# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:57:50 2022
#   Inital geometry file: a 129 line input string
#   Ligand name: methyl (2E)-2-(2-{[6-(2-cyanophenoxy)pyrimidin-4-yl]oxy}phenyl)-3-methoxyprop-2-enoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO\C=C(C(=O)OC)/c1ccccc1Oc2cc(Oc3ccccc3C#N)ncn2
#
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
 AZO  AZO  'methyl (2E)-2-(2-{[6-(2-cyanophenoxy)pyrimidin-4-yl]oxy}phenyl)-3-methoxyprop-2-enoate'  ligand  47  30  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AZO
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
 AZO  N1    N  NS    0  -0.239  -4.3342   2.4768  -1.3332
 AZO  C1    C  CSP   0   0.053  -4.5465   1.4161  -0.9377
 AZO  C2    C  CR6   0  -0.024  -4.8100   0.1043  -0.4490
 AZO  C3    C  CR16  0  -0.253  -6.0356  -0.1982   0.1420
 AZO  C4    C  CR16  0  -0.247  -6.2751  -1.4803   0.6056
 AZO  C5    C  CR16  0  -0.237  -5.2968  -2.4574   0.4771
 AZO  C6    C  CR16  0  -0.306  -4.0713  -2.1629  -0.1063
 AZO  C7    C  CR6   0   0.374  -3.8331  -0.8842  -0.5676
 AZO  O1    O  O2    0  -0.498  -2.6568  -0.6064  -1.2128
 AZO  C8    C  CR6   0   0.558  -1.6928   0.0705  -0.5637
 AZO  C9    C  CR16  0  -0.460  -0.5248   0.3367  -1.2555
 AZO  C10   C  CR6   0   0.560   0.4278   1.0324  -0.5266
 AZO  N3    N  N     0  -0.435   0.2373   1.4304   0.7200
 AZO  C11   C  CR16  0   0.080  -0.9195   1.1050   1.2645
 AZO  N2    N  N     0  -0.449  -1.9031   0.4353   0.6868
 AZO  O2    O  O2    0  -0.501   1.5810   1.3241  -1.1354
 AZO  C12   C  CR6   0   0.329   2.6575   1.7207  -0.3681
 AZO  C13   C  CR16  0  -0.313   3.0874   3.0309  -0.4577
 AZO  C14   C  CR16  0  -0.267   4.2041   3.4271   0.2667
 AZO  C15   C  CR16  0  -0.246   4.8666   2.5145   1.0745
 AZO  C16   C  CR16  0  -0.301   4.4195   1.2018   1.1485
 AZO  C17   C  CR6   0   0.098   3.3095   0.7805   0.4244
 AZO  C18   C  C     0  -0.343   2.8297  -0.6161   0.4768
 AZO  C19   C  C     0   0.587   3.0149  -1.4277  -0.7303
 AZO  O3    O  O     0  -0.457   3.5732  -1.0224  -1.7242
 AZO  O4    O  O2    0  -0.468   2.5112  -2.6552  -0.6306
 AZO  C20   C  CH3   0  -0.420   2.6748  -3.5258  -1.7472
 AZO  C21   C  C1    0   0.164   2.2492  -1.1235   1.5806
 AZO  O5    O  O2    0  -0.419   2.0770  -0.3967   2.6682
 AZO  C22   C  CH3   0  -0.429   1.3872  -1.0221   3.7468
 AZO  H3    H  HCR6  0   0.291  -6.7891   0.5717   0.2341
 AZO  H4    H  HCR6  0   0.280  -7.2254  -1.7179   1.0626
 AZO  H5    H  HCR6  0   0.283  -5.4848  -3.4602   0.8359
 AZO  H6    H  HCR6  0   0.290  -3.3084  -2.9231  -0.2079
 AZO  H9    H  HCR6  0   0.301  -0.3625   0.0187  -2.2754
 AZO  H11   H  HCR6  0   0.275  -1.0837   1.4207   2.2881
 AZO  H13   H  HCR6  0   0.272   2.5581   3.7331  -1.0890
 AZO  H14   H  HCR6  0   0.265   4.5487   4.4505   0.2011
 AZO  H15   H  HCR6  0   0.260   5.7364   2.8201   1.6405
 AZO  H16   H  HCR6  0   0.258   4.9445   0.4876   1.7700
 AZO  H201  H  HCH3  0   0.236   2.1867  -3.1324  -2.6387
 AZO  H202  H  HCH3  0   0.237   3.7275  -3.7054  -1.9654
 AZO  H203  H  HCH3  0   0.250   2.2031  -4.4625  -1.4651
