# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 08:52:40 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2E)-3-(3-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(Oc2cccc(\C=C\C#N)c2)c(OCCN3C=CC(=O)NC3=O)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
 1YQ  1YQ  (2E)-3-(3-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile  ligand  45  29  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1YQ
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
 1YQ  O12  O   O     0  -0.462  -3.4877   1.2672  -3.1640
 1YQ  C17  C   CSP   0   0.088   6.0496   3.3932   2.5034
 1YQ  C00  C   CR16  0  -0.344  -1.9376  -2.0883  -0.0254
 1YQ  C01  C   CR6   0  -0.026  -2.0844  -2.8206  -1.1963
 1YQ  C02  C   CR16  0  -0.246  -1.0052  -3.1883  -1.9756
 1YQ  C03  C   CR16  0  -0.312   0.2631  -2.7953  -1.5667
 1YQ  C04  C   CR6   0   0.229   0.4330  -2.0552  -0.4152
 1YQ  C05  C   CR6   0   0.374  -0.6682  -1.6838   0.3707
 1YQ  O0A  O   O2    0  -0.507   1.6887  -1.7084   0.0048
 1YQ  O0B  O   O2    0  -0.470  -0.3755  -0.9643   1.4649
 1YQ  C0C  C   CR6   0   0.404   2.1103  -0.4294  -0.2118
 1YQ  C0D  C   CR16  0  -0.349   1.6657   0.3448  -1.2737
 1YQ  C0E  C   CR16  0  -0.231   2.1777   1.6280  -1.4382
 1YQ  C0F  C   CR16  0  -0.319   3.1188   2.1387  -0.5650
 1YQ  C0G  C   CR6   0   0.152   3.5732   1.3537   0.4997
 1YQ  C0H  C   CR16  0  -0.389   3.0620   0.0682   0.6671
 1YQ  C0M  C   C1    0  -0.204   4.5629   1.8194   1.4636
 1YQ  C0O  C   CH2   0  -0.220  -1.3842  -0.4917   2.3449
 1YQ  C0P  C   CH2   0  -0.345  -1.7640   0.9423   2.0207
 1YQ  N0S  N   NR6   0  -0.520  -2.2395   1.1098   0.6535
 1YQ  C0V  C   CR6   0   0.725  -3.5424   0.7722   0.3549
 1YQ  N0W  N   NR16  0  -0.728  -3.8718   0.8698  -0.9696
 1YQ  C0X  C   CR6   0   0.569  -3.0547   1.2461  -2.0272
 1YQ  C0Y  C   CR16  0  -0.507  -1.7155   1.5918  -1.6208
 1YQ  C0Z  C   CR16  0   0.106  -1.3775   1.5119  -0.3233
 1YQ  C15  C   C1    0  -0.351   5.0874   3.0518   1.5180
 1YQ  N19  N   NS    0  -0.268   6.8269   3.6916   3.3022
 1YQ  H1   H   HCR6  0   0.299  -2.8176  -1.8663   0.5610
 1YQ  H2   H   HCR6  0   0.284  -1.1375  -3.7619  -2.8816
 1YQ  H3   H   HCR6  0   0.288   1.1302  -3.0726  -2.1524
 1YQ  H7   H   HCR6  0   0.289   0.9349  -0.0355  -1.9753
 1YQ  H8   H   HCR6  0   0.275   1.8323   2.2300  -2.2684
 1YQ  H9   H   HCR6  0   0.265   3.5009   3.1381  -0.7236
 1YQ  H10  H   HCR6  0   0.277   3.4067  -0.5503   1.4872
 1YQ  H11  H   H     0   0.292   4.8877   1.0874   2.1951
 1YQ  H12  H   HCH2  0   0.256  -2.2563  -1.1449   2.3617
 1YQ  H13  H   HCH2  0   0.285  -0.9516  -0.5099   3.3452
 1YQ  H14  H   HCH2  0   0.293  -2.5265   1.2777   2.7212
 1YQ  H15  H   HCH2  0   0.285  -0.9014   1.5947   2.1452
 1YQ  H16  H   HNR6  0   0.427  -4.8271   0.6216  -1.1970
 1YQ  H17  H   HCR6  0   0.288  -0.9998   1.9190  -2.3592
