# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 00:16:42 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  32  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  -0.436  -4.5786   1.8916  -0.0324
 88R  O2    O  O2    0  -0.464  -4.0001   0.6171   0.1571
 88R  C3    C  CR6   0   0.297  -2.7137   0.4461  -0.2021
 88R  C4    C  CR16  0  -0.371  -1.9085   1.4134  -0.7757
 88R  C5    C  CR16  0  -0.318  -0.5823   1.1287  -1.1051
 88R  C6    C  CR6   0   0.111  -0.0472  -0.1221  -0.8662
 88R  C7    C  CR16  0  -0.437  -0.8633  -1.1041  -0.2935
 88R  C8    C  CR6   0   0.327  -2.1802  -0.8388   0.0371
 88R  O9    O  O2    0  -0.465  -3.0319  -1.7270   0.5832
 88R  C10   C  CH3   0  -0.438  -2.5580  -3.0325   0.8418
 88R  C11   C  CH2   0  -0.513   1.3929  -0.4319  -1.1695
 88R  C12   C  CH1   0  -0.499   2.2654  -0.3514   0.0893
 88R  C13   C  C     0   0.584   3.7189  -0.6681  -0.2038
 88R  O14   O  O     0  -0.420   4.1351  -1.0900  -1.2492
 88R  O15   O  OH1   0  -0.590   4.4758  -0.4387   0.8596
 88R  C16   C  C     0   0.562   2.1789   1.0373   0.6904
 88R  O17   O  O     0  -0.431   2.5941   2.0174   0.1258
 88R  O18   O  OH1   0  -0.574   1.5877   1.0541   1.8710
 88R  H11C  H  HCH3  0   0.259  -5.5987   1.8264   0.3384
 88R  H12C  H  HCH3  0   0.227  -4.0491   2.6679   0.5268
 88R  H13C  H  HCH3  0   0.227  -4.6054   2.1760  -1.0878
 88R  H4    H  HCR6  0   0.280  -2.2938   2.4031  -0.9811
 88R  H5    H  HCR6  0   0.249   0.0227   1.9048  -1.5571
 88R  H7    H  HCR6  0   0.276  -0.4459  -2.0877  -0.1155
 88R  H111  H  HCH2  0   0.274   1.4808  -1.4388  -1.5800
 88R  H112  H  HCH2  0   0.267   1.7769   0.2547  -1.9257
 88R  H101  H  HCH3  0   0.260  -3.3857  -3.5801   1.2855
 88R  H102  H  HCH3  0   0.228  -2.2492  -3.5443  -0.0738
 88R  H103  H  HCH3  0   0.227  -1.7187  -3.0317   1.5422
 88R  H12   H  HCH1  0   0.327   1.9184  -1.0878   0.8210
 88R  H15   H  HOH1  0   0.488   5.4036  -0.6472   0.6699
 88R  H18   H  HOH1  0   0.485   1.5313   1.9641   2.2023

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    1.412  0.020  1.412
 88R  O2   C3    single    1.346  0.020  1.346
 88R  C3   C4    aromatic  1.383  0.020  1.383
 88R  C3   C8    aromatic  1.412  0.020  1.412
 88R  C4   C5    aromatic  1.396  0.020  1.396
 88R  C5   C6    aromatic  1.381  0.020  1.381
 88R  C6   C7    aromatic  1.399  0.020  1.399
 88R  C6   C11   single    1.504  0.020  1.504
 88R  C7   C8    aromatic  1.383  0.020  1.383
 88R  C8   O9    single    1.346  0.020  1.346
 88R  O9   C10   single    1.413  0.020  1.413
 88R  C11  C12   single    1.534  0.020  1.534
 88R  C12  C13   single    1.516  0.020  1.516
 88R  C12  C16   single    1.516  0.020  1.516
 88R  C13  O14   double    1.202  0.020  1.202
 88R  C13  O15   single    1.325  0.020  1.325
 88R  C16  O17   double    1.205  0.020  1.205
 88R  C16  O18   single    1.320  0.020  1.320
 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
 88R  O15  H15   single    0.850  0.020  0.980
 88R  O18  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
 88R  H13C  C1   H12C  108.71  3.000
 88R  H13C  C1   H11C  108.77  3.000
 88R  H12C  C1   H11C  108.81  3.000
 88R  H13C  C1   O2    111.98  3.000
 88R  H12C  C1   O2    111.94  3.000
 88R  H11C  C1   O2    106.53  3.000
 88R  C3    O2   C1    118.04  3.000
 88R  C8    C3   C4    119.13  3.000
 88R  C8    C3   O2    115.56  3.000
 88R  C4    C3   O2    125.31  3.000
 88R  H4    C4   C5    118.70  3.000
 88R  H4    C4   C3    120.75  3.000
 88R  C5    C4   C3    120.55  3.000
 88R  H5    C5   C6    120.31  3.000
 88R  H5    C5   C4    118.89  3.000
 88R  C6    C5   C4    120.80  3.000
 88R  C11   C6   C7    119.76  3.000
 88R  C11   C6   C5    121.51  3.000
 88R  C7    C6   C5    118.70  3.000
 88R  H7    C7   C8    120.11  3.000
 88R  H7    C7   C6    118.67  3.000
 88R  C8    C7   C6    121.22  3.000
 88R  O9    C8   C7    124.93  3.000
 88R  O9    C8   C3    115.48  3.000
 88R  C7    C8   C3    119.59  3.000
 88R  C10   O9   C8    118.15  3.000
 88R  H103  C10  H102  108.67  3.000
 88R  H103  C10  H101  108.87  3.000
 88R  H102  C10  H101  108.72  3.000
 88R  H103  C10  O9    111.97  3.000
 88R  H102  C10  O9    111.96  3.000
 88R  H101  C10  O9    106.54  3.000
 88R  H112  C11  H111  106.96  3.000
 88R  H112  C11  C12   109.61  3.000
 88R  H111  C11  C12   108.14  3.000
 88R  H112  C11  C6    110.31  3.000
 88R  H111  C11  C6    110.07  3.000
 88R  C12   C11  C6    111.62  3.000
 88R  H12   C12  C16   109.46  3.000
 88R  H12   C12  C13   107.02  3.000
 88R  C16   C12  C13   108.83  3.000
 88R  H12   C12  C11   109.45  3.000
 88R  C16   C12  C11   109.94  3.000
 88R  C13   C12  C11   112.07  3.000
 88R  O15   C13  O14   124.12  3.000
 88R  O15   C13  C12   110.87  3.000
 88R  O14   C13  C12   125.00  3.000
 88R  H15   O15  C13   110.63  3.000
 88R  O18   C16  O17   124.25  3.000
 88R  O18   C16  C12   113.07  3.000
 88R  O17   C16  C12   122.67  3.000
 88R  H18   O18  C16   110.08  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  CONST_16  H15   O15  C13  C12   180.00   0.0  0
 88R  CONST_17  H18   O18  C16  C12   180.00   0.0  0
 88R  Var_01    C4    C3   O2   C1     -1.58  30.0  2
 88R  Var_02    C12   C11  C6   C5     98.87  30.0  2
 88R  Var_03    C13   C12  C11  C6    179.75  30.0  3
 88R  Var_04    H11C  C1   O2   C3   -178.63  30.0  3
 88R  Var_05    H101  C10  O9   C8    179.42  30.0  3
 88R  Var_06    O14   C13  C12  C11    -8.48  30.0  3
 88R  Var_07    O17   C16  C12  C11   -65.36  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-2  H15  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
 88R  plan-3  H18  0.020

