# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 20:52:54 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: (3E)-3-[(2,4-dimethoxyphenyl)methylidene]-3,4,5,6-tetrahydro-2,3'-bipyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(\C=C2/CCCN=C2c3cccnc3)c(OC)c1
#
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
 ZY7  ZY7  (3E)-3-[(2,4-dimethoxyphenyl)methylidene]-3,4,5,6-tetrahydro-2,3'-bipyridine  ligand  43  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ZY7
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
 ZY7  C7    C  C1    0  -0.326   0.1116   0.0497  -0.0054
 ZY7  C4    C  CR6   0  -0.039  -1.3439  -0.0134   0.1123
 ZY7  C3    C  CR6   0   0.379  -2.0680  -0.9911  -0.6035
 ZY7  O21   O  O2    0  -0.462  -1.3400  -1.7832  -1.4071
 ZY7  C22   C  CH3   0  -0.439  -1.9858  -2.8268  -2.1109
 ZY7  C2    C  CR16  0  -0.486  -3.4435  -1.0921  -0.4737
 ZY7  C5    C  CR16  0  -0.275  -2.0629   0.8167   0.9642
 ZY7  C6    C  CR16  0  -0.404  -3.4410   0.7311   1.1116
 ZY7  C1    C  CR6   0   0.403  -4.1344  -0.2273   0.3805
 ZY7  O20   O  O2    0  -0.468  -5.4646  -0.4061   0.4311
 ZY7  C8    C  C     0   0.063   0.8678   1.1610  -0.0531
 ZY7  C13   C  CH2   0  -0.516   0.3351   2.5608  -0.1512
 ZY7  C12   C  CH2   0  -0.475   1.1415   3.3241  -1.1948
 ZY7  C11   C  CH2   0  -0.322   2.6164   3.2876  -0.8407
 ZY7  N10   N  N     0  -0.378   3.1320   1.9959  -0.4473
 ZY7  C9    C  C     0   0.209   2.3415   1.0540  -0.1138
 ZY7  C14   C  CR6   0  -0.061   2.9983  -0.2293   0.2511
 ZY7  C19   C  CR16  0  -0.076   3.9533  -0.7815  -0.5988
 ZY7  N18   N  N     0  -0.403   4.6233  -1.8945  -0.3349
 ZY7  C17   C  CR16  0  -0.066   4.3776  -2.5102   0.8164
 ZY7  C16   C  CR16  0  -0.319   3.4551  -2.0458   1.7416
 ZY7  C15   C  CR16  0  -0.172   2.7499  -0.8893   1.4506
 ZY7  C23   C  CH3   0  -0.437  -6.2302   0.4376   1.2700
 ZY7  H7    H  H     0   0.255   0.6154  -0.9087  -0.0658
 ZY7  H221  H  HCH3  0   0.264  -1.2090  -3.3563  -2.6564
 ZY7  H222  H  HCH3  0   0.231  -2.4827  -3.5270  -1.4351
 ZY7  H223  H  HCH3  0   0.231  -2.7184  -2.4422  -2.8246
 ZY7  H2    H  HCR6  0   0.284  -4.0120  -1.8311  -1.0230
 ZY7  H5    H  HCR6  0   0.269  -1.5291   1.5425   1.5636
 ZY7  H6    H  HCR6  0   0.278  -3.9393   1.4002   1.7990
 ZY7  H131  H  HCH2  0   0.258  -0.7220   2.5543  -0.4160
 ZY7  H132  H  HCH2  0   0.248   0.4135   3.0691   0.8164
 ZY7  H121  H  HCH2  0   0.234   0.9797   2.8728  -2.1777
 ZY7  H122  H  HCH2  0   0.245   0.8025   4.3593  -1.2617
 ZY7  H111  H  HCH2  0   0.242   3.2231   3.6439  -1.6769
 ZY7  H112  H  HCH2  0   0.238   2.8234   3.9801  -0.0165
 ZY7  H19   H  HCR6  0   0.259   4.1731  -0.2952  -1.5433
