxypyrimidin-2-yl)oxy]benzoic acid'  ligand  49  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6QL
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
 6QL  O01  O  OH1   0  -0.579  -1.0546  -0.6122  -1.6803
 6QL  C02  C  C     0   0.519   0.0867  -0.1835  -1.1685
 6QL  C03  C  CR6   0  -0.165   0.0339  -0.0553   0.3144
 6QL  C04  C  CR6   0   0.372   1.1079  -0.4945   1.0864
 6QL  O05  O  O2    0  -0.492   2.1551  -1.1341   0.4719
 6QL  C06  C  CR6   0   0.599   3.2231  -0.4065   0.1048
 6QL  N07  N  N     0  -0.507   4.1302  -1.0993  -0.5483
 6QL  C08  C  CR6   0   0.569   5.2051  -0.4173  -0.9220
 6QL  O09  O  O2    0  -0.460   6.1651  -1.0384  -1.5856
 6QL  C10  C  CH3   0  -0.420   6.0068  -2.4223  -1.8845
 6QL  C11  C  CR16  0  -0.509   5.3751   0.9352  -0.6482
 6QL  C12  C  CR6   0   0.572   4.3377   1.5282   0.0583
 6QL  O13  O  O2    0  -0.460   4.4381   2.8106   0.3627
 6QL  C14  C  CH3   0  -0.417   3.3583   3.4282   1.0595
 6QL  N15  N  N     0  -0.501   3.2571   0.8600   0.4399
 6QL  C16  C  CR16  0  -0.300   1.0984  -0.3919   2.4638
 6QL  C17  C  CR16  0  -0.262   0.0083   0.1886   3.0924
 6QL  C18  C  CR16  0  -0.297  -1.0642   0.6575   2.3519
 6QL  C19  C  CR6   0   0.383  -1.0471   0.5235   0.9761
 6QL  O20  O  O2    0  -0.492  -2.0646   1.0709   0.2351
 6QL  C21  C  CR6   0   0.598  -3.1916   0.3623   0.0533
 6QL  N22  N  N     0  -0.503  -3.3028  -0.7963   0.6559
 6QL  C23  C  CR6   0   0.573  -4.4383  -1.4496   0.4435
 6QL  O24  O  O2    0  -0.459  -4.6190  -2.6249   1.0200
 6QL  C25  C  CH3   0  -0.417  -3.5869  -3.1355   1.8609
 6QL  C26  C  CR16  0  -0.507  -5.4508  -0.9496  -0.3637
 6QL  C27  C  CR6   0   0.569  -5.1935   0.2928  -0.9324
 6QL  O28  O  O2    0  -0.460  -6.1224   0.8206  -1.7106
 6QL  C29  C  CH3   0  -0.421  -5.8699   2.0854  -2.3167
 6QL  N30  N  N     0  -0.504  -4.0647   0.9593  -0.7278
 6QL  O31  O  O     0  -0.418   1.0672   0.0591  -1.8246
 6QL  H1   H  HOH1  0   0.491  -0.9933  -0.6470  -2.6478
 6QL  H2   H  HCH3  0   0.252   6.9003  -2.7074  -2.4329
 6QL  H3   H  HCH3  0   0.237   5.9311  -3.0237  -0.9787
 6QL  H4   H  HCH3  0   0.237   5.1291  -2.6017  -2.5052
 6QL  H5   H  HCR6  0   0.283   6.2514   1.4829  -0.9625
 6QL  H6   H  HCH3  0   0.237   3.1634   2.9418   2.0147
 6QL  H7   H  HCH3  0   0.250   3.6687   4.4552   1.2295
 6QL  H8   H  HCH3  0   0.237   2.4437   3.4169   0.4670
 6QL  H9   H  HCR6  0   0.280   1.9371  -0.7625   3.0378
 6QL  H10  H  HCR6  0   0.279  -0.0029   0.2813   4.1697
 6QL  H11  H  HCR6  0   0.281  -1.9089   1.1267   2.8380
 6QL  H12  H  HCH3  0   0.237  -3.3927  -2.4741   2.7047
 6QL  H13  H  HCH3  0   0.251  -3.9526  -4.0913   2.2249
 6QL  H14  H  HCH3  0   0.238  -2.6585  -3.2857   1.3109
 6QL  H15  H  HCR6  0   0.284  -6.3733  -1.4842  -0.5360
 6QL  H16  H  HCH3  0   0.252  -6.7518   2.3061  -2.9115
 6QL  H17  H  HCH3  0   0.237  -5.7299   2.8674  -1.5706
 6QL  H18  H  HCH3  0   0.237  -4.9940   2.0519  -2.9639

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