 AZO  H21   H  H     0   0.271   1.8994  -2.1519   1.6150
 AZO  H221  H  HCH3  0   0.260   1.3457  -0.2981   4.5553
 AZO  H222  H  HCH3  0   0.239   0.3705  -1.2930   3.4580
 AZO  H223  H  HCH3  0   0.245   1.9160  -1.9131   4.0879

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
 AZO  N1   C1    triple    1.152  0.020  1.152
 AZO  C1   C2    single    1.424  0.020  1.424
 AZO  C2   C3    aromatic  1.394  0.020  1.394
 AZO  C2   C7    aromatic  1.395  0.020  1.395
 AZO  C3   C4    aromatic  1.384  0.020  1.384
 AZO  C3   H3    single    0.930  0.020  1.080
 AZO  C4   C5    aromatic  1.389  0.020  1.389
 AZO  C4   H4    single    0.930  0.020  1.080
 AZO  C5   C6    aromatic  1.389  0.020  1.389
 AZO  C5   H5    single    0.930  0.020  1.080
 AZO  C6   C7    aromatic  1.380  0.020  1.380
 AZO  C6   H6    single    0.930  0.020  1.080
 AZO  C7   O1    single    1.370  0.020  1.370
 AZO  O1   C8    single    1.345  0.020  1.345
 AZO  C8   C9    aromatic  1.383  0.020  1.383
 AZO  C8   N2    aromatic  1.320  0.020  1.320
 AZO  C9   C10   aromatic  1.387  0.020  1.387
 AZO  C9   H9    single    0.930  0.020  1.080
 AZO  C10  N3    aromatic  1.322  0.020  1.322
 AZO  C10  O2    single    1.336  0.020  1.336
 AZO  N3   C11   aromatic  1.319  0.020  1.319
 AZO  C11  N2    aromatic  1.323  0.020  1.323
 AZO  C11  H11   single    0.930  0.020  1.080
 AZO  O2   C12   single    1.380  0.020  1.380
 AZO  C12  C13   aromatic  1.382  0.020  1.382
 AZO  C12  C17   aromatic  1.392  0.020  1.392
 AZO  C13  C14   aromatic  1.389  0.020  1.389
 AZO  C13  H13   single    0.930  0.020  1.080
 AZO  C14  C15   aromatic  1.387  0.020  1.387
 AZO  C14  H14   single    0.930  0.020  1.080
 AZO  C15  C16   aromatic  1.389  0.020  1.389
 AZO  C15  H15   single    0.930  0.020  1.080
 AZO  C16  C17   aromatic  1.391  0.020  1.391
 AZO  C16  H16   single    0.930  0.020  1.080
 AZO  C17  C18   single    1.478  0.020  1.478
 AZO  C18  C19   single    1.466  0.020  1.466
 AZO  C18  C21   double    1.346  0.020  1.346
 AZO  C19  O3    double    1.210  0.020  1.210
 AZO  C19  O4    single    1.331  0.020  1.331
 AZO  O4   C20   single    1.425  0.020  1.425
 AZO  C20  H201  single    0.970  0.020  1.090
 AZO  C20  H202  single    0.970  0.020  1.090
 AZO  C20  H203  single    0.970  0.020  1.090
 AZO  C21  O5    single    1.319  0.020  1.319
 AZO  C21  H21   single    0.930  0.020  1.080
 AZO  O5   C22   single    1.425  0.020  1.425
 AZO  C22  H221  single    0.970  0.020  1.090
 AZO  C22  H222  single    0.970  0.020  1.090
 AZO  C22  H223  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
 AZO  C2    C1   N1    180.00  3.000
 AZO  C7    C2   C3    119.87  3.000
 AZO  C7    C2   C1    119.60  3.000
 AZO  C3    C2   C1    120.53  3.000
 AZO  H3    C3   C4    120.69  3.000
 AZO  H3    C3   C2    119.63  3.000
 AZO  C4    C3   C2    119.68  3.000
 AZO  H4    C4   C5    120.25  3.000
 AZO  H4    C4   C3    119.82  3.000
 AZO  C5    C4   C3    119.93  3.000
 AZO  H5    C5   C6    119.30  3.000
 AZO  H5    C5   C4    119.96  3.000
