# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 05:57:12 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: (3,4-dimethoxybenzyl)propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CC(C(O)=O)C(O)=O)cc1OC
#
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
 88R  88R  '(3,4-dimethoxybenzyl)propanedioic acid'  ligand  30  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_88R
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
 88R  C1    C  CH3    0  -0.433  -4.6386   1.8588   0.0038
 88R  O2    O  O2     0  -0.468  -4.0636   0.5785   0.1471
 88R  C3    C  C      0   0.284  -2.7615   0.4305  -0.1804
 88R  C4    C  C1     0  -0.371  -1.9414   1.4316  -0.6709
 88R  C5    C  C1     0  -0.321  -0.6051   1.1696  -0.9773
 88R  C6    C  C      0   0.133  -0.0669  -0.0926  -0.8041
 88R  C7    C  C1     0  -0.448  -0.9010  -1.1032  -0.3114
 88R  C8    C  C      0   0.321  -2.2282  -0.8612   0.0007
 88R  O9    O  O2     0  -0.468  -3.0903  -1.7847   0.4755
 88R  C10   C  CH3    0  -0.435  -2.6128  -3.0969   0.6814
 88R  C11   C  CH2    0  -0.489   1.3777  -0.3900  -1.0951
 88R  C12   C  CH1    0  -0.464   2.2629  -0.2722   0.1451
 88R  C13   C  C      0   0.411   3.7270  -0.6905  -0.1065
 88R  O14   O  O      0  -0.607   4.0556  -1.0451  -1.2563
 88R  O15   O  OC    -1  -0.628   4.4840  -0.6364   0.8862
 88R  C16   C  C      0   0.421   2.2761   1.1678   0.6910
 88R  O17   O  O      0  -0.626   2.6256   2.0542  -0.1196
 88R  O18   O  OC    -1  -0.624   1.9605   1.3523   1.8834
 88R  H11C  H  HCH3   0   0.255  -5.6724   1.7736   0.3309
 88R  H12C  H  HCH3   0   0.224  -4.1351   2.6069   0.6229
 88R  H13C  H  HCH3   0   0.224  -4.6273   2.2007  -1.0351
 88R  H4    H  H      0   0.272  -2.3246   2.4318  -0.8253
 88R  H5    H  H      0   0.234   0.0165   1.9739  -1.3491
 88R  H7    H  H      0   0.266  -0.4847  -2.0944  -0.1776
 88R  H111  H  HCH2   0   0.216   1.4618  -1.4004  -1.5016
 88R  H112  H  HCH2   0   0.217   1.7477   0.2861  -1.8665
 88R  H101  H  HCH3   0   0.257  -3.4462  -3.6708   1.0797
 88R  H102  H  HCH3   0   0.225  -2.2798  -3.5644  -0.2496
 88R  H103  H  HCH3   0   0.225  -1.7895  -3.1272   1.4002
 88R  H12   H  HCH1   0   0.199   1.8612  -0.9339   0.9223

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
 88R  C1   O2    single    1.411  0.020  1.411
 88R  O2   C3    single    1.351  0.020  1.351
 88R  C3   C4    aromatic  1.384  0.020  1.384
 88R  C3   C8    aromatic  1.409  0.020  1.409
 88R  C4   C5    aromatic  1.396  0.020  1.396
 88R  C5   C6    aromatic  1.383  0.020  1.383
 88R  C6   C7    aromatic  1.400  0.020  1.400
 88R  C6   C11   single    1.503  0.020  1.503
 88R  C7   C8    aromatic  1.385  0.020  1.385
 88R  C8   O9    single    1.350  0.020  1.350
 88R  O9   C10   single    1.411  0.020  1.411
 88R  C11  C12   single    1.528  0.020  1.528
 88R  C12  C13   single    1.543  0.020  1.543
 88R  C12  C16   single    1.540  0.020  1.540
 88R  C13  O14   deloc     1.247  0.020  1.247
 88R  C13  O15   deloc     1.250  0.020  1.250
 88R  C16  O17   deloc     1.251  0.020  1.251
 88R  C16  O18   deloc     1.247  0.020  1.247
 88R  C1   H11C  single    0.970  0.020  1.090
 88R  C1   H12C  single    0.970  0.020  1.090
 88R  C1   H13C  single    0.970  0.020  1.090
 88R  C4   H4    single    0.930  0.020  1.080
 88R  C5   H5    single    0.930  0.020  1.080
 88R  C7   H7    single    0.930  0.020  1.080
 88R  C11  H111  single    0.970  0.020  1.090
 88R  C11  H112  single    0.970  0.020  1.090
 88R  C10  H101  single    0.970  0.020  1.090
 88R  C10  H102  single    0.970  0.020  1.090
 88R  C10  H103  single    0.970  0.020  1.090