 1YQ  H18  H   HCR6  0   0.317  -0.3849   1.7725   0.0162
 1YQ  H19  H   H     0   0.322   4.8135   3.8441   0.8327
 1YQ  O10  O   O     0  -0.475  -4.3326   0.4036   1.2003
 1YQ  CL1  CL  CL    0  -0.118  -3.6832  -3.2786  -1.6809

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
 1YQ  O12  C0X  double    1.217  0.020  1.217
 1YQ  C17  C15  single    1.419  0.020  1.419
 1YQ  C17  N19  triple    1.154  0.020  1.154
 1YQ  C00  C01  aromatic  1.389  0.020  1.389
 1YQ  C00  C05  aromatic  1.390  0.020  1.390
 1YQ  C01  C02  aromatic  1.381  0.020  1.381
 1YQ  C02  C03  aromatic  1.389  0.020  1.389
 1YQ  C03  C04  aromatic  1.379  0.020  1.379
 1YQ  C04  C05  aromatic  1.403  0.020  1.403
 1YQ  C04  O0A  single    1.369  0.020  1.369
 1YQ  C05  O0B  single    1.342  0.020  1.342
 1YQ  O0A  C0C  single    1.364  0.020  1.364
 1YQ  O0B  C0O  single    1.420  0.020  1.420
 1YQ  C0C  C0D  aromatic  1.387  0.020  1.387
 1YQ  C0C  C0H  aromatic  1.388  0.020  1.388
 1YQ  C0D  C0E  aromatic  1.391  0.020  1.391
 1YQ  C0E  C0F  aromatic  1.382  0.020  1.382
 1YQ  C0F  C0G  aromatic  1.399  0.020  1.399
 1YQ  C0G  C0H  aromatic  1.393  0.020  1.393
 1YQ  C0G  C0M  single    1.458  0.020  1.458
 1YQ  C0M  C15  double    1.340  0.020  1.340
 1YQ  C0O  C0P  single    1.519  0.020  1.519
 1YQ  C0P  N0S  single    1.457  0.020  1.457
 1YQ  N0S  C0V  single    1.379  0.020  1.379
 1YQ  N0S  C0Z  single    1.363  0.020  1.363
 1YQ  C0V  N0W  single    1.368  0.020  1.368
 1YQ  C0V  O10  double    1.214  0.020  1.214
 1YQ  N0W  C0X  single    1.388  0.020  1.388
 1YQ  C0X  C0Y  single    1.442  0.020  1.442
 1YQ  C0Y  C0Z  double    1.343  0.020  1.343
 1YQ  C01  CL1  single    1.732  0.020  1.732
 1YQ  C00  H1   single    0.930  0.020  1.080
 1YQ  C02  H2   single    0.930  0.020  1.080
 1YQ  C03  H3   single    0.930  0.020  1.080
 1YQ  C0D  H7   single    0.930  0.020  1.080
 1YQ  C0E  H8   single    0.930  0.020  1.080
 1YQ  C0F  H9   single    0.930  0.020  1.080
 1YQ  C0H  H10  single    0.930  0.020  1.080
 1YQ  C0M  H11  single    0.930  0.020  1.080
 1YQ  C0O  H12  single    0.970  0.020  1.090
 1YQ  C0O  H13  single    0.970  0.020  1.090
 1YQ  C0P  H14  single    0.970  0.020  1.090
 1YQ  C0P  H15  single    0.970  0.020  1.090
 1YQ  N0W  H16  single    0.860  0.020  1.020
 1YQ  C0Y  H17  single    0.930  0.020  1.080
 1YQ  C0Z  H18  single    0.930  0.020  1.080
 1YQ  C15  H19  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
 1YQ  N19  C17  C15  180.00  3.000
 1YQ  H1   C00  C05  121.96  3.000
 1YQ  H1   C00  C01  118.67  3.000
 1YQ  C05  C00  C01  119.36  3.000
 1YQ  CL1  C01  C02  119.54  3.000
 1YQ  CL1  C01  C00  118.22  3.000
 1YQ  C02  C01  C00  122.25  3.000
 1YQ  H2   C02  C03  120.58  3.000
 1YQ  H2   C02  C01  121.26  3.000
 1YQ  C03  C02  C01  118.16  3.000
 1YQ  H3   C03  C04  119.37  3.000
 1YQ  H3   C03  C02  119.97  3.000
