# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:40:18 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2E)-3-(3-bromo-5-{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(Oc2cc(Br)cc(/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
 1YR  1YR  (2E)-3-(3-bromo-5-{4-chloro-2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile  ligand  45  30  .  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_1YR
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
 1YR  C15  C   C1    0  -0.338  -3.4644  -2.2489   2.2527
 1YR  C17  C   CSP   0   0.088  -4.4254  -2.6172   3.2309
 1YR  C00  C   CR16  0  -0.340   2.9482   3.2069  -1.0547
 1YR  C01  C   CR6   0  -0.028   2.5567   4.1674  -1.9784
 1YR  C02  C   CR16  0  -0.244   1.2413   4.5705  -2.1058
 1YR  C03  C   CR16  0  -0.305   0.2886   3.9817  -1.2840
 1YR  C04  C   CR6   0   0.221   0.6543   3.0279  -0.3571
 1YR  C05  C   CR6   0   0.368   1.9917   2.6329  -0.2252
 1YR  O0A  O   O2    0  -0.499  -0.2937   2.4949   0.4745
 1YR  O0B  O   O2    0  -0.456   2.2494   1.7045   0.7053
 1YR  C0C  C   CR6   0   0.417  -0.7502   1.2358   0.2523
 1YR  C0D  C   CR16  0  -0.315  -0.3087   0.4333  -0.7915
 1YR  C0E  C   CR6   0  -0.093  -0.8589  -0.8350  -0.9244
 1YR  C0F  C   CR16  0  -0.294  -1.8222  -1.3171  -0.0617
 1YR  C0G  C   CR6   0   0.140  -2.2493  -0.4990   0.9864
 1YR  C0H  C   CR16  0  -0.378  -1.7261   0.7805   1.1294
 1YR  C0M  C   C1    0  -0.203  -3.2204  -0.9621   1.9724
 1YR  C0O  C   CH2   0  -0.197   3.5273   1.0910   0.7119
 1YR  C0P  C   CH2   0  -0.354   3.5383   0.0521   1.8085
 1YR  N0S  N   NR6   0  -0.519   2.4861  -0.9477   1.6821
 1YR  C0V  C   CR6   0   0.733   2.6424  -1.9600   0.7616
 1YR  N0W  N   NR16  0  -0.729   1.6305  -2.8836   0.7454
 1YR  C0X  C   CR6   0   0.578   0.4994  -2.9229   1.5472
 1YR  C0Y  C   CR16  0  -0.497   0.4068  -1.8127   2.4595
 1YR  C0Z  C   CR16  0   0.105   1.3817  -0.8894   2.4808
 1YR  O10  O   O     0  -0.479   3.6049  -2.0338   0.0257
 1YR  O12  O   O     0  -0.467  -0.2999  -3.8363   1.4417
 1YR  N19  N   NS    0  -0.264  -5.1997  -2.9379   4.0235
 1YR  H1   H   H     0   0.320  -2.9343  -3.0660   1.7787
 1YR  H3   H   HCR6  0   0.310   3.9899   2.9260  -0.9883
 1YR  H4   H   HCR6  0   0.286   0.9530   5.3195  -2.8292
 1YR  H5   H   HCR6  0   0.288  -0.7512   4.2708  -1.3656
 1YR  H9   H   HCR6  0   0.302   0.4293   0.7870  -1.4989
 1YR  H10  H   HCR6  0   0.284  -2.2463  -2.3006  -0.2048
 1YR  H11  H   HCR6  0   0.282  -2.0654   1.4216   1.9338
 1YR  H12  H   H     0   0.299  -3.7456  -0.1930   2.5279
 1YR  H14  H   HCH2  0   0.252   3.7390   0.6439  -0.2628
 1YR  H15  H   HCH2  0   0.258   4.3152   1.8189   0.9291
 1YR  H16  H   HCH2  0   0.294   4.5111  -0.4374   1.8156
 1YR  H17  H   HCH2  0   0.286   3.4165   0.5312   2.7789
 1YR  H18  H   HNR6  0   0.422   1.7434  -3.6355   0.0765
 1YR  H19  H   HCR6  0   0.289  -0.4390  -1.7357   3.1240