 AZO  C6    C5   C4    120.75  3.000
 AZO  H6    C6   C7    119.87  3.000
 AZO  H6    C6   C5    120.84  3.000
 AZO  C7    C6   C5    119.29  3.000
 AZO  O1    C7   C6    119.57  3.000
 AZO  O1    C7   C2    119.84  3.000
 AZO  C6    C7   C2    120.48  3.000
 AZO  C8    O1   C7    119.35  3.000
 AZO  N2    C8   C9    123.73  3.000
 AZO  N2    C8   O1    118.84  3.000
 AZO  C9    C8   O1    117.43  3.000
 AZO  H9    C9   C10   122.72  3.000
 AZO  H9    C9   C8    122.83  3.000
 AZO  C10   C9   C8    114.44  3.000
 AZO  O2    C10  N3    119.22  3.000
 AZO  O2    C10  C9    117.58  3.000
 AZO  N3    C10  C9    123.20  3.000
 AZO  C11   N3   C10   116.18  3.000
 AZO  H11   C11  N2    116.57  3.000
 AZO  H11   C11  N3    116.80  3.000
 AZO  N2    C11  N3    126.63  3.000
 AZO  C11   N2   C8    115.81  3.000
 AZO  C12   O2   C10   118.85  3.000
 AZO  C17   C12  C13   122.11  3.000
 AZO  C17   C12  O2    119.20  3.000
 AZO  C13   C12  O2    118.63  3.000
 AZO  H13   C13  C14   120.82  3.000
 AZO  H13   C13  C12   120.04  3.000
 AZO  C14   C13  C12   119.14  3.000
 AZO  H14   C14  C15   120.36  3.000
 AZO  H14   C14  C13   119.63  3.000
 AZO  C15   C14  C13   120.00  3.000
 AZO  H15   C15  C16   119.87  3.000
 AZO  H15   C15  C14   120.18  3.000
 AZO  C16   C15  C14   119.94  3.000
 AZO  H16   C16  C17   119.09  3.000
 AZO  H16   C16  C15   119.87  3.000
 AZO  C17   C16  C15   121.04  3.000
 AZO  C18   C17  C16   121.80  3.000
 AZO  C18   C17  C12   120.43  3.000
 AZO  C16   C17  C12   117.76  3.000
 AZO  C21   C18  C19   121.38  3.000
 AZO  C21   C18  C17   121.68  3.000
 AZO  C19   C18  C17   116.93  3.000
 AZO  O4    C19  O3    123.05  3.000
 AZO  O4    C19  C18   113.65  3.000
 AZO  O3    C19  C18   123.30  3.000
 AZO  C20   O4   C19   117.47  3.000
 AZO  H203  C20  H202  109.24  3.000
 AZO  H203  C20  H201  109.22  3.000
 AZO  H202  C20  H201  109.17  3.000
 AZO  H203  C20  O4    105.87  3.000
 AZO  H202  C20  O4    111.61  3.000
 AZO  H201  C20  O4    111.65  3.000
 AZO  H21   C21  O5    116.95  3.000
 AZO  H21   C21  C18   121.42  3.000
 AZO  O5    C21  C18   121.63  3.000
 AZO  C22   O5   C21   116.45  3.000
 AZO  H223  C22  H222  109.37  3.000
 AZO  H223  C22  H221  109.28  3.000
 AZO  H222  C22  H221  109.08  3.000
 AZO  H223  C22  O5    111.14  3.000
 AZO  H222  C22  O5    111.08  3.000
 AZO  H221  C22  O5    106.83  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
 AZO  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 AZO  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 AZO  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 AZO  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 AZO  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 AZO  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 AZO  CONST_07  N3    C10  C9   C8      0.00   0.0  0
 AZO  CONST_08  N3    C11  N2   C8      0.00   0.0  0
 AZO  CONST_09  C11   N2   C8   C9      0.00   0.0  0
 AZO  CONST_10  C11   N3   C10  C9      0.00   0.0  0
 AZO  CONST_11  N2    C8   C9   C10     0.00   0.0  0
 AZO  CONST_12  N2    C11  N3   C10     0.00   0.0  0