 1YQ  C04  C03  C02  120.66  3.000
 1YQ  O0A  C04  C05  118.76  3.000
 1YQ  O0A  C04  C03  120.34  3.000
 1YQ  C05  C04  C03  120.87  3.000
 1YQ  O0B  C05  C04  115.31  3.000
 1YQ  O0B  C05  C00  125.99  3.000
 1YQ  C04  C05  C00  118.70  3.000
 1YQ  C0C  O0A  C04  118.19  3.000
 1YQ  C0O  O0B  C05  121.94  3.000
 1YQ  C0H  C0C  C0D  120.30  3.000
 1YQ  C0H  C0C  O0A  116.59  3.000
 1YQ  C0D  C0C  O0A  123.07  3.000
 1YQ  H7   C0D  C0E  119.74  3.000
 1YQ  H7   C0D  C0C  121.11  3.000
 1YQ  C0E  C0D  C0C  119.16  3.000
 1YQ  H8   C0E  C0F  119.78  3.000
 1YQ  H8   C0E  C0D  119.10  3.000
 1YQ  C0F  C0E  C0D  121.12  3.000
 1YQ  H9   C0F  C0G  121.03  3.000
 1YQ  H9   C0F  C0E  119.31  3.000
 1YQ  C0G  C0F  C0E  119.66  3.000
 1YQ  C0M  C0G  C0H  117.66  3.000
 1YQ  C0M  C0G  C0F  122.99  3.000
 1YQ  C0H  C0G  C0F  119.35  3.000
 1YQ  H10  C0H  C0G  120.06  3.000
 1YQ  H10  C0H  C0C  119.53  3.000
 1YQ  C0G  C0H  C0C  120.41  3.000
 1YQ  H11  C0M  C15  118.42  3.000
 1YQ  H11  C0M  C0G  115.70  3.000
 1YQ  C15  C0M  C0G  125.88  3.000
 1YQ  H13  C0O  H12  107.07  3.000
 1YQ  H13  C0O  C0P  108.12  3.000
 1YQ  H12  C0O  C0P  111.67  3.000
 1YQ  H13  C0O  O0B  106.34  3.000
 1YQ  H12  C0O  O0B  112.25  3.000
 1YQ  C0P  C0O  O0B  111.08  3.000
 1YQ  H15  C0P  H14  107.26  3.000
 1YQ  H15  C0P  N0S  107.27  3.000
 1YQ  H14  C0P  N0S  109.87  3.000
 1YQ  H15  C0P  C0O  110.08  3.000
 1YQ  H14  C0P  C0O  109.20  3.000
 1YQ  N0S  C0P  C0O  112.98  3.000
 1YQ  C0Z  N0S  C0V  120.97  3.000
 1YQ  C0Z  N0S  C0P  119.99  3.000
 1YQ  C0V  N0S  C0P  118.91  3.000
 1YQ  O10  C0V  N0W  122.61  3.000
 1YQ  O10  C0V  N0S  122.58  3.000
 1YQ  N0W  C0V  N0S  114.81  3.000
 1YQ  H16  N0W  C0X  116.77  3.000
 1YQ  H16  N0W  C0V  115.27  3.000
 1YQ  C0X  N0W  C0V  127.95  3.000
 1YQ  C0Y  C0X  N0W  113.39  3.000
 1YQ  C0Y  C0X  O12  126.15  3.000
 1YQ  N0W  C0X  O12  120.47  3.000
 1YQ  H17  C0Y  C0Z  120.80  3.000
 1YQ  H17  C0Y  C0X  119.73  3.000
 1YQ  C0Z  C0Y  C0X  119.46  3.000
 1YQ  H18  C0Z  C0Y  121.35  3.000
 1YQ  H18  C0Z  N0S  115.25  3.000
 1YQ  C0Y  C0Z  N0S  123.40  3.000
 1YQ  H19  C15  C0M  123.24  3.000
 1YQ  H19  C15  C17  115.78  3.000
 1YQ  C0M  C15  C17  120.98  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
 1YQ  CONST_01  C03  C02  C01  C00    0.00   0.0  0
 1YQ  CONST_02  C03  C04  C05  C00    0.00   0.0  0
 1YQ  CONST_03  C04  C05  C00  C01    0.00   0.0  0
 1YQ  CONST_04  C04  C03  C02  C01    0.00   0.0  0
 1YQ  CONST_05  C05  C00  C01  C02    0.00   0.0  0
 1YQ  CONST_06  C05  C04  C03  C02    0.00   0.0  0
 1YQ  CONST_07  C0F  C0E  C0D  C0C    0.00   0.0  0
 1YQ  CONST_08  C0F  C0G  C0H  C0C    0.00   0.0  0
 1YQ  CONST_09  C0G  C0H  C0C  C0D    0.00   0.0  0
 1YQ  CONST_10  C0G  C0F  C0E  C0D    0.00   0.0  0
 1YQ  CONST_11  C0H  C0C  C0D  C0E    0.00   0.0  0
 1YQ  CONST_12  C0H  C0G  C0F  C0E    0.00   0.0  0