 1YR  H20  H   HCR6  0   0.322   1.3438  -0.0480   3.1573
 1YR  BR1  BR  BR    0  -0.026  -0.2669  -1.9297  -2.3424
 1YR  CL1  CL  CL    0  -0.118   3.7664   4.8747  -2.9961

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
 1YR  C15  C17  single    1.420  0.020  1.420
 1YR  C15  C0M  double    1.339  0.020  1.339
 1YR  C17  N19  triple    1.153  0.020  1.153
 1YR  C00  C01  aromatic  1.389  0.020  1.389
 1YR  C00  C05  aromatic  1.390  0.020  1.390
 1YR  C01  C02  aromatic  1.382  0.020  1.382
 1YR  C02  C03  aromatic  1.389  0.020  1.389
 1YR  C03  C04  aromatic  1.379  0.020  1.379
 1YR  C04  C05  aromatic  1.401  0.020  1.401
 1YR  C04  O0A  single    1.369  0.020  1.369
 1YR  C05  O0B  single    1.339  0.020  1.339
 1YR  O0A  C0C  single    1.358  0.020  1.358
 1YR  O0B  C0O  single    1.418  0.020  1.418
 1YR  C0C  C0D  aromatic  1.389  0.020  1.389
 1YR  C0C  C0H  aromatic  1.389  0.020  1.389
 1YR  C0D  C0E  aromatic  1.389  0.020  1.389
 1YR  C0E  C0F  aromatic  1.380  0.020  1.380
 1YR  C0E  BR1  single    1.887  0.020  1.887
 1YR  C0F  C0G  aromatic  1.397  0.020  1.397
 1YR  C0G  C0H  aromatic  1.390  0.020  1.390
 1YR  C0G  C0M  single    1.459  0.020  1.459
 1YR  C0O  C0P  single    1.511  0.020  1.511
 1YR  C0P  N0S  single    1.457  0.020  1.457
 1YR  N0S  C0V  single    1.377  0.020  1.377
 1YR  N0S  C0Z  single    1.364  0.020  1.364
 1YR  C0V  N0W  single    1.370  0.020  1.370
 1YR  C0V  O10  double    1.214  0.020  1.214
 1YR  N0W  C0X  single    1.387  0.020  1.387
 1YR  C0X  C0Y  single    1.440  0.020  1.440
 1YR  C0X  O12  double    1.218  0.020  1.218
 1YR  C0Y  C0Z  double    1.343  0.020  1.343
 1YR  C01  CL1  single    1.732  0.020  1.732
 1YR  C15  H1   single    0.930  0.020  1.080
 1YR  C00  H3   single    0.930  0.020  1.080
 1YR  C02  H4   single    0.930  0.020  1.080
 1YR  C03  H5   single    0.930  0.020  1.080
 1YR  C0D  H9   single    0.930  0.020  1.080
 1YR  C0F  H10  single    0.930  0.020  1.080
 1YR  C0H  H11  single    0.930  0.020  1.080
 1YR  C0M  H12  single    0.930  0.020  1.080
 1YR  C0O  H14  single    0.970  0.020  1.090
 1YR  C0O  H15  single    0.970  0.020  1.090
 1YR  C0P  H16  single    0.970  0.020  1.090
 1YR  C0P  H17  single    0.970  0.020  1.090
 1YR  N0W  H18  single    0.860  0.020  1.020
 1YR  C0Y  H19  single    0.930  0.020  1.080
 1YR  C0Z  H20  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
 1YR  H1   C15  C0M  122.96  3.000
 1YR  H1   C15  C17  115.92  3.000
 1YR  C0M  C15  C17  121.11  3.000
 1YR  N19  C17  C15  180.00  3.000
 1YR  H3   C00  C05  121.27  3.000
 1YR  H3   C00  C01  119.49  3.000
 1YR  C05  C00  C01  119.24  3.000
 1YR  CL1  C01  C02  119.45  3.000
 1YR  CL1  C01  C00  118.45  3.000
 1YR  C02  C01  C00  122.10  3.000
 1YR  H4   C02  C03  120.45  3.000
 1YR  H4   C02  C01  121.20  3.000
 1YR  C03  C02  C01  118.34  3.000