 AZO  CONST_13  C15   C14  C13  C12     0.00   0.0  0
 AZO  CONST_14  C15   C16  C17  C12     0.00   0.0  0
 AZO  CONST_15  C16   C17  C12  C13     0.00   0.0  0
 AZO  CONST_16  C16   C15  C14  C13     0.00   0.0  0
 AZO  CONST_17  C17   C12  C13  C14     0.00   0.0  0
 AZO  CONST_18  C17   C16  C15  C14     0.00   0.0  0
 AZO  CONST_19  C4    C3   C2   C1    180.00   0.0  0
 AZO  CONST_20  C6    C7   C2   C1    180.00   0.0  0
 AZO  CONST_21  O1    C7   C2   C3    180.00   0.0  0
 AZO  CONST_22  O1    C7   C6   C5    180.00   0.0  0
 AZO  CONST_23  C10   C9   C8   O1    180.00   0.0  0
 AZO  CONST_24  C11   N2   C8   O1    180.00   0.0  0
 AZO  CONST_25  O2    C10  C9   C8    180.00   0.0  0
 AZO  CONST_26  O2    C10  N3   C11   180.00   0.0  0
 AZO  CONST_27  C14   C13  C12  O2    180.00   0.0  0
 AZO  CONST_28  C16   C17  C12  O2    180.00   0.0  0
 AZO  CONST_29  C18   C17  C12  C13   180.00   0.0  0
 AZO  CONST_30  C18   C17  C16  C15   180.00   0.0  0
 AZO  CONST_31  H4    C4   C3   C2    180.00   0.0  0
 AZO  CONST_32  H6    C6   C7   C2    180.00   0.0  0
 AZO  CONST_33  H5    C5   C4   C3    180.00   0.0  0
 AZO  CONST_34  H3    C3   C4   C5    180.00   0.0  0
 AZO  CONST_35  H11   C11  N2   C8    180.00   0.0  0
 AZO  CONST_36  H9    C9   C10  N3    180.00   0.0  0
 AZO  CONST_37  H14   C14  C13  C12   180.00   0.0  0
 AZO  CONST_38  H16   C16  C17  C12   180.00   0.0  0
 AZO  CONST_39  H15   C15  C14  C13   180.00   0.0  0
 AZO  CONST_40  H13   C13  C14  C15   180.00   0.0  0
 AZO  Var_01    C9    C8   O1   C7   -179.60  30.0  2
 AZO  Var_02    C13   C12  O2   C10  -110.87  30.0  2
 AZO  Var_03    C19   C18  C17  C12    69.83  30.0  2
 AZO  Var_04    O5    C21  C18  C17     0.20   0.0  2
 AZO  Var_05    O3    C19  C18  C17     2.64  30.0  2
 AZO  Var_06    H201  C20  O4   C19   -61.39  30.0  3
 AZO  Var_07    H221  C22  O5   C21   179.25  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
 AZO  plan-1  N1   0.020
 AZO  plan-1  C1   0.020
 AZO  plan-1  C2   0.020
 AZO  plan-1  C3   0.020
 AZO  plan-1  C4   0.020
 AZO  plan-1  C5   0.020
 AZO  plan-1  C6   0.020
 AZO  plan-1  C7   0.020
 AZO  plan-1  O1   0.020
 AZO  plan-1  H3   0.020
 AZO  plan-1  H4   0.020
 AZO  plan-1  H5   0.020
 AZO  plan-1  H6   0.020
 AZO  plan-2  O1   0.020
 AZO  plan-2  C8   0.020
 AZO  plan-2  C9   0.020
 AZO  plan-2  C10  0.020
 AZO  plan-2  N3   0.020
 AZO  plan-2  C11  0.020
 AZO  plan-2  N2   0.020
 AZO  plan-2  O2   0.020
 AZO  plan-2  H9   0.020
 AZO  plan-2  H11  0.020
 AZO  plan-3  O2   0.020
 AZO  plan-3  C12  0.020
 AZO  plan-3  C13  0.020
 AZO  plan-3  C14  0.020
 AZO  plan-3  C15  0.020
 AZO  plan-3  C16  0.020
 AZO  plan-3  C17  0.020
 AZO  plan-3  C18  0.020
 AZO  plan-3  H13  0.020
 AZO  plan-3  H14  0.020
 AZO  plan-3  H15  0.020
 AZO  plan-3  H16  0.020
 AZO  plan-4  C17  0.020
 AZO  plan-4  C18  0.020
 AZO  plan-4  C19  0.020
 AZO  plan-4  C21  0.020
 AZO  plan-4  O5   0.020
 AZO  plan-4  H21  0.020
 AZO  plan-5  C18  0.020
 AZO  plan-5  C19  0.020
 AZO  plan-5  O3   0.020
 AZO  plan-5  O4   0.020

