# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 20:26:32 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-[(E)-5,6-dihydro-2,3'-bipyridin-3(4H)-ylidenemethyl]-3-methoxyphenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(O)ccc1\C=C2/CCCN=C2c3cccnc3
#
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
 ZY5  ZY5  4-[(E)-5,6-dihydro-2,3'-bipyridin-3(4H)-ylidenemethyl]-3-methoxyphenol  ligand  40  22  .  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_ZY5
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
 ZY5  C7    C  C1    0  -0.326  -0.1973   0.0393   0.0489
 ZY5  C4    C  CR6   0  -0.044  -1.6455  -0.0074   0.2416
 ZY5  C3    C  CR6   0   0.378  -2.4262  -0.9154  -0.5031
 ZY5  O21   O  O2    0  -0.462  -1.7613  -1.6492  -1.4096
 ZY5  C22   C  CH3   0  -0.439  -2.4673  -2.6148  -2.1647
 ZY5  C2    C  CR16  0  -0.476  -3.7959  -1.0130  -0.2993
 ZY5  C5    C  CR16  0  -0.274  -2.2978   0.7658   1.1982
 ZY5  C6    C  CR16  0  -0.407  -3.6633   0.6812   1.4172
 ZY5  C1    C  CR6   0   0.372  -4.4138  -0.2110   0.6595
 ZY5  O20   O  OH1   0  -0.627  -5.7426  -0.3537   0.8090
 ZY5  C8    C  C     0   0.061   0.5784   1.1377   0.0397
 ZY5  C13   C  CH2   0  -0.515   0.0737   2.5506   0.0605
 ZY5  C12   C  CH2   0  -0.475   0.8349   3.3543  -0.9874
 ZY5  C11   C  CH2   0  -0.323   2.3263   3.2751  -0.7185
 ZY5  N10   N  N     0  -0.378   2.8371   1.9581  -0.4119
 ZY5  C9    C  C     0   0.210   2.0461   1.0115  -0.0931
 ZY5  C14   C  CR6   0  -0.060   2.6956  -0.2973   0.1836
 ZY5  C19   C  CR16  0  -0.076   3.6258  -0.8120  -0.7163
 ZY5  N18   N  N     0  -0.403   4.2880  -1.9449  -0.5281
 ZY5  C17   C  CR16  0  -0.067   4.0596  -2.6205   0.5927
 ZY5  C16   C  CR16  0  -0.318   3.1629  -2.1978   1.5620
 ZY5  C15   C  CR16  0  -0.172   2.4654  -1.0196   1.3503
 ZY5  H7    H  H     0   0.254   0.2816  -0.9218  -0.1032
 ZY5  H5    H  HCR6  0   0.269  -1.7151   1.4341   1.8187
 ZY5  H2    H  HCR6  0   0.287  -4.4078  -1.6989  -0.8697
 ZY5  H221  H  HCH3  0   0.231  -3.2386  -2.1575  -2.7891
 ZY5  H222  H  HCH3  0   0.263  -1.7356  -3.0968  -2.8079
 ZY5  H223  H  HCH3  0   0.232  -2.9299  -3.3721  -1.5269
 ZY5  H6    H  HCR6  0   0.270  -4.1307   1.2925   2.1800
 ZY5  H20   H  HOH1  0   0.477  -6.0680   0.2353   1.4990
 ZY5  H131  H  HCH2  0   0.257  -0.9979   2.5857  -0.1350
 ZY5  H132  H  HCH2  0   0.248   0.2301   2.9953   1.0493
 ZY5  H121  H  HCH2  0   0.235   0.6113   2.9549  -1.9805
 ZY5  H122  H  HCH2  0   0.245   0.5128   4.3970  -0.9846
 ZY5  H111  H  HCH2  0   0.242   2.8931   3.6575  -1.5711
 ZY5  H112  H  HCH2  0   0.237   2.5931   3.9259   0.1223
 ZY5  H19   H  HCR6  0   0.259   3.8314  -0.2774  -1.6377
 ZY5  H15   H  HCR6  0   0.272   1.7620  -0.6613   2.0913
 ZY5  H17   H  HCR6  0   0.266   4.6159  -3.5415   0.7269
 ZY5  H16   H  HCR6  0   0.273   3.0183  -2.7788   2.4622

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
 ZY5  C7   C4    single    1.462  0.020  1.462
 ZY5  C7   C8    double    1.345  0.020  1.345
 ZY5  C4   C3    aromatic  1.410  0.020  1.410
 ZY5  C4   C5    aromatic  1.392  0.020  1.392
 ZY5  C3   O21   single    1.342  0.020  1.342
 ZY5  C3   C2    aromatic  1.388  0.020  1.388
 ZY5  O21  C22   single    1.415  0.020  1.415
 ZY5  C2   C1    aromatic  1.394  0.020  1.394
 ZY5  C5   C6    aromatic  1.386  0.020  1.386
 ZY5  C6   C1    aromatic  1.390  0.020  1.390