 1YR  H5   C03  C04  119.35  3.000
 1YR  H5   C03  C02  120.07  3.000
 1YR  C04  C03  C02  120.58  3.000
 1YR  O0A  C04  C05  119.61  3.000
 1YR  O0A  C04  C03  119.59  3.000
 1YR  C05  C04  C03  120.76  3.000
 1YR  O0B  C05  C04  116.40  3.000
 1YR  O0B  C05  C00  124.64  3.000
 1YR  C04  C05  C00  118.96  3.000
 1YR  C0C  O0A  C04  119.63  3.000
 1YR  C0O  O0B  C05  118.46  3.000
 1YR  C0H  C0C  C0D  120.57  3.000
 1YR  C0H  C0C  O0A  115.91  3.000
 1YR  C0D  C0C  O0A  123.51  3.000
 1YR  H9   C0D  C0E  120.42  3.000
 1YR  H9   C0D  C0C  121.30  3.000
 1YR  C0E  C0D  C0C  118.27  3.000
 1YR  BR1  C0E  C0F  119.09  3.000
 1YR  BR1  C0E  C0D  118.52  3.000
 1YR  C0F  C0E  C0D  122.39  3.000
 1YR  H10  C0F  C0G  120.84  3.000
 1YR  H10  C0F  C0E  120.60  3.000
 1YR  C0G  C0F  C0E  118.56  3.000
 1YR  C0M  C0G  C0H  118.24  3.000
 1YR  C0M  C0G  C0F  121.65  3.000
 1YR  C0H  C0G  C0F  120.09  3.000
 1YR  H11  C0H  C0G  120.22  3.000
 1YR  H11  C0H  C0C  119.67  3.000
 1YR  C0G  C0H  C0C  120.09  3.000
 1YR  H12  C0M  C0G  116.32  3.000
 1YR  H12  C0M  C15  119.08  3.000
 1YR  C0G  C0M  C15  124.58  3.000
 1YR  H15  C0O  H14  108.03  3.000
 1YR  H15  C0O  C0P  107.95  3.000
 1YR  H14  C0O  C0P  111.38  3.000
 1YR  H15  C0O  O0B  111.23  3.000
 1YR  H14  C0O  O0B  110.33  3.000
 1YR  C0P  C0O  O0B  107.91  3.000
 1YR  H17  C0P  H16  106.97  3.000
 1YR  H17  C0P  N0S  107.36  3.000
 1YR  H16  C0P  N0S  109.71  3.000
 1YR  H17  C0P  C0O  110.09  3.000
 1YR  H16  C0P  C0O  108.68  3.000
 1YR  N0S  C0P  C0O  113.81  3.000
 1YR  C0Z  N0S  C0V  120.97  3.000
 1YR  C0Z  N0S  C0P  120.30  3.000
 1YR  C0V  N0S  C0P  118.72  3.000
 1YR  O10  C0V  N0W  122.51  3.000
 1YR  O10  C0V  N0S  122.68  3.000
 1YR  N0W  C0V  N0S  114.81  3.000
 1YR  H18  N0W  C0X  116.86  3.000
 1YR  H18  N0W  C0V  115.22  3.000
 1YR  C0X  N0W  C0V  127.91  3.000
 1YR  O12  C0X  C0Y  126.21  3.000
 1YR  O12  C0X  N0W  120.41  3.000
 1YR  C0Y  C0X  N0W  113.39  3.000
 1YR  H19  C0Y  C0Z  120.70  3.000
 1YR  H19  C0Y  C0X  119.73  3.000
 1YR  C0Z  C0Y  C0X  119.57  3.000
 1YR  H20  C0Z  C0Y  121.33  3.000
 1YR  H20  C0Z  N0S  115.36  3.000
 1YR  C0Y  C0Z  N0S  123.30  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
 1YR  CONST_01  C03  C02  C01  C00     0.00   0.0  0
 1YR  CONST_02  C03  C04  C05  C00     0.00   0.0  0
 1YR  CONST_03  C04  C05  C00  C01     0.00   0.0  0
 1YR  CONST_04  C04  C03  C02  C01     0.00   0.0  0
 1YR  CONST_05  C05  C00  C01  C02     0.00   0.0  0
 1YR  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 1YR  CONST_07  C0F  C0E  C0D  C0C     0.00   0.0  0
 1YR  CONST_08  C0F  C0G  C0H  C0C     0.00   0.0  0
 1YR  CONST_09  C0G  C0H  C0C  C0D     0.00   0.0  0
 1YR  CONST_10  C0G  C0F  C0E  C0D     0.00   0.0  0
 1YR  CONST_11  C0H  C0C  C0D  C0E     0.00   0.0  0
 1YR  CONST_12  C0H  C0G  C0F  C0E     0.00   0.0  0
 1YR  CONST_13  C0X  N0W  C0V  N0S     0.00   0.0  0