 88R  C12  H12   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
 88R  H13C  C1   H12C  108.61  3.000
 88R  H13C  C1   H11C  108.66  3.000
 88R  H12C  C1   H11C  108.71  3.000
 88R  H13C  C1   O2    112.09  3.000
 88R  H12C  C1   O2    112.06  3.000
 88R  H11C  C1   O2    106.61  3.000
 88R  C3    O2   C1    117.88  3.000
 88R  C8    C3   C4    118.97  3.000
 88R  C8    C3   O2    115.72  3.000
 88R  C4    C3   O2    125.31  3.000
 88R  H4    C4   C5    118.76  3.000
 88R  H4    C4   C3    120.61  3.000
 88R  C5    C4   C3    120.62  3.000
 88R  H5    C5   C6    119.85  3.000
 88R  H5    C5   C4    119.06  3.000
 88R  C6    C5   C4    121.09  3.000
 88R  C11   C6   C7    119.86  3.000
 88R  C11   C6   C5    122.02  3.000
 88R  C7    C6   C5    118.10  3.000
 88R  H7    C7   C8    120.03  3.000
 88R  H7    C7   C6    118.36  3.000
 88R  C8    C7   C6    121.62  3.000
 88R  O9    C8   C7    124.88  3.000
 88R  O9    C8   C3    115.51  3.000
 88R  C7    C8   C3    119.60  3.000
 88R  C10   O9   C8    118.12  3.000
 88R  H103  C10  H102  108.57  3.000
 88R  H103  C10  H101  108.76  3.000
 88R  H102  C10  H101  108.64  3.000
 88R  H103  C10  O9    112.11  3.000
 88R  H102  C10  O9    112.10  3.000
 88R  H101  C10  O9    106.54  3.000
 88R  H112  C11  H111  106.51  3.000
 88R  H112  C11  C12   109.25  3.000
 88R  H111  C11  C12   109.19  3.000
 88R  H112  C11  C6    109.90  3.000
 88R  H111  C11  C6    109.21  3.000
 88R  C12   C11  C6    112.60  3.000
 88R  H12   C12  C16   108.42  3.000
 88R  H12   C12  C13   107.42  3.000
 88R  C16   C12  C13   107.64  3.000
 88R  H12   C12  C11   108.44  3.000
 88R  C16   C12  C11   111.39  3.000
 88R  C13   C12  C11   113.35  3.000
 88R  O15   C13  O14   125.81  3.000
 88R  O15   C13  C12   115.69  3.000
 88R  O14   C13  C12   118.50  3.000
 88R  O18   C16  O17   125.83  3.000
 88R  O18   C16  C12   118.36  3.000
 88R  O17   C16  C12   115.80  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
 88R  CONST_01  C6    C5   C4   C3      0.00   0.0  0
 88R  CONST_02  C6    C7   C8   C3      0.00   0.0  0
 88R  CONST_03  C7    C8   C3   C4      0.00   0.0  0
 88R  CONST_04  C7    C6   C5   C4      0.00   0.0  0
 88R  CONST_05  C8    C3   C4   C5      0.00   0.0  0
 88R  CONST_06  C8    C7   C6   C5      0.00   0.0  0
 88R  CONST_07  C5    C4   C3   O2    180.00   0.0  0
 88R  CONST_08  C7    C8   C3   O2    180.00   0.0  0
 88R  CONST_09  O9    C8   C3   C4    180.00   0.0  0
 88R  CONST_10  C11   C6   C5   C4    180.00   0.0  0
 88R  CONST_11  O9    C8   C7   C6    180.00   0.0  0
 88R  CONST_12  C11   C6   C7   C8    180.00   0.0  0
 88R  CONST_13  H5    C5   C4   C3    180.00   0.0  0
 88R  CONST_14  H7    C7   C8   C3    180.00   0.0  0
 88R  CONST_15  H4    C4   C5   C6    180.00   0.0  0
 88R  Var_01    C4    C3   O2   C1     -1.19  30.0  2
 88R  Var_02    C12   C11  C6   C5     93.88  30.0  2
 88R  Var_03    C13   C12  C11  C6    175.07  30.0  3
 88R  Var_04    H11C  C1   O2   C3   -179.01  30.0  3
 88R  Var_05    H101  C10  O9   C8    178.90  30.0  3
 88R  Var_06    O14   C13  C12  C11     1.49  30.0  3
 88R  Var_07    O17   C16  C12  C11   -56.05  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
 88R  plan-1  O2   0.020
 88R  plan-1  C3   0.020
 88R  plan-1  C4   0.020
 88R  plan-1  C5   0.020
 88R  plan-1  C6   0.020
 88R  plan-1  C7   0.020
 88R  plan-1  C8   0.020
 88R  plan-1  O9   0.020
 88R  plan-1  C11  0.020
 88R  plan-1  H4   0.020
 88R  plan-1  H5   0.020
 88R  plan-1  H7   0.020
 88R  plan-2  C12  0.020
 88R  plan-2  C13  0.020
 88R  plan-2  O14  0.020
 88R  plan-2  O15  0.020
 88R  plan-3  C12  0.020
 88R  plan-3  C16  0.020
 88R  plan-3  O17  0.020
 88R  plan-3  O18  0.020

