# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 01:33:13 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2E)-3-(3-chloro-5-{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: Clc1cc(Oc2ccccc2OCCN3C=CC(=O)NC3=O)cc(\C=C\C#N)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
 3X6  3X6  (2E)-3-(3-chloro-5-{2-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenoxy}phenyl)prop-2-enenitrile  ligand  45  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3X6
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
 3X6  C10  C   CR6   0   0.735   3.9462   0.5105  -1.2620
 3X6  C12  C   CR6   0   0.567   3.5519   2.7609  -0.3024
 3X6  C13  C   CR16  0  -0.505   2.1427   2.5277  -0.4920
 3X6  C14  C   CR16  0   0.128   1.7318   1.3650  -1.0255
 3X6  C00  C   CR16  0  -0.385   1.0927  -3.6686   1.2030
 3X6  C01  C   CR16  0  -0.244   0.6007  -4.4412   2.2498
 3X6  C02  C   CR16  0  -0.279  -0.1635  -3.8713   3.2535
 3X6  C03  C   CR16  0  -0.311  -0.4380  -2.5089   3.2126
 3X6  C04  C   CR6   0   0.224   0.0542  -1.7362   2.1800
 3X6  C05  C   CR6   0   0.372   0.8227  -2.3059   1.1552
 3X6  C0C  C   CR6   0   0.406  -0.9066   0.2228   1.2634
 3X6  C0D  C   CR16  0  -0.307  -0.8543   1.6111   1.2440
 3X6  C0E  C   CR6   0  -0.018  -1.6069   2.2909   0.3007
 3X6  C0F  C   CR16  0  -0.290  -2.4037   1.6355  -0.6183
 3X6  C0G  C   CR6   0   0.147  -2.4603   0.2414  -0.5780
 3X6  C0H  C   CR16  0  -0.388  -1.7147  -0.4627   0.3674
 3X6  CL1  CL  CL    0  -0.103  -1.5216   4.0195   0.2632
 3X6  C0M  C   C1    0  -0.206  -3.2814  -0.5364  -1.5004
 3X6  C0V  C   C1    0  -0.346  -4.0035  -0.0458  -2.5165
 3X6  C0X  C   CSP   0   0.090  -4.7705  -0.9024  -3.3491
 3X6  N0Z  N   NS    0  -0.263  -5.4014  -1.5797  -4.0374
 3X6  O0B  O   O2    0  -0.464   1.2307  -1.4669   0.1895
 3X6  C0O  C   CH2   0  -0.190   1.9879  -1.9709  -0.8944
 3X6  N0S  N   NR6   0  -0.519   2.5832   0.3754  -1.4149
 3X6  N11  N   NR16  0  -0.731   4.3470   1.7033  -0.7212
 3X6  O15  O   O     0  -0.478   4.7301  -0.3584  -1.5833
 3X6  O17  O   O     0  -0.466   4.0559   3.7631   0.1704
 3X6  H1   H   HCR6  0   0.274   1.4307   3.2884  -0.2115
 3X6  H2   H   HCR6  0   0.303   0.6829   1.1621  -1.1892
 3X6  H3   H   HCR6  0   0.289   1.6896  -4.1434   0.4364
 3X6  H4   H   HCR6  0   0.265   0.8267  -5.4989   2.2714
 3X6  H5   H   HCR6  0   0.262  -0.5471  -4.4746   4.0646
 3X6  H6   H   HCR6  0   0.275  -1.0254  -2.0377   3.9904
 3X6  H7   H   HCR6  0   0.303  -0.2297   2.1427   1.9497
 3X6  H8   H   HCR6  0   0.285  -2.9713   2.2043  -1.3413
 3X6  H9   H   HCR6  0   0.293  -1.7796  -1.5432   0.3915
 3X6  H10  H   H     0   0.297  -3.2904  -1.6069  -1.3280
 3X6  H11  H   H     0   0.325  -4.0452   1.0075  -2.7637
 3X6  H12  H   HCH2  0   0.249   2.9845  -2.2717  -0.5596
 3X6  H13  H   HCH2  0   0.255   1.5067  -2.8405  -1.3520
 3X6  H14  H   HCH2  0   0.296   2.6702  -1.2156  -2.7721