 ZY5  C1   O20   single    1.345  0.020  1.345
 ZY5  C8   C13   single    1.501  0.020  1.501
 ZY5  C8   C9    single    1.479  0.020  1.479
 ZY5  C13  C12   single    1.524  0.020  1.524
 ZY5  C12  C11   single    1.518  0.020  1.518
 ZY5  C11  N10   single    1.445  0.020  1.445
 ZY5  N10  C9    double    1.274  0.020  1.274
 ZY5  C9   C14   single    1.487  0.020  1.487
 ZY5  C14  C19   aromatic  1.393  0.020  1.393
 ZY5  C14  C15   aromatic  1.391  0.020  1.391
 ZY5  C19  N18   aromatic  1.326  0.020  1.326
 ZY5  N18  C17   aromatic  1.328  0.020  1.328
 ZY5  C17  C16   aromatic  1.386  0.020  1.386
 ZY5  C16  C15   aromatic  1.385  0.020  1.385
 ZY5  C7   H7    single    0.930  0.020  1.080
 ZY5  C5   H5    single    0.930  0.020  1.080
 ZY5  C2   H2    single    0.930  0.020  1.080
 ZY5  C22  H221  single    0.970  0.020  1.090
 ZY5  C22  H222  single    0.970  0.020  1.090
 ZY5  C22  H223  single    0.970  0.020  1.090
 ZY5  C6   H6    single    0.930  0.020  1.080
 ZY5  O20  H20   single    0.850  0.020  0.980
 ZY5  C13  H131  single    0.970  0.020  1.090
 ZY5  C13  H132  single    0.970  0.020  1.090
 ZY5  C12  H121  single    0.970  0.020  1.090
 ZY5  C12  H122  single    0.970  0.020  1.090
 ZY5  C11  H111  single    0.970  0.020  1.090
 ZY5  C11  H112  single    0.970  0.020  1.090
 ZY5  C19  H19   single    0.930  0.020  1.080
 ZY5  C15  H15   single    0.930  0.020  1.080
 ZY5  C17  H17   single    0.930  0.020  1.080
 ZY5  C16  H16   single    0.930  0.020  1.080

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
 ZY5  H7    C7   C8    117.92  3.000
 ZY5  H7    C7   C4    115.32  3.000
 ZY5  C8    C7   C4    126.76  3.000
 ZY5  C5    C4   C3    117.46  3.000
 ZY5  C5    C4   C7    122.48  3.000
 ZY5  C3    C4   C7    119.96  3.000
 ZY5  C2    C3   O21   123.32  3.000
 ZY5  C2    C3   C4    120.93  3.000
 ZY5  O21   C3   C4    115.74  3.000
 ZY5  C22   O21  C3    119.10  3.000
 ZY5  H223  C22  H222  108.85  3.000
 ZY5  H223  C22  H221  108.95  3.000
 ZY5  H222  C22  H221  108.82  3.000
 ZY5  H223  C22  O21   111.89  3.000
 ZY5  H222  C22  O21   106.41  3.000
 ZY5  H221  C22  O21   111.81  3.000
 ZY5  H2    C2   C1    118.46  3.000
 ZY5  H2    C2   C3    121.69  3.000
 ZY5  C1    C2   C3    119.85  3.000
 ZY5  H5    C5   C6    118.53  3.000
 ZY5  H5    C5   C4    118.99  3.000
 ZY5  C6    C5   C4    122.44  3.000
 ZY5  H6    C6   C1    120.85  3.000
 ZY5  H6    C6   C5    120.13  3.000
 ZY5  C1    C6   C5    119.01  3.000
 ZY5  O20   C1   C6    122.74  3.000
 ZY5  O20   C1   C2    116.95  3.000
 ZY5  C6    C1   C2    120.30  3.000
 ZY5  H20   O20  C1    110.39  3.000
 ZY5  C9    C8   C13   114.54  3.000
 ZY5  C9    C8   C7    120.22  3.000
 ZY5  C13   C8   C7    125.10  3.000
 ZY5  H132  C13  H131  106.81  3.000
 ZY5  H132  C13  C12   109.59  3.000
 ZY5  H131  C13  C12   110.53  3.000
 ZY5  H132  C13  C8    110.28  3.000
 ZY5  H131  C13  C8    111.01  3.000
 ZY5  C12   C13  C8    108.60  3.000
 ZY5  H122  C12  H121  106.91  3.000
 ZY5  H122  C12  C11   109.85  3.000
 ZY5  H121  C12  C11   110.05  3.000
 ZY5  H122  C12  C13   110.77  3.000
 ZY5  H121  C12  C13   109.25  3.000
 ZY5  C11   C12  C13   109.97  3.000
 ZY5  H112  C11  H111  105.33  3.000
 ZY5  H112  C11  N10   106.99  3.000
 ZY5  H111  C11  N10   107.52  3.000
 ZY5  H112  C11  C12   110.12  3.000
 ZY5  H111  C11  C12   110.68  3.000
