# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 04:48:25 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (~{E})-3-(3-azanyl-4-methoxy-phenyl)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)prop-2-en-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(/C=C/C(=O)c2ccc(OC)c3C=CC(C)(C)Oc23)cc1N
#
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
 Y50  Y50  (~{E})-3-(3-azanyl-4-methoxy-phenyl)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)prop-2-en-1-one  ligand  50  27  .  2021-08-25  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y50
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
 Y50  C1   C  CH3   0  -0.435  -7.6370   1.5580  -1.2980
 Y50  O2   O  O2    0  -0.470  -7.2645   0.4051  -0.5691
 Y50  C3   C  CR6   0   0.346  -5.9597   0.1934  -0.3157
 Y50  C4   C  CR16  0  -0.364  -4.9258   1.0116  -0.7537
 Y50  C5   C  CR16  0  -0.337  -3.6067   0.7153  -0.4452
 Y50  C6   C  CR6   0   0.141  -3.3005  -0.4093   0.3182
 Y50  C7   C  C1    0  -0.235  -1.9443  -0.7781   0.6903
 Y50  C8   C  C1    0  -0.400  -0.8148  -0.1114   0.4040
 Y50  C9   C  C     0   0.357   0.5032  -0.6164   0.8316
 Y50  O10  O  O     0  -0.417   0.6374  -1.7163   1.3410
 Y50  C11  C  CR6   0  -0.165   1.6600   0.2859   0.6133
 Y50  C12  C  CR16  0  -0.278   1.5076   1.6655   0.7471
 Y50  C13  C  CR16  0  -0.404   2.5633   2.5485   0.6155
 Y50  C14  C  CR6   0   0.362   3.8322   2.0499   0.3268
 Y50  O15  O  O2    0  -0.457   4.9202   2.8139   0.1784
 Y50  C16  C  CH3   0  -0.439   4.8062   4.2150   0.3545
 Y50  C17  C  CR66  0  -0.134   4.0293   0.6702   0.1720
 Y50  C18  C  CR16  0  -0.204   5.3369   0.0810  -0.0771
 Y50  C19  C  CR16  0  -0.246   5.4219  -1.1908  -0.4603
 Y50  C20  C  CR6   0   0.146   4.1734  -1.9948  -0.6900
 Y50  C21  C  CH3   0  -0.665   4.3800  -3.4513  -0.3112
 Y50  C22  C  CH3   0  -0.651   3.7197  -1.8650  -2.1413
 Y50  O23  O  O     0  -0.467   3.1268  -1.5183   0.1803
 Y50  C24  C  CR66  0   0.373   2.9441  -0.1990   0.3131
 Y50  C25  C  CR16  0  -0.386  -4.3512  -1.2240   0.7596
 Y50  C26  C  CR6   0   0.232  -5.6780  -0.9519   0.4592
 Y50  N27  N  NH2   0  -0.851  -6.7035  -1.7932   0.8477
 Y50  H1   H  HCH3  0   0.231  -7.3211   2.4758  -0.7956
 Y50  H2   H  HCH3  0   0.231  -7.2265   1.5490  -2.3110
 Y50  H3   H  HCH3  0   0.262  -8.7221   1.5471  -1.3593
 Y50  H4   H  HCR6  0   0.282  -5.1374   1.8925  -1.3447
 Y50  H5   H  HCR6  0   0.252  -2.8283   1.3739  -0.8066
 Y50  H6   H  H     0   0.258  -1.8561  -1.6934   1.2691
 Y50  H7   H  H     0   0.266  -0.8414   0.8088  -0.1656
 Y50  H8   H  HCR6  0   0.270   0.5334   2.0724   0.9852
 Y50  H9   H  HCR6  0   0.285   2.3837   3.6065   0.7409
 Y50  H10  H  HCH3  0   0.235   4.1288   4.6611  -0.3768
 Y50  H11  H  HCH3  0   0.235   4.4646   4.4701   1.3598
 Y50  H12  H  HCH3  0   0.264   5.8021   4.6233   0.2054
 Y50  H13  H  HCR6  0   0.258   6.2276   0.6771   0.0677
 Y50  H14  H  HCR6  0   0.262   6.3778  -1.6644  -0.6477
 Y50  H15  H  HCH3  0   0.243   4.6948  -3.5502   0.7282
 Y50  H16  H  HCH3  0   0.244   3.4656  -4.0277  -0.4551