 ZY7  H17   H  HCR6  0   0.266   4.9407  -3.4158   1.0133
 ZY7  H16   H  HCR6  0   0.273   3.2964  -2.5778   2.6694
 ZY7  H15   H  HCR6  0   0.272   2.0260  -0.4988   2.1546
 ZY7  H231  H  HCH3  0   0.230  -5.9450   0.3352   2.3198
 ZY7  H232  H  HCH3  0   0.230  -6.1426   1.4878   0.9810
 ZY7  H233  H  HCH3  0   0.261  -7.2659   0.1282   1.1558

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
 ZY7  C7   C4    single    1.462  0.020  1.462
 ZY7  C7   C8    double    1.345  0.020  1.345
 ZY7  C4   C3    aromatic  1.412  0.020  1.412
 ZY7  C4   C5    aromatic  1.390  0.020  1.390
 ZY7  C3   O21   single    1.343  0.020  1.343
 ZY7  C3   C2    aromatic  1.385  0.020  1.385
 ZY7  O21  C22   single    1.415  0.020  1.415
 ZY7  C2   C1    aromatic  1.398  0.020  1.398
 ZY7  C5   C6    aromatic  1.389  0.020  1.389
 ZY7  C6   C1    aromatic  1.391  0.020  1.391
 ZY7  C1   O20   single    1.343  0.020  1.343
 ZY7  O20  C23   single    1.415  0.020  1.415
 ZY7  C8   C13   single    1.501  0.020  1.501
 ZY7  C8   C9    single    1.479  0.020  1.479
 ZY7  C13  C12   single    1.524  0.020  1.524
 ZY7  C12  C11   single    1.517  0.020  1.517
 ZY7  C11  N10   single    1.445  0.020  1.445
 ZY7  N10  C9    double    1.274  0.020  1.274
 ZY7  C9   C14   single    1.487  0.020  1.487
 ZY7  C14  C19   aromatic  1.393  0.020  1.393
 ZY7  C14  C15   aromatic  1.391  0.020  1.391
 ZY7  C19  N18   aromatic  1.326  0.020  1.326
 ZY7  N18  C17   aromatic  1.328  0.020  1.328
 ZY7  C17  C16   aromatic  1.387  0.020  1.387
 ZY7  C16  C15   aromatic  1.385  0.020  1.385
 ZY7  C7   H7    single    0.930  0.020  1.080
 ZY7  C22  H221  single    0.970  0.020  1.090
 ZY7  C22  H222  single    0.970  0.020  1.090
 ZY7  C22  H223  single    0.970  0.020  1.090
 ZY7  C2   H2    single    0.930  0.020  1.080
 ZY7  C5   H5    single    0.930  0.020  1.080
 ZY7  C6   H6    single    0.930  0.020  1.080
 ZY7  C13  H131  single    0.970  0.020  1.090
 ZY7  C13  H132  single    0.970  0.020  1.090
 ZY7  C12  H121  single    0.970  0.020  1.090
 ZY7  C12  H122  single    0.970  0.020  1.090
 ZY7  C11  H111  single    0.970  0.020  1.090
 ZY7  C11  H112  single    0.970  0.020  1.090
 ZY7  C19  H19   single    0.930  0.020  1.080
 ZY7  C17  H17   single    0.930  0.020  1.080
 ZY7  C16  H16   single    0.930  0.020  1.080
 ZY7  C15  H15   single    0.930  0.020  1.080
 ZY7  C23  H231  single    0.970  0.020  1.090
 ZY7  C23  H232  single    0.970  0.020  1.090
 ZY7  C23  H233  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
 ZY7  H7    C7   C8    117.84  3.000
 ZY7  H7    C7   C4    115.40  3.000
 ZY7  C8    C7   C4    126.75  3.000