 ZY5  N10   C11  C12   115.62  3.000
 ZY5  C9    N10  C11   120.71  3.000
 ZY5  C14   C9   N10   115.43  3.000
 ZY5  C14   C9   C8    119.46  3.000
 ZY5  N10   C9   C8    125.10  3.000
 ZY5  C15   C14  C19   117.42  3.000
 ZY5  C15   C14  C9    122.73  3.000
 ZY5  C19   C14  C9    119.78  3.000
 ZY5  H19   C19  N18   116.55  3.000
 ZY5  H19   C19  C14   119.56  3.000
 ZY5  N18   C19  C14   123.89  3.000
 ZY5  C17   N18  C19   117.94  3.000
 ZY5  H17   C17  C16   120.28  3.000
 ZY5  H17   C17  N18   116.63  3.000
 ZY5  C16   C17  N18   123.09  3.000
 ZY5  H16   C16  C15   121.13  3.000
 ZY5  H16   C16  C17   120.32  3.000
 ZY5  C15   C16  C17   118.56  3.000
 ZY5  H15   C15  C16   120.26  3.000
 ZY5  H15   C15  C14   120.64  3.000
 ZY5  C16   C15  C14   119.10  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
 ZY5  CONST_01  C1    C2   C3   C4     0.00   0.0  0
 ZY5  CONST_02  C1    C6   C5   C4     0.00   0.0  0
 ZY5  CONST_03  C6    C5   C4   C3     0.00   0.0  0
 ZY5  CONST_04  C6    C1   C2   C3     0.00   0.0  0
 ZY5  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 ZY5  CONST_06  C5    C6   C1   C2     0.00   0.0  0
 ZY5  CONST_07  C17   N18  C19  C14    0.00   0.0  0
 ZY5  CONST_08  C17   C16  C15  C14    0.00   0.0  0
 ZY5  CONST_09  C16   C15  C14  C19    0.00   0.0  0
 ZY5  CONST_10  C16   C17  N18  C19    0.00   0.0  0
 ZY5  CONST_11  C15   C14  C19  N18    0.00   0.0  0
 ZY5  CONST_12  C15   C16  C17  N18    0.00   0.0  0
 ZY5  CONST_13  N18   C19  C14  C9   180.00   0.0  0
 ZY5  CONST_14  C16   C15  C14  C9   180.00   0.0  0
 ZY5  CONST_15  C2    C3   C4   C7   180.00   0.0  0
 ZY5  CONST_16  C6    C5   C4   C7   180.00   0.0  0
 ZY5  CONST_17  O20   C1   C2   C3   180.00   0.0  0
 ZY5  CONST_18  C5    C4   C3   O21  180.00   0.0  0
 ZY5  CONST_19  C1    C2   C3   O21  180.00   0.0  0
 ZY5  CONST_20  O20   C1   C6   C5   180.00   0.0  0
 ZY5  CONST_21  H2    C2   C3   C4   180.00   0.0  0
 ZY5  CONST_22  H6    C6   C5   C4   180.00   0.0  0
 ZY5  CONST_23  H5    C5   C4   C3   180.00   0.0  0
 ZY5  CONST_24  H19   C19  C14  C9     0.00   0.0  0
 ZY5  CONST_25  H15   C15  C14  C9     0.00   0.0  0
 ZY5  CONST_26  H16   C16  C15  C14  180.00   0.0  0
 ZY5  CONST_27  H17   C17  N18  C19  180.00   0.0  0
 ZY5  Var_01    C11   C12  C13  C8   -56.92  30.0  1
 ZY5  Var_02    C19   C14  C9   C8   132.23  30.0  2
 ZY5  Var_03    N10   C9   C8   C13  -12.62  30.0  1
 ZY5  Var_04    N10   C11  C12  C13   45.18  30.0  1
 ZY5  Var_05    C9    C8   C13  C12   41.59  30.0  1
 ZY5  Var_06    C13   C8   C7   C4    -7.94  30.0  2
 ZY5  Var_07    C8    C7   C4   C3   141.45  30.0  3
 ZY5  Var_08    C2    C3   O21  C22   -2.75  30.0  1
 ZY5  Var_09    H221  C22  O21  C3    62.61  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
 ZY5  plan-1  C7   0.020
 ZY5  plan-1  C4   0.020
 ZY5  plan-1  C3   0.020
 ZY5  plan-1  O21  0.020
 ZY5  plan-1  C2   0.020
 ZY5  plan-1  C5   0.020
 ZY5  plan-1  C6   0.020
 ZY5  plan-1  C1   0.020
 ZY5  plan-1  O20  0.020
 ZY5  plan-1  H5   0.020
 ZY5  plan-1  H2   0.020
 ZY5  plan-1  H6   0.020
 ZY5  plan-2  C9   0.020
 ZY5  plan-2  C14  0.020
 ZY5  plan-2  C19  0.020
 ZY5  plan-2  N18  0.020
 ZY5  plan-2  C17  0.020
 ZY5  plan-2  C16  0.020
 ZY5  plan-2  C15  0.020
 ZY5  plan-2  H19  0.020
 ZY5  plan-2  H15  0.020
 ZY5  plan-2  H17  0.020
 ZY5  plan-2  H16  0.020