 1YR  CONST_14  C0Y  C0X  N0W  C0V     0.00   0.0  0
 1YR  CONST_15  C0Z  N0S  C0V  N0W     0.00   0.0  0
 1YR  CONST_16  O0A  C04  C05  C00   180.00   0.0  0
 1YR  CONST_17  O0B  C05  C00  C01   180.00   0.0  0
 1YR  CONST_18  O0A  C04  C03  C02   180.00   0.0  0
 1YR  CONST_19  CL1  C01  C02  C03   180.00   0.0  0
 1YR  CONST_20  O0B  C05  C04  C03   180.00   0.0  0
 1YR  CONST_21  CL1  C01  C00  C05   180.00   0.0  0
 1YR  CONST_22  C0E  C0D  C0C  O0A   180.00   0.0  0
 1YR  CONST_23  C0G  C0H  C0C  O0A   180.00   0.0  0
 1YR  CONST_24  BR1  C0E  C0D  C0C   180.00   0.0  0
 1YR  CONST_25  C0M  C0G  C0H  C0C   180.00   0.0  0
 1YR  CONST_26  C0M  C0G  C0F  C0E   180.00   0.0  0
 1YR  CONST_27  BR1  C0E  C0F  C0G   180.00   0.0  0
 1YR  CONST_28  N0W  C0V  N0S  C0P   180.00   0.0  0
 1YR  CONST_29  O12  C0X  N0W  C0V   180.00   0.0  0
 1YR  CONST_30  O10  C0V  N0W  C0X   180.00   0.0  0
 1YR  CONST_31  O10  C0V  N0S  C0Z   180.00   0.0  0
 1YR  CONST_32  H4   C02  C01  C00   180.00   0.0  0
 1YR  CONST_33  H5   C03  C02  C01   180.00   0.0  0
 1YR  CONST_34  H3   C00  C01  C02   180.00   0.0  0
 1YR  CONST_35  H11  C0H  C0C  C0D   180.00   0.0  0
 1YR  CONST_36  H10  C0F  C0E  C0D   180.00   0.0  0
 1YR  CONST_37  H9   C0D  C0E  C0F   180.00   0.0  0
 1YR  CONST_38  H18  N0W  C0V  N0S   180.00   0.0  0
 1YR  CONST_39  O10  C0V  N0S  C0P     0.00   0.0  0
 1YR  CONST_40  C0G  C0M  C15  C17   180.00   0.0  0
 1YR  CONST_41  H1   C15  C0M  C0G     0.00   0.0  0
 1YR  CONST_42  H12  C0M  C15  C17     0.00   0.0  0
 1YR  Var_01    C0D  C0C  O0A  C04    -0.11  30.0  2
 1YR  Var_02    C0F  C0G  C0M  C15    22.45  30.0  2
 1YR  Var_03    C0V  N0S  C0P  C0O    77.56  30.0  3
 1YR  Var_04    C0P  C0O  O0B  C05  -177.62  30.0  3
 1YR  Var_05    N0S  C0P  C0O  O0B    56.65  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
 1YR  plan-1  C00  0.020
 1YR  plan-1  C01  0.020
 1YR  plan-1  C02  0.020
 1YR  plan-1  C03  0.020
 1YR  plan-1  C04  0.020
 1YR  plan-1  C05  0.020
 1YR  plan-1  O0A  0.020
 1YR  plan-1  O0B  0.020
 1YR  plan-1  H3   0.020
 1YR  plan-1  H4   0.020
 1YR  plan-1  H5   0.020
 1YR  plan-1  CL1  0.020
 1YR  plan-2  O0A  0.020
 1YR  plan-2  C0C  0.020
 1YR  plan-2  C0D  0.020
 1YR  plan-2  C0E  0.020
 1YR  plan-2  C0F  0.020
 1YR  plan-2  C0G  0.020
 1YR  plan-2  C0H  0.020
 1YR  plan-2  C0M  0.020
 1YR  plan-2  H9   0.020
 1YR  plan-2  H10  0.020
 1YR  plan-2  H11  0.020
 1YR  plan-2  BR1  0.020
 1YR  plan-3  C0P  0.020
 1YR  plan-3  N0S  0.020
 1YR  plan-3  C0V  0.020
 1YR  plan-3  N0W  0.020
 1YR  plan-3  C0X  0.020
 1YR  plan-3  C0Y  0.020
 1YR  plan-3  C0Z  0.020
 1YR  plan-3  O10  0.020
 1YR  plan-3  O12  0.020
 1YR  plan-3  H18  0.020
 1YR  plan-3  H19  0.020
 1YR  plan-3  H20  0.020
 1YR  plan-4  C15  0.020
 1YR  plan-4  C17  0.020
 1YR  plan-4  C0G  0.020
 1YR  plan-4  C0M  0.020
 1YR  plan-4  H1   0.020
 1YR  plan-4  H12  0.020