 6QL  C14  O13  single    1.426  0.020  1.426
 6QL  O13  C12  single    1.322  0.020  1.322
 6QL  C25  O24  single    1.426  0.020  1.426
 6QL  O24  C23  single    1.321  0.020  1.321
 6QL  C12  N15  aromatic  1.327  0.020  1.327
 6QL  C12  C11  aromatic  1.388  0.020  1.388
 6QL  N15  C06  aromatic  1.311  0.020  1.311
 6QL  O31  C02  double    1.204  0.020  1.204
 6QL  C11  C08  aromatic  1.390  0.020  1.390
 6QL  C23  C26  aromatic  1.388  0.020  1.388
 6QL  C23  N22  aromatic  1.327  0.020  1.327
 6QL  C26  C27  aromatic  1.390  0.020  1.390
 6QL  C06  O05  single    1.343  0.020  1.343
 6QL  C06  N07  aromatic  1.315  0.020  1.315
 6QL  C02  O01  single    1.322  0.020  1.322
 6QL  C02  C03  single    1.489  0.020  1.489
 6QL  O05  C04  single    1.372  0.020  1.372
 6QL  N22  C21  aromatic  1.311  0.020  1.311
 6QL  C08  N07  aromatic  1.327  0.020  1.327
 6QL  C08  O09  single    1.322  0.020  1.322
 6QL  C27  O28  single    1.322  0.020  1.322
 6QL  C27  N30  aromatic  1.327  0.020  1.327
 6QL  O28  C29  single    1.425  0.020  1.425
 6QL  C04  C03  aromatic  1.394  0.020  1.394
 6QL  C04  C16  aromatic  1.381  0.020  1.381
 6QL  C03  C19  aromatic  1.393  0.020  1.393
 6QL  C10  O09  single    1.425  0.020  1.425
 6QL  C21  N30  aromatic  1.315  0.020  1.315
 6QL  C21  O20  single    1.344  0.020  1.344
 6QL  C16  C17  aromatic  1.386  0.020  1.386
 6QL  C19  O20  single    1.373  0.020  1.373
 6QL  C19  C18  aromatic  1.382  0.020  1.382
 6QL  C17  C18  aromatic  1.385  0.020  1.385
 6QL  O01  H1   single    0.850  0.020  0.980
 6QL  C10  H2   single    0.970  0.020  1.090
 6QL  C10  H3   single    0.970  0.020  1.090
 6QL  C10  H4   single    0.970  0.020  1.090
 6QL  C11  H5   single    0.930  0.020  1.080
 6QL  C14  H6   single    0.970  0.020  1.090
 6QL  C14  H7   single    0.970  0.020  1.090
 6QL  C14  H8   single    0.970  0.020  1.090
 6QL  C16  H9   single    0.930  0.020  1.080
 6QL  C17  H10  single    0.930  0.020  1.080
 6QL  C18  H11  single    0.930  0.020  1.080
 6QL  C25  H12  single    0.970  0.020  1.090
 6QL  C25  H13  single    0.970  0.020  1.090
 6QL  C25  H14  single    0.970  0.020  1.090
 6QL  C26  H15  single    0.930  0.020  1.080
 6QL  C29  H16  single    0.970  0.020  1.090
 6QL  C29  H17  single    0.970  0.020  1.090
 6QL  C29  H18  single    0.970  0.020  1.090

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
 6QL  H1   O01  C02  110.07  3.000
 6QL  O31  C02  C03  123.64  3.000
 6QL  C03  C02  O01  112.50  3.000
 6QL  O31  C02  O01  123.86  3.000
 6QL  C19  C03  C04  117.76  3.000
 6QL  C19  C03  C02  122.42  3.000
 6QL  C04  C03  C02  119.81  3.000
 6QL  C16  C04  O05  119.11  3.000
 6QL  C16  C04  C03  121.58  3.000
 6QL  O05  C04  C03  119.13  3.000
 6QL  C06  O05  C04  118.47  3.000
 6QL  N15  C06  N07  128.19  3.000
 6QL  N07  C06  O05  113.51  3.000
 6QL  N15  C06  O05  118.30  3.000
 6QL  C08  N07  C06  115.34  3.000
 6QL  C11  C08  O09  117.85  3.000
 6QL  O09  C08  N07  119.23  3.000
 6QL  C11  C08  N07  122.93  3.000