 ZY7  C5    C4   C3    117.33  3.000
 ZY7  C5    C4   C7    122.60  3.000
 ZY7  C3    C4   C7    119.99  3.000
 ZY7  C2    C3   O21   123.46  3.000
 ZY7  C2    C3   C4    120.82  3.000
 ZY7  O21   C3   C4    115.72  3.000
 ZY7  C22   O21  C3    119.04  3.000
 ZY7  H223  C22  H222  108.94  3.000
 ZY7  H223  C22  H221  108.83  3.000
 ZY7  H222  C22  H221  108.86  3.000
 ZY7  H223  C22  O21   111.80  3.000
 ZY7  H222  C22  O21   111.88  3.000
 ZY7  H221  C22  O21   106.43  3.000
 ZY7  H2    C2   C1    118.22  3.000
 ZY7  H2    C2   C3    121.59  3.000
 ZY7  C1    C2   C3    120.19  3.000
 ZY7  H5    C5   C6    118.17  3.000
 ZY7  H5    C5   C4    119.00  3.000
 ZY7  C6    C5   C4    122.80  3.000
 ZY7  H6    C6   C1    122.08  3.000
 ZY7  H6    C6   C5    119.13  3.000
 ZY7  C1    C6   C5    118.79  3.000
 ZY7  O20   C1   C6    124.46  3.000
 ZY7  O20   C1   C2    115.48  3.000
 ZY7  C6    C1   C2    120.07  3.000
 ZY7  C23   O20  C1    118.62  3.000
 ZY7  C9    C8   C13   114.74  3.000
 ZY7  C9    C8   C7    120.13  3.000
 ZY7  C13   C8   C7    124.98  3.000
 ZY7  H132  C13  H131  106.66  3.000
 ZY7  H132  C13  C12   109.54  3.000
 ZY7  H131  C13  C12   110.48  3.000
 ZY7  H132  C13  C8    110.46  3.000
 ZY7  H131  C13  C8    110.77  3.000
 ZY7  C12   C13  C8    108.91  3.000
 ZY7  H122  C12  H121  106.88  3.000
 ZY7  H122  C12  C11   109.83  3.000
 ZY7  H121  C12  C11   110.10  3.000
 ZY7  H122  C12  C13   110.66  3.000
 ZY7  H121  C12  C13   109.30  3.000
 ZY7  C11   C12  C13   110.03  3.000
 ZY7  H112  C11  H111  105.34  3.000
 ZY7  H112  C11  N10   107.01  3.000
 ZY7  H111  C11  N10   107.56  3.000
 ZY7  H112  C11  C12   110.10  3.000
 ZY7  H111  C11  C12   110.68  3.000
 ZY7  N10   C11  C12   115.58  3.000
 ZY7  C9    N10  C11   120.71  3.000
 ZY7  C14   C9   N10   115.36  3.000
 ZY7  C14   C9   C8    119.50  3.000
 ZY7  N10   C9   C8    125.14  3.000
 ZY7  C15   C14  C19   117.42  3.000
 ZY7  C15   C14  C9    122.82  3.000
 ZY7  C19   C14  C9    119.69  3.000
 ZY7  H19   C19  N18   116.57  3.000
 ZY7  H19   C19  C14   119.51  3.000
 ZY7  N18   C19  C14   123.92  3.000
 ZY7  C17   N18  C19   117.92  3.000
 ZY7  H17   C17  C16   120.27  3.000
 ZY7  H17   C17  N18   116.64  3.000
 ZY7  C16   C17  N18   123.09  3.000
 ZY7  H16   C16  C15   121.09  3.000
 ZY7  H16   C16  C17   120.35  3.000
 ZY7  C15   C16  C17   118.56  3.000
 ZY7  H15   C15  C16   120.32  3.000
 ZY7  H15   C15  C14   120.59  3.000
 ZY7  C16   C15  C14   119.09  3.000
 ZY7  H233  C23  H232  108.80  3.000
 ZY7  H233  C23  H231  108.84  3.000
 ZY7  H232  C23  H231  108.85  3.000
 ZY7  H233  C23  O20   106.48  3.000
 ZY7  H232  C23  O20   111.89  3.000