 3X6  H15  H   HCH2  0   0.279   1.0629  -0.6762  -2.3331
 3X6  H16  H   HNR6  0   0.426   5.3478   1.8130  -0.6106
 3X6  C0P  C   CH2   0  -0.355   2.0577  -0.8781  -1.9383
 3X6  O0A  O   O2    0  -0.498  -0.1487  -0.3794   2.2099

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
 3X6  O15  C10  double    1.214  0.020  1.214
 3X6  C0P  C0O  single    1.513  0.020  1.513
 3X6  C0P  N0S  single    1.457  0.020  1.457
 3X6  C10  N0S  single    1.378  0.020  1.378
 3X6  C10  N11  single    1.370  0.020  1.370
 3X6  C0O  O0B  single    1.415  0.020  1.415
 3X6  N0S  C14  single    1.362  0.020  1.362
 3X6  N11  C12  single    1.388  0.020  1.388
 3X6  C14  C13  double    1.344  0.020  1.344
 3X6  O0B  C05  single    1.343  0.020  1.343
 3X6  C00  C05  aromatic  1.390  0.020  1.390
 3X6  C00  C01  aromatic  1.391  0.020  1.391
 3X6  C12  C13  single    1.441  0.020  1.441
 3X6  C12  O17  double    1.217  0.020  1.217
 3X6  C05  C04  aromatic  1.402  0.020  1.402
 3X6  C01  C02  aromatic  1.384  0.020  1.384
 3X6  C04  O0A  single    1.372  0.020  1.372
 3X6  C04  C03  aromatic  1.380  0.020  1.380
 3X6  C02  C03  aromatic  1.390  0.020  1.390
 3X6  O0A  C0C  single    1.354  0.020  1.354
 3X6  C0D  C0C  aromatic  1.389  0.020  1.389
 3X6  C0D  C0E  aromatic  1.385  0.020  1.385
 3X6  C0C  C0H  aromatic  1.388  0.020  1.388
 3X6  CL1  C0E  single    1.731  0.020  1.731
 3X6  C0E  C0F  aromatic  1.382  0.020  1.382
 3X6  C0H  C0G  aromatic  1.395  0.020  1.395
 3X6  C0F  C0G  aromatic  1.396  0.020  1.396
 3X6  C0G  C0M  single    1.459  0.020  1.459
 3X6  C0M  C0V  double    1.340  0.020  1.340
 3X6  C0V  C0X  single    1.420  0.020  1.420
 3X6  C0X  N0Z  triple    1.154  0.020  1.154
 3X6  C13  H1   single    0.930  0.020  1.080
 3X6  C14  H2   single    0.930  0.020  1.080
 3X6  C00  H3   single    0.930  0.020  1.080
 3X6  C01  H4   single    0.930  0.020  1.080
 3X6  C02  H5   single    0.930  0.020  1.080
 3X6  C03  H6   single    0.930  0.020  1.080
 3X6  C0D  H7   single    0.930  0.020  1.080
 3X6  C0F  H8   single    0.930  0.020  1.080
 3X6  C0H  H9   single    0.930  0.020  1.080
 3X6  C0M  H10  single    0.930  0.020  1.080
 3X6  C0V  H11  single    0.930  0.020  1.080
 3X6  C0O  H12  single    0.970  0.020  1.090
 3X6  C0O  H13  single    0.970  0.020  1.090
 3X6  C0P  H14  single    0.970  0.020  1.090
 3X6  C0P  H15  single    0.970  0.020  1.090
 3X6  N11  H16  single    0.860  0.020  1.020

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
 3X6  O15  C10  N11  122.62  3.000
 3X6  N11  C10  N0S  114.74  3.000
 3X6  O15  C10  N0S  122.63  3.000
 3X6  O17  C12  N11  120.49  3.000
 3X6  O17  C12  C13  126.11  3.000
 3X6  N11  C12  C13  113.41  3.000
 3X6  H1   C13  C14  120.77  3.000
 3X6  H1   C13  C12  119.80  3.000
 3X6  C14  C13  C12  119.43  3.000
 3X6  H2   C14  N0S  115.27  3.000
 3X6  H2   C14  C13  121.28  3.000
 3X6  N0S  C14  C13  123.44  3.000