 6QL  C10  O09  C08  118.75  3.000
 6QL  H4   C10  H3   109.06  3.000
 6QL  H4   C10  H2   109.37  3.000
 6QL  H3   C10  H2   109.38  3.000
 6QL  H4   C10  O09  111.65  3.000
 6QL  H3   C10  O09  111.68  3.000
 6QL  H2   C10  O09  105.63  3.000
 6QL  H5   C11  C12  122.54  3.000
 6QL  H5   C11  C08  122.35  3.000
 6QL  C12  C11  C08  115.11  3.000
 6QL  N15  C12  O13  118.97  3.000
 6QL  N15  C12  C11  122.68  3.000
 6QL  O13  C12  C11  118.35  3.000
 6QL  C14  O13  C12  118.37  3.000
 6QL  H8   C14  H7   109.56  3.000
 6QL  H8   C14  H6   108.77  3.000
 6QL  H7   C14  H6   109.63  3.000
 6QL  H8   C14  O13  111.44  3.000
 6QL  H7   C14  O13  105.64  3.000
 6QL  H6   C14  O13  111.75  3.000
 6QL  C12  N15  C06  115.74  3.000
 6QL  H9   C16  C17  120.85  3.000
 6QL  H9   C16  C04  119.89  3.000
 6QL  C17  C16  C04  119.26  3.000
 6QL  H10  C17  C18  119.70  3.000
 6QL  H10  C17  C16  119.74  3.000
 6QL  C18  C17  C16  120.56  3.000
 6QL  H11  C18  C19  119.93  3.000
 6QL  H11  C18  C17  120.75  3.000
 6QL  C19  C18  C17  119.32  3.000
 6QL  O20  C19  C18  119.31  3.000
 6QL  C18  C19  C03  121.50  3.000
 6QL  O20  C19  C03  118.98  3.000
 6QL  C21  O20  C19  118.98  3.000
 6QL  N30  C21  N22  128.19  3.000
 6QL  N30  C21  O20  113.44  3.000
 6QL  N22  C21  O20  118.37  3.000
 6QL  C23  N22  C21  115.73  3.000
 6QL  C26  C23  O24  118.32  3.000
 6QL  C26  C23  N22  122.67  3.000
 6QL  O24  C23  N22  119.01  3.000
 6QL  C25  O24  C23  118.48  3.000
 6QL  H14  C25  H13  109.56  3.000
 6QL  H14  C25  H12  108.83  3.000
 6QL  H13  C25  H12  109.55  3.000
 6QL  H14  C25  O24  111.63  3.000
 6QL  H13  C25  O24  105.61  3.000
 6QL  H12  C25  O24  111.62  3.000
 6QL  H15  C26  C27  122.35  3.000
 6QL  H15  C26  C23  122.51  3.000
 6QL  C27  C26  C23  115.14  3.000
 6QL  N30  C27  O28  119.22  3.000
 6QL  N30  C27  C26  122.91  3.000
 6QL  O28  C27  C26  117.88  3.000
 6QL  C29  O28  C27  118.70  3.000
 6QL  H18  C29  H17  108.99  3.000
 6QL  H18  C29  H16  109.49  3.000
 6QL  H17  C29  H16  109.47  3.000
 6QL  H18  C29  O28  111.58  3.000
 6QL  H17  C29  O28  111.62  3.000
 6QL  H16  C29  O28  105.62  3.000
 6QL  C27  N30  C21  115.36  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
 6QL  CONST_01  C17  C16  C04  C03     0.00   0.0  0
 6QL  CONST_02  C17  C18  C19  C03     0.00   0.0  0
 6QL  CONST_03  C18  C19  C03  C04     0.00   0.0  0
 6QL  CONST_04  C18  C17  C16  C04     0.00   0.0  0
 6QL  CONST_05  C11  C12  N15  C06     0.00   0.0  0
 6QL  CONST_06  C11  C08  N07  C06     0.00   0.0  0
 6QL  CONST_07  C12  N15  C06  N07     0.00   0.0  0
 6QL  CONST_08  C12  C11  C08  N07     0.00   0.0  0
 6QL  CONST_09  N15  C12  C11  C08     0.00   0.0  0
 6QL  CONST_10  N15  C06  N07  C08     0.00   0.0  0
 6QL  CONST_11  C19  C03  C04  C16     0.00   0.0  0
 6QL  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 6QL  CONST_13  C26  C23  N22  C21     0.00   0.0  0
 6QL  CONST_14  C26  C27  N30  C21     0.00   0.0  0
 6QL  CONST_15  C27  C26  C23  N22     0.00   0.0  0