 1YQ  CONST_13  C0X  N0W  C0V  N0S    0.00   0.0  0
 1YQ  CONST_14  C0Y  C0X  N0W  C0V    0.00   0.0  0
 1YQ  CONST_15  C0Z  N0S  C0V  N0W    0.00   0.0  0
 1YQ  CONST_16  O0A  C04  C05  C00  180.00   0.0  0
 1YQ  CONST_17  O0B  C05  C00  C01  180.00   0.0  0
 1YQ  CONST_18  O0A  C04  C03  C02  180.00   0.0  0
 1YQ  CONST_19  CL1  C01  C02  C03  180.00   0.0  0
 1YQ  CONST_20  O0B  C05  C04  C03  180.00   0.0  0
 1YQ  CONST_21  CL1  C01  C00  C05  180.00   0.0  0
 1YQ  CONST_22  C0E  C0D  C0C  O0A  180.00   0.0  0
 1YQ  CONST_23  C0G  C0H  C0C  O0A  180.00   0.0  0
 1YQ  CONST_24  C0M  C0G  C0H  C0C  180.00   0.0  0
 1YQ  CONST_25  C0M  C0G  C0F  C0E  180.00   0.0  0
 1YQ  CONST_26  C0V  N0W  C0X  O12  180.00   0.0  0
 1YQ  CONST_27  N0W  C0V  N0S  C0P  180.00   0.0  0
 1YQ  CONST_28  O10  C0V  N0W  C0X  180.00   0.0  0
 1YQ  CONST_29  O10  C0V  N0S  C0Z  180.00   0.0  0
 1YQ  CONST_30  H2   C02  C01  C00  180.00   0.0  0
 1YQ  CONST_31  H3   C03  C02  C01  180.00   0.0  0
 1YQ  CONST_32  H1   C00  C01  C02  180.00   0.0  0
 1YQ  CONST_33  H8   C0E  C0D  C0C  180.00   0.0  0
 1YQ  CONST_34  H10  C0H  C0C  C0D  180.00   0.0  0
 1YQ  CONST_35  H9   C0F  C0E  C0D  180.00   0.0  0
 1YQ  CONST_36  H7   C0D  C0E  C0F  180.00   0.0  0
 1YQ  CONST_37  H16  N0W  C0V  N0S  180.00   0.0  0
 1YQ  CONST_38  O10  C0V  N0S  C0P    0.00   0.0  0
 1YQ  CONST_39  C0G  C0M  C15  C17  180.00   0.0  0
 1YQ  CONST_40  H19  C15  C0M  C0G    0.00   0.0  0
 1YQ  CONST_41  H11  C0M  C15  C17    0.00   0.0  0
 1YQ  Var_01    C0D  C0C  O0A  C04  -29.10  30.0  2
 1YQ  Var_02    C15  C0M  C0G  C0F    4.81  30.0  2
 1YQ  Var_03    C0V  N0S  C0P  C0O   80.18  30.0  3
 1YQ  Var_04    C0P  C0O  O0B  C05  -96.34  30.0  3
 1YQ  Var_05    N0S  C0P  C0O  O0B   58.25  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
 1YQ  plan-1  C00  0.020
 1YQ  plan-1  C01  0.020
 1YQ  plan-1  C02  0.020
 1YQ  plan-1  C03  0.020
 1YQ  plan-1  C04  0.020
 1YQ  plan-1  C05  0.020
 1YQ  plan-1  O0A  0.020
 1YQ  plan-1  O0B  0.020
 1YQ  plan-1  H1   0.020
 1YQ  plan-1  H2   0.020
 1YQ  plan-1  H3   0.020
 1YQ  plan-1  CL1  0.020
 1YQ  plan-2  O0A  0.020
 1YQ  plan-2  C0C  0.020
 1YQ  plan-2  C0D  0.020
 1YQ  plan-2  C0E  0.020
 1YQ  plan-2  C0F  0.020
 1YQ  plan-2  C0G  0.020
 1YQ  plan-2  C0H  0.020
 1YQ  plan-2  C0M  0.020
 1YQ  plan-2  H7   0.020
 1YQ  plan-2  H8   0.020
 1YQ  plan-2  H9   0.020
 1YQ  plan-2  H10  0.020
 1YQ  plan-3  O12  0.020
 1YQ  plan-3  C0P  0.020
 1YQ  plan-3  N0S  0.020
 1YQ  plan-3  C0V  0.020
 1YQ  plan-3  N0W  0.020
 1YQ  plan-3  C0X  0.020
 1YQ  plan-3  C0Y  0.020
 1YQ  plan-3  C0Z  0.020
 1YQ  plan-3  H16  0.020
 1YQ  plan-3  H17  0.020
 1YQ  plan-3  H18  0.020
 1YQ  plan-3  O10  0.020
 1YQ  plan-4  C17  0.020
 1YQ  plan-4  C0G  0.020
 1YQ  plan-4  C0M  0.020
 1YQ  plan-4  C15  0.020
 1YQ  plan-4  H11  0.020
 1YQ  plan-4  H19  0.020