 Y50  H17  H  HCH3  0   0.236   5.1552  -3.8882  -0.9403
 Y50  H18  H  HCH3  0   0.241   4.5057  -2.2223  -2.8078
 Y50  H19  H  HCH3  0   0.239   2.8236  -2.4599  -2.3273
 Y50  H20  H  HCH3  0   0.238   3.5107  -0.8263  -2.4025
 Y50  H21  H  HCR6  0   0.260  -4.1238  -2.0987   1.3600
 Y50  H22  H  HNH2  0   0.377  -7.5970  -1.3496   0.9905
 Y50  H23  H  HNH2  0   0.378  -6.4730  -2.3994   1.6191

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
 Y50  C16  O15  single    1.417  0.020  1.417
 Y50  O15  C14  single    1.338  0.020  1.338
 Y50  C13  C14  aromatic  1.394  0.020  1.394
 Y50  C13  C12  aromatic  1.383  0.020  1.383
 Y50  C14  C17  aromatic  1.402  0.020  1.402
 Y50  C12  C11  aromatic  1.394  0.020  1.394
 Y50  C17  C18  single    1.456  0.020  1.456
 Y50  C17  C24  aromatic  1.398  0.020  1.398
 Y50  C18  C19  double    1.331  0.020  1.331
 Y50  C11  C24  aromatic  1.405  0.020  1.405
 Y50  C11  C9   single    1.483  0.020  1.483
 Y50  C24  O23  single    1.338  0.020  1.338
 Y50  C19  C20  single    1.503  0.020  1.503
 Y50  O10  C9   double    1.220  0.020  1.220
 Y50  C22  C20  single    1.526  0.020  1.526
 Y50  C20  O23  single    1.442  0.020  1.442
 Y50  C20  C21  single    1.519  0.020  1.519
 Y50  C9   C8   single    1.475  0.020  1.475
 Y50  C8   C7   double    1.342  0.020  1.342
 Y50  C7   C6   single    1.454  0.020  1.454
 Y50  C5   C6   aromatic  1.393  0.020  1.393
 Y50  C5   C4   aromatic  1.387  0.020  1.387
 Y50  C6   C25  aromatic  1.401  0.020  1.401
 Y50  C4   C3   aromatic  1.389  0.020  1.389
 Y50  C25  C26  aromatic  1.387  0.020  1.387
 Y50  C3   C26  aromatic  1.411  0.020  1.411
 Y50  C3   O2   single    1.346  0.020  1.346
 Y50  C26  N27  single    1.382  0.020  1.382
 Y50  O2   C1   single    1.414  0.020  1.414
 Y50  C1   H1   single    0.970  0.020  1.090
 Y50  C1   H2   single    0.970  0.020  1.090
 Y50  C1   H3   single    0.970  0.020  1.090
 Y50  C4   H4   single    0.930  0.020  1.080
 Y50  C5   H5   single    0.930  0.020  1.080
 Y50  C7   H6   single    0.930  0.020  1.080
 Y50  C8   H7   single    0.930  0.020  1.080
 Y50  C12  H8   single    0.930  0.020  1.080
 Y50  C13  H9   single    0.930  0.020  1.080
 Y50  C16  H10  single    0.970  0.020  1.090
 Y50  C16  H11  single    0.970  0.020  1.090
 Y50  C16  H12  single    0.970  0.020  1.090
 Y50  C18  H13  single    0.930  0.020  1.080
 Y50  C19  H14  single    0.930  0.020  1.080
 Y50  C21  H15  single    0.970  0.020  1.090
 Y50  C21  H16  single    0.970  0.020  1.090
 Y50  C21  H17  single    0.970  0.020  1.090
 Y50  C22  H18  single    0.970  0.020  1.090
 Y50  C22  H19  single    0.970  0.020  1.090
 Y50  C22  H20  single    0.970  0.020  1.090
 Y50  C25  H21  single    0.930  0.020  1.080
 Y50  N27  H22  single    0.890  0.020  1.040
 Y50  N27  H23  single    0.890  0.020  1.040

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
 Y50  H3   C1   H2   108.82  3.000
 Y50  H3   C1   H1   108.84  3.000
 Y50  H2   C1   H1   108.93  3.000
 Y50  H3   C1   O2   106.49  3.000
 Y50  H2   C1   O2   111.85  3.000