 6QL  CONST_16  C27  N30  C21  N22     0.00   0.0  0
 6QL  CONST_17  N30  C27  C26  C23     0.00   0.0  0
 6QL  CONST_18  N30  C21  N22  C23     0.00   0.0  0
 6QL  CONST_19  C16  C04  C03  C02   180.00   0.0  0
 6QL  CONST_20  C18  C19  C03  C02   180.00   0.0  0
 6QL  CONST_21  O20  C19  C03  C04   180.00   0.0  0
 6QL  CONST_22  C12  N15  C06  O05   180.00   0.0  0
 6QL  CONST_23  C08  N07  C06  O05   180.00   0.0  0
 6QL  CONST_24  C19  C03  C04  O05   180.00   0.0  0
 6QL  CONST_25  C17  C16  C04  O05   180.00   0.0  0
 6QL  CONST_26  O13  C12  N15  C06   180.00   0.0  0
 6QL  CONST_27  O09  C08  N07  C06   180.00   0.0  0
 6QL  CONST_28  O13  C12  C11  C08   180.00   0.0  0
 6QL  CONST_29  C12  C11  C08  O09   180.00   0.0  0
 6QL  CONST_30  O20  C19  C18  C17   180.00   0.0  0
 6QL  CONST_31  C23  N22  C21  O20   180.00   0.0  0
 6QL  CONST_32  C27  N30  C21  O20   180.00   0.0  0
 6QL  CONST_33  O24  C23  N22  C21   180.00   0.0  0
 6QL  CONST_34  O28  C27  N30  C21   180.00   0.0  0
 6QL  CONST_35  O28  C27  C26  C23   180.00   0.0  0
 6QL  CONST_36  C27  C26  C23  O24   180.00   0.0  0
 6QL  CONST_37  H9   C16  C04  C03   180.00   0.0  0
 6QL  CONST_38  H11  C18  C19  C03   180.00   0.0  0
 6QL  CONST_39  H10  C17  C16  C04   180.00   0.0  0
 6QL  CONST_40  H5   C11  C08  N07   180.00   0.0  0
 6QL  CONST_41  H15  C26  C23  N22   180.00   0.0  0
 6QL  CONST_42  H1   O01  C02  C03   180.00   0.0  0
 6QL  Var_01    N15  C06  O05  C04     5.00  30.0  3
 6QL  Var_02    C16  C04  O05  C06   -90.44  30.0  2
 6QL  Var_03    N22  C21  O20  C19     3.78  30.0  3
 6QL  Var_04    C04  C03  C02  O01   137.10  30.0  2
 6QL  Var_05    C11  C08  O09  C10  -179.58  30.0  3
 6QL  Var_06    N15  C12  O13  C14    -1.67  30.0  2
 6QL  Var_07    C26  C23  O24  C25  -179.37  30.0  2
 6QL  Var_08    N30  C27  O28  C29     0.72  30.0  3
 6QL  Var_09    H2   C10  O09  C08   179.46  30.0  3
 6QL  Var_10    H6   C14  O13  C12    59.00  30.0  3
 6QL  Var_11    H12  C25  O24  C23    60.54  30.0  3
 6QL  Var_12    H16  C29  O28  C27   179.18  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
 6QL  plan-1  C02  0.020
 6QL  plan-1  C03  0.020
 6QL  plan-1  C04  0.020
 6QL  plan-1  O05  0.020
 6QL  plan-1  C16  0.020
 6QL  plan-1  C17  0.020
 6QL  plan-1  C18  0.020
 6QL  plan-1  C19  0.020
 6QL  plan-1  O20  0.020
 6QL  plan-1  H9   0.020
 6QL  plan-1  H10  0.020
 6QL  plan-1  H11  0.020
 6QL  plan-2  O05  0.020
 6QL  plan-2  C06  0.020
 6QL  plan-2  N07  0.020
 6QL  plan-2  C08  0.020
 6QL  plan-2  O09  0.020
 6QL  plan-2  C11  0.020
 6QL  plan-2  C12  0.020
 6QL  plan-2  O13  0.020
 6QL  plan-2  N15  0.020
 6QL  plan-2  H5   0.020
 6QL  plan-3  O20  0.020
 6QL  plan-3  C21  0.020
 6QL  plan-3  N22  0.020
 6QL  plan-3  C23  0.020
 6QL  plan-3  O24  0.020
 6QL  plan-3  C26  0.020
 6QL  plan-3  C27  0.020
 6QL  plan-3  O28  0.020
 6QL  plan-3  N30  0.020
 6QL  plan-3  H15  0.020
 6QL  plan-4  O01  0.020
 6QL  plan-4  C02  0.020
 6QL  plan-4  C03  0.020
 6QL  plan-4  O31  0.020
 6QL  plan-4  H1   0.020