 ZY7  H231  C23  O20   111.87  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
 ZY7  CONST_01  C1    C2   C3   C4      0.00   0.0  0
 ZY7  CONST_02  C1    C6   C5   C4      0.00   0.0  0
 ZY7  CONST_03  C6    C5   C4   C3      0.00   0.0  0
 ZY7  CONST_04  C6    C1   C2   C3      0.00   0.0  0
 ZY7  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 ZY7  CONST_06  C5    C6   C1   C2      0.00   0.0  0
 ZY7  CONST_07  C17   N18  C19  C14     0.00   0.0  0
 ZY7  CONST_08  C17   C16  C15  C14     0.00   0.0  0
 ZY7  CONST_09  C16   C15  C14  C19     0.00   0.0  0
 ZY7  CONST_10  C16   C17  N18  C19     0.00   0.0  0
 ZY7  CONST_11  C15   C14  C19  N18     0.00   0.0  0
 ZY7  CONST_12  C15   C16  C17  N18     0.00   0.0  0
 ZY7  CONST_13  N18   C19  C14  C9    180.00   0.0  0
 ZY7  CONST_14  C16   C15  C14  C9    180.00   0.0  0
 ZY7  CONST_15  C2    C3   C4   C7    180.00   0.0  0
 ZY7  CONST_16  C6    C5   C4   C7    180.00   0.0  0
 ZY7  CONST_17  O20   C1   C2   C3    180.00   0.0  0
 ZY7  CONST_18  C5    C4   C3   O21   180.00   0.0  0
 ZY7  CONST_19  C1    C2   C3   O21   180.00   0.0  0
 ZY7  CONST_20  O20   C1   C6   C5    180.00   0.0  0
 ZY7  CONST_21  H2    C2   C3   C4    180.00   0.0  0
 ZY7  CONST_22  H6    C6   C5   C4    180.00   0.0  0
 ZY7  CONST_23  H5    C5   C4   C3    180.00   0.0  0
 ZY7  CONST_24  H19   C19  C14  C9      0.00   0.0  0
 ZY7  CONST_25  H15   C15  C14  C9      0.00   0.0  0
 ZY7  CONST_26  H16   C16  C15  C14   180.00   0.0  0
 ZY7  CONST_27  H17   C17  N18  C19   180.00   0.0  0
 ZY7  Var_01    C11   C12  C13  C8    -56.25  30.0  1
 ZY7  Var_02    C19   C14  C9   C8    130.72  30.0  2
 ZY7  Var_03    N10   C9   C8   C13   -11.73  30.0  1
 ZY7  Var_04    N10   C11  C12  C13    45.57  30.0  1
 ZY7  Var_05    C9    C8   C13  C12    40.35  30.0  1
 ZY7  Var_06    C13   C8   C7   C4     -7.40  30.0  2
 ZY7  Var_07    C8    C7   C4   C3    141.57  30.0  3
 ZY7  Var_08    C2    C3   O21  C22    -3.52  30.0  1
 ZY7  Var_09    H221  C22  O21  C3   -177.65  30.0  3
 ZY7  Var_10    H231  C23  O20  C1    -61.54  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
 ZY7  plan-1  C7   0.020
 ZY7  plan-1  C4   0.020
 ZY7  plan-1  C3   0.020
 ZY7  plan-1  O21  0.020
 ZY7  plan-1  C2   0.020
 ZY7  plan-1  C5   0.020
 ZY7  plan-1  C6   0.020
 ZY7  plan-1  C1   0.020
 ZY7  plan-1  O20  0.020
 ZY7  plan-1  H2   0.020
 ZY7  plan-1  H5   0.020
 ZY7  plan-1  H6   0.020
 ZY7  plan-2  C9   0.020
 ZY7  plan-2  C14  0.020
 ZY7  plan-2  C19  0.020
 ZY7  plan-2  N18  0.020
 ZY7  plan-2  C17  0.020
 ZY7  plan-2  C16  0.020
 ZY7  plan-2  C15  0.020
 ZY7  plan-2  H19  0.020
 ZY7  plan-2  H17  0.020
 ZY7  plan-2  H16  0.020
 ZY7  plan-2  H15  0.020