 3X6  H3   C00  C05  120.88  3.000
 3X6  H3   C00  C01  119.00  3.000
 3X6  C05  C00  C01  120.11  3.000
 3X6  H4   C01  C02  120.22  3.000
 3X6  H4   C01  C00  118.96  3.000
 3X6  C02  C01  C00  120.82  3.000
 3X6  H5   C02  C03  119.92  3.000
 3X6  H5   C02  C01  120.67  3.000
 3X6  C03  C02  C01  119.41  3.000
 3X6  H6   C03  C04  119.16  3.000
 3X6  H6   C03  C02  120.83  3.000
 3X6  C04  C03  C02  120.01  3.000
 3X6  O0A  C04  C05  119.92  3.000
 3X6  O0A  C04  C03  118.98  3.000
 3X6  C05  C04  C03  120.99  3.000
 3X6  O0B  C05  C04  116.00  3.000
 3X6  C04  C05  C00  118.67  3.000
 3X6  O0B  C05  C00  125.33  3.000
 3X6  C0H  C0C  C0D  120.44  3.000
 3X6  C0H  C0C  O0A  123.89  3.000
 3X6  C0D  C0C  O0A  115.67  3.000
 3X6  H7   C0D  C0E  121.12  3.000
 3X6  H7   C0D  C0C  120.24  3.000
 3X6  C0E  C0D  C0C  118.65  3.000
 3X6  CL1  C0E  C0F  119.19  3.000
 3X6  C0F  C0E  C0D  122.25  3.000
 3X6  CL1  C0E  C0D  118.56  3.000
 3X6  H8   C0F  C0G  121.57  3.000
 3X6  H8   C0F  C0E  119.88  3.000
 3X6  C0G  C0F  C0E  118.55  3.000
 3X6  C0M  C0G  C0H  117.39  3.000
 3X6  C0M  C0G  C0F  122.47  3.000
 3X6  C0H  C0G  C0F  120.14  3.000
 3X6  H9   C0H  C0G  119.13  3.000
 3X6  H9   C0H  C0C  120.90  3.000
 3X6  C0G  C0H  C0C  119.97  3.000
 3X6  H10  C0M  C0V  118.54  3.000
 3X6  H10  C0M  C0G  115.49  3.000
 3X6  C0V  C0M  C0G  125.98  3.000
 3X6  H11  C0V  C0X  115.61  3.000
 3X6  H11  C0V  C0M  123.38  3.000
 3X6  C0X  C0V  C0M  121.01  3.000
 3X6  N0Z  C0X  C0V  180.00  3.000
 3X6  C0O  O0B  C05  119.40  3.000
 3X6  H13  C0O  H12  108.08  3.000
 3X6  H13  C0O  C0P  107.80  3.000
 3X6  H12  C0O  C0P  111.59  3.000
 3X6  H13  C0O  O0B  111.60  3.000
 3X6  H12  C0O  O0B  110.56  3.000
 3X6  C0P  C0O  O0B  107.22  3.000
 3X6  C0P  N0S  C14  120.16  3.000
 3X6  C14  N0S  C10  121.01  3.000
 3X6  C0P  N0S  C10  118.75  3.000
 3X6  H16  N11  C12  116.78  3.000
 3X6  H16  N11  C10  115.25  3.000
 3X6  C12  N11  C10  127.96  3.000
 3X6  H15  C0P  H14  107.09  3.000
 3X6  H15  C0P  N0S  107.47  3.000
 3X6  H14  C0P  N0S  109.82  3.000
 3X6  H15  C0P  C0O  109.99  3.000
 3X6  H14  C0P  C0O  109.31  3.000
 3X6  N0S  C0P  C0O  112.98  3.000
 3X6  C0C  O0A  C04  120.49  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
 3X6  CONST_01  C03  C04  C05  C00     0.00   0.0  0
 3X6  CONST_02  C03  C02  C01  C00     0.00   0.0  0
 3X6  CONST_03  C04  C05  C00  C01     0.00   0.0  0
 3X6  CONST_04  C04  C03  C02  C01     0.00   0.0  0
 3X6  CONST_05  C05  C00  C01  C02     0.00   0.0  0
 3X6  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 3X6  CONST_07  C0F  C0E  C0D  C0C     0.00   0.0  0
 3X6  CONST_08  C0F  C0G  C0H  C0C     0.00   0.0  0
 3X6  CONST_09  C0G  C0H  C0C  C0D     0.00   0.0  0
 3X6  CONST_10  C0G  C0F  C0E  C0D     0.00   0.0  0
 3X6  CONST_11  C0H  C0C  C0D  C0E     0.00   0.0  0
 3X6  CONST_12  C0H  C0G  C0F  C0E     0.00   0.0  0