 Y50  H1   C1   O2   111.81  3.000
 Y50  C3   O2   C1   118.73  3.000
 Y50  C26  C3   C4   120.17  3.000
 Y50  C26  C3   O2   115.12  3.000
 Y50  C4   C3   O2   124.71  3.000
 Y50  H4   C4   C5   118.79  3.000
 Y50  H4   C4   C3   120.42  3.000
 Y50  C5   C4   C3   120.80  3.000
 Y50  H5   C5   C6   121.09  3.000
 Y50  H5   C5   C4   118.69  3.000
 Y50  C6   C5   C4   120.22  3.000
 Y50  C25  C6   C7   118.13  3.000
 Y50  C25  C6   C5   118.51  3.000
 Y50  C7   C6   C5   123.36  3.000
 Y50  H6   C7   C8   117.62  3.000
 Y50  H6   C7   C6   115.20  3.000
 Y50  C8   C7   C6   127.18  3.000
 Y50  H7   C8   C9   117.75  3.000
 Y50  H7   C8   C7   120.91  3.000
 Y50  C9   C8   C7   121.34  3.000
 Y50  C11  C9   O10  121.62  3.000
 Y50  O10  C9   C8   121.89  3.000
 Y50  C11  C9   C8   116.49  3.000
 Y50  C24  C11  C12  117.51  3.000
 Y50  C24  C11  C9   122.29  3.000
 Y50  C12  C11  C9   120.17  3.000
 Y50  H8   C12  C13  117.92  3.000
 Y50  H8   C12  C11  119.43  3.000
 Y50  C13  C12  C11  122.64  3.000
 Y50  H9   C13  C14  121.72  3.000
 Y50  H9   C13  C12  119.17  3.000
 Y50  C14  C13  C12  119.11  3.000
 Y50  C17  C14  O15  115.81  3.000
 Y50  C17  C14  C13  120.19  3.000
 Y50  O15  C14  C13  124.00  3.000
 Y50  C16  O15  C14  119.05  3.000
 Y50  H12  C16  H11  108.98  3.000
 Y50  H12  C16  H10  108.86  3.000
 Y50  H11  C16  H10  109.09  3.000
 Y50  H12  C16  O15  106.31  3.000
 Y50  H11  C16  O15  111.75  3.000
 Y50  H10  C16  O15  111.75  3.000
 Y50  C24  C17  C18  117.58  3.000
 Y50  C24  C17  C14  119.45  3.000
 Y50  C18  C17  C14  122.91  3.000
 Y50  H13  C18  C19  120.83  3.000
 Y50  H13  C18  C17  119.59  3.000
 Y50  C19  C18  C17  119.56  3.000
 Y50  H14  C19  C20  118.23  3.000
 Y50  H14  C19  C18  121.60  3.000
 Y50  C20  C19  C18  120.14  3.000
 Y50  O23  C20  C22  109.27  3.000
 Y50  O23  C20  C21  105.37  3.000
 Y50  C22  C20  C21  111.05  3.000
 Y50  C21  C20  C19  111.21  3.000
 Y50  O23  C20  C19  109.51  3.000
 Y50  C22  C20  C19  110.30  3.000
 Y50  H17  C21  H16  107.96  3.000
 Y50  H17  C21  H15  107.97  3.000
 Y50  H16  C21  H15  108.66  3.000
 Y50  H17  C21  C20  109.70  3.000
 Y50  H16  C21  C20  111.09  3.000
 Y50  H15  C21  C20  111.34  3.000
 Y50  H20  C22  H19  108.71  3.000
 Y50  H20  C22  H18  107.68  3.000
 Y50  H19  C22  H18  108.00  3.000
 Y50  H20  C22  C20  111.44  3.000
 Y50  H19  C22  C20  111.08  3.000
 Y50  H18  C22  C20  109.82  3.000
 Y50  C24  O23  C20  118.98  3.000
 Y50  O23  C24  C17  119.80  3.000
 Y50  O23  C24  C11  119.09  3.000
 Y50  C17  C24  C11  121.10  3.000
 Y50  H21  C25  C26  118.58  3.000
 Y50  H21  C25  C6   119.08  3.000
 Y50  C26  C25  C6   122.34  3.000
 Y50  N27  C26  C25  121.96  3.000
 Y50  N27  C26  C3   120.02  3.000
 Y50  C25  C26  C3   117.97  3.000
 Y50  H23  N27  H22  111.04  3.000
 Y50  H23  N27  C26  114.31  3.000
 Y50  H22  N27  C26  115.45  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
 Y50  CONST_01  C6   C5   C4   C3      0.00   0.0  0
 Y50  CONST_02  C6   C25  C26  C3      0.00   0.0  0
 Y50  CONST_03  C25  C6   C5   C4      0.00   0.0  0