 3X6  CONST_13  C13  C12  N11  C10     0.00   0.0  0
 3X6  CONST_14  N0S  C10  N11  C12     0.00   0.0  0
 3X6  CONST_15  N11  C10  N0S  C14     0.00   0.0  0
 3X6  CONST_16  O0A  C04  C05  C00   180.00   0.0  0
 3X6  CONST_17  O0B  C05  C00  C01   180.00   0.0  0
 3X6  CONST_18  O0A  C04  C03  C02   180.00   0.0  0
 3X6  CONST_19  O0B  C05  C04  C03   180.00   0.0  0
 3X6  CONST_20  C0E  C0D  C0C  O0A   180.00   0.0  0
 3X6  CONST_21  C0G  C0H  C0C  O0A   180.00   0.0  0
 3X6  CONST_22  CL1  C0E  C0D  C0C   180.00   0.0  0
 3X6  CONST_23  C0M  C0G  C0H  C0C   180.00   0.0  0
 3X6  CONST_24  C0M  C0G  C0F  C0E   180.00   0.0  0
 3X6  CONST_25  CL1  C0E  C0F  C0G   180.00   0.0  0
 3X6  CONST_26  O17  C12  N11  C10   180.00   0.0  0
 3X6  CONST_27  O15  C10  N11  C12   180.00   0.0  0
 3X6  CONST_28  O15  C10  N0S  C14   180.00   0.0  0
 3X6  CONST_29  N11  C10  N0S  C0P   180.00   0.0  0
 3X6  CONST_30  H5   C02  C01  C00   180.00   0.0  0
 3X6  CONST_31  H6   C03  C02  C01   180.00   0.0  0
 3X6  CONST_32  H3   C00  C01  C02   180.00   0.0  0
 3X6  CONST_33  H4   C01  C02  C03   180.00   0.0  0
 3X6  CONST_34  H9   C0H  C0C  C0D   180.00   0.0  0
 3X6  CONST_35  H8   C0F  C0E  C0D   180.00   0.0  0
 3X6  CONST_36  H7   C0D  C0E  C0F   180.00   0.0  0
 3X6  CONST_37  H16  N11  C12  C13   180.00   0.0  0
 3X6  CONST_38  O15  C10  N0S  C0P     0.00   0.0  0
 3X6  CONST_39  C0X  C0V  C0M  C0G   180.00   0.0  0
 3X6  CONST_40  H11  C0V  C0M  C0G     0.00   0.0  0
 3X6  CONST_41  H10  C0M  C0V  C0X     0.00   0.0  0
 3X6  Var_01    C0D  C0C  O0A  C04  -168.97  30.0  2
 3X6  Var_02    C0O  C0P  N0S  C10    79.44  30.0  2
 3X6  Var_03    C0V  C0M  C0G  C0F     3.86  30.0  2
 3X6  Var_04    C0P  C0O  O0B  C05   168.80  30.0  1
 3X6  Var_05    N0S  C0P  C0O  O0B    55.01  30.0  2

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
 3X6  plan-1  C10  0.020
 3X6  plan-1  C12  0.020
 3X6  plan-1  C13  0.020
 3X6  plan-1  C14  0.020
 3X6  plan-1  N0S  0.020
 3X6  plan-1  N11  0.020
 3X6  plan-1  O15  0.020
 3X6  plan-1  O17  0.020
 3X6  plan-1  H1   0.020
 3X6  plan-1  H2   0.020
 3X6  plan-1  H16  0.020
 3X6  plan-1  C0P  0.020
 3X6  plan-2  C00  0.020
 3X6  plan-2  C01  0.020
 3X6  plan-2  C02  0.020
 3X6  plan-2  C03  0.020
 3X6  plan-2  C04  0.020
 3X6  plan-2  C05  0.020
 3X6  plan-2  O0B  0.020
 3X6  plan-2  H3   0.020
 3X6  plan-2  H4   0.020
 3X6  plan-2  H5   0.020
 3X6  plan-2  H6   0.020
 3X6  plan-2  O0A  0.020
 3X6  plan-3  C0C  0.020
 3X6  plan-3  C0D  0.020
 3X6  plan-3  C0E  0.020
 3X6  plan-3  C0F  0.020
 3X6  plan-3  C0G  0.020
 3X6  plan-3  C0H  0.020
 3X6  plan-3  CL1  0.020
 3X6  plan-3  C0M  0.020
 3X6  plan-3  H7   0.020
 3X6  plan-3  H8   0.020
 3X6  plan-3  H9   0.020
 3X6  plan-3  O0A  0.020
 3X6  plan-4  C0G  0.020
 3X6  plan-4  C0M  0.020
 3X6  plan-4  C0V  0.020
 3X6  plan-4  C0X  0.020
 3X6  plan-4  H10  0.020
 3X6  plan-4  H11  0.020