 Y50  CONST_04  C25  C26  C3   C4      0.00   0.0  0
 Y50  CONST_05  C26  C25  C6   C5      0.00   0.0  0
 Y50  CONST_06  C26  C3   C4   C5      0.00   0.0  0
 Y50  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 Y50  CONST_08  C14  C17  C24  C11     0.00   0.0  0
 Y50  CONST_09  C17  C14  C13  C12     0.00   0.0  0
 Y50  CONST_10  C17  C24  C11  C12     0.00   0.0  0
 Y50  CONST_11  C24  C17  C14  C13     0.00   0.0  0
 Y50  CONST_12  C24  C11  C12  C13     0.00   0.0  0
 Y50  CONST_13  C5   C4   C3   O2    180.00   0.0  0
 Y50  CONST_14  C25  C26  C3   O2    180.00   0.0  0
 Y50  CONST_15  C7   C6   C5   C4    180.00   0.0  0
 Y50  CONST_16  N27  C26  C3   C4    180.00   0.0  0
 Y50  CONST_17  N27  C26  C25  C6    180.00   0.0  0
 Y50  CONST_18  C26  C25  C6   C7    180.00   0.0  0
 Y50  CONST_19  C13  C12  C11  C9    180.00   0.0  0
 Y50  CONST_20  C17  C24  C11  C9    180.00   0.0  0
 Y50  CONST_21  O23  C24  C11  C9      0.00   0.0  0
 Y50  CONST_22  O15  C14  C13  C12   180.00   0.0  0
 Y50  CONST_23  C18  C17  C14  O15     0.00   0.0  0
 Y50  CONST_24  C24  C17  C14  O15   180.00   0.0  0
 Y50  CONST_25  H5   C5   C4   C3    180.00   0.0  0
 Y50  CONST_26  H21  C25  C26  C3    180.00   0.0  0
 Y50  CONST_27  H4   C4   C5   C6    180.00   0.0  0
 Y50  CONST_28  H9   C13  C12  C11   180.00   0.0  0
 Y50  CONST_29  H8   C12  C13  C14   180.00   0.0  0
 Y50  Var_01    C19  C18  C17  C14  -167.48  30.0  1
 Y50  Var_02    C20  C19  C18  C17     2.58  30.0  1
 Y50  Var_03    O23  C20  C19  C18   -30.34  30.0  1
 Y50  Var_04    C4   C3   O2   C1     -1.98  30.0  2
 Y50  Var_05    C8   C7   C6   C5      1.76  30.0  2
 Y50  Var_06    C12  C11  C9   C8     35.13  30.0  2
 Y50  Var_07    C17  C14  O15  C16  -178.38  30.0  2
 Y50  Var_08    H18  C22  C20  C19    59.51  30.0  3
 Y50  Var_09    H15  C21  C20  C19    57.33  30.0  3
 Y50  Var_10    C9   C8   C7   C6   -179.08   0.0  2
 Y50  Var_11    C11  C9   C8   C7   -172.39  30.0  1
 Y50  Var_12    H1   C1   O2   C3    -59.49  30.0  3
 Y50  Var_13    H10  C16  O15  C14   -62.34  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
 Y50  plan-1  O2   0.020
 Y50  plan-1  C3   0.020
 Y50  plan-1  C4   0.020
 Y50  plan-1  C5   0.020
 Y50  plan-1  C6   0.020
 Y50  plan-1  C7   0.020
 Y50  plan-1  C25  0.020
 Y50  plan-1  C26  0.020
 Y50  plan-1  N27  0.020
 Y50  plan-1  H4   0.020
 Y50  plan-1  H5   0.020
 Y50  plan-1  H21  0.020
 Y50  plan-2  C9   0.020
 Y50  plan-2  C11  0.020
 Y50  plan-2  C12  0.020
 Y50  plan-2  C13  0.020
 Y50  plan-2  C14  0.020
 Y50  plan-2  O15  0.020
 Y50  plan-2  C17  0.020
 Y50  plan-2  C18  0.020
 Y50  plan-2  O23  0.020
 Y50  plan-2  C24  0.020
 Y50  plan-2  H8   0.020
 Y50  plan-2  H9   0.020
 Y50  plan-3  C26  0.020
 Y50  plan-3  N27  0.020
 Y50  plan-3  H22  0.020
 Y50  plan-3  H23  0.020
 Y50  plan-4  C8   0.020
 Y50  plan-4  C9   0.020
 Y50  plan-4  O10  0.020
 Y50  plan-4  C11  0.020
 Y50  plan-5  C6   0.020
 Y50  plan-5  C7   0.020
 Y50  plan-5  C8   0.020
 Y50  plan-5  C9   0.020
 Y50  plan-5  H6   0.020
 Y50  plan-5  H7   0.020

