# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 21:47:47 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: 5-[3-(3-chloro-5-propoxyphenyl)-2-oxo-2H-[1,3'-bipyridin]-5-yl]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1cc(Cl)cc(c1)C2=CC(=CN(C2=O)c3cccnc3)C4=CNC(=O)NC4=O
#
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
 YSG  YSG  5-[3-(3-chloro-5-propoxyphenyl)-2-oxo-2H-[1,3'-bipyridin]-5-yl]pyrimidine-2,4(1H,3H)-dione  ligand  51  32  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YSG
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
 YSG  N1   N   NR16  0  -0.719  -24.4771  -4.0336  -22.3326
 YSG  C2   C   CR6   0  -0.164  -21.7327  -4.3448  -27.7518
 YSG  N3   N   NR6   0  -0.620  -20.1696  -4.8126  -26.0040
 YSG  C4   C   CR16  0  -0.305  -22.9191  -2.9977  -29.4555
 YSG  C5   C   CR6   0  -0.004  -23.2203  -2.7299  -30.7822
 YSG  C6   C   CR16  0  -0.325  -22.6620  -3.4446  -31.8212
 YSG  C8   C   CH2   0  -0.191  -20.2470  -6.1055  -32.3751
 YSG  C1   C   CR6   0   0.539  -20.3530  -4.5667  -27.3652
 YSG  C10  C   CH3   0  -0.661  -19.0431  -5.3969  -34.4966
 YSG  C11  C   CR16  0  -0.418  -21.4681  -4.7778  -30.1983
 YSG  C12  C   CR16  0  -0.205  -22.7188  -4.3707  -26.8094
 YSG  C13  C   CR6   0  -0.011  -22.4632  -4.6236  -25.4384
 YSG  C14  C   CR6   0  -0.243  -23.5401  -4.6537  -24.4415
 YSG  C15  C   CR6   0   0.560  -23.3841  -3.9443  -23.1784
 YSG  C16  C   CR16  0   0.066  -24.7059  -5.2955  -24.6666
 YSG  C17  C   CR6   0   0.681  -25.6625  -4.6902  -22.5490
 YSG  C18  C   CR16  0   0.030  -21.1683  -4.8441  -25.0868
 YSG  C19  C   CR6   0   0.176  -18.8353  -5.0420  -25.5530
 YSG  C20  C   CR16  0  -0.138  -18.3473  -6.3291  -25.4144
 YSG  C21  C   CR16  0  -0.330  -17.0538  -6.4857  -24.9431
 YSG  C22  C   CR16  0  -0.055  -16.3162  -5.3506  -24.6417
 YSG  C23  C   CR16  0  -0.052  -18.0246  -3.9666  -25.2240
 YSG  C3   C   CR6   0   0.121  -22.0372  -4.0344  -29.1625
 YSG  C7   C   CR6   0   0.415  -21.7725  -4.4795  -31.5220
 YSG  C9   C   CH2   0  -0.458  -19.7149  -6.5270  -33.7276
 YSG  N2   N   NR16  0  -0.673  -25.7253  -5.3064  -23.7708
 YSG  N4   N   N     0  -0.398  -16.7869  -4.1157  -24.7770
 YSG  O2   O   O2    0  -0.471  -21.2607  -5.1290  -32.5783
 YSG  O3   O   O     0  -0.436  -22.4021  -3.3104  -22.8447
 YSG  O4   O   O     0  -0.462  -26.5620  -4.7200  -21.7386
 YSG  CL1  CL  CL    0  -0.127  -24.3144  -1.4353  -31.1495
 YSG  H12  H   HNR6  0   0.427  -24.3974  -3.5569  -21.4422
 YSG  H1   H   HCR6  0   0.275  -23.3463  -2.3947  -28.6658
 YSG  H2   H   HCR6  0   0.283  -22.8951  -3.2126  -32.8520
 YSG  H3   H   HCH2  0   0.235  -20.6555  -6.9680  -31.8375
 YSG  H4   H   HCH2  0   0.223  -19.4360  -5.6875  -31.7674
 YSG  H8   H   HCH3  0   0.231  -18.6120  -5.7646  -35.4276
 YSG  H7   H   HCH3  0   0.226  -19.7466  -4.6049  -34.7513
 YSG  H9   H   HCH3  0   0.219  -18.2362  -4.9519  -33.9117
 YSG  H10  H   HCR6  0   0.279  -20.7983  -5.5897  -29.9588
 YSG  H11  H   HCR6  0   0.278  -23.7425  -4.1907  -27.1182
 YSG  H13  H   HCR6  0   0.322  -24.8941  -5.8472  -25.5775
 YSG  H15  H   HCR6  0   0.315  -20.8626  -5.0664  -24.0754
 YSG  H16  H   HCR6  0   0.288  -18.9638  -7.1832  -25.6643
 YSG  H17  H   HCR6  0   0.282  -16.6242  -7.4688  -24.8111
 YSG  H18  H   HCR6  0   0.274  -15.3013  -5.4432  -24.2723
 YSG  H19  H   HCR6  0   0.280  -18.3999  -2.9533  -25.3246
 YSG  H5   H   HCH2  0   0.232  -20.5219  -6.9659  -34.3198
 YSG  H6   H   HCH2  0   0.235  -18.9958  -7.3300  -33.5482
 YSG  H14  H   HNR6  0   0.439  -26.5725  -5.8096  -23.9926
 YSG  O1   O   O     0  -0.464  -19.3854  -4.5399  -28.1108

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
 YSG  C10  C9   single    1.523  0.020  1.523
 YSG  C9   C8   single    1.513  0.020  1.513
 YSG  O2   C8   single    1.422  0.020  1.422
 YSG  O2   C7   single    1.341  0.020  1.341
 YSG  C6   C7   aromatic  1.397  0.020  1.397
 YSG  C6   C5   aromatic  1.379  0.020  1.379
 YSG  C7   C11  aromatic  1.391  0.020  1.391
 YSG  CL1  C5   single    1.734  0.020  1.734
 YSG  C5   C4   aromatic  1.387  0.020  1.387
 YSG  C11  C3   aromatic  1.396  0.020  1.396
 YSG  C4   C3   aromatic  1.392  0.020  1.392
 YSG  C3   C2   single    1.476  0.020  1.476
 YSG  O1   C1   double    1.222  0.020  1.222
 YSG  C2   C1   single    1.450  0.020  1.450
 YSG  C2   C12  double    1.364  0.020  1.364
 YSG  C1   N3   single    1.395  0.020  1.395
 YSG  C12  C13  single    1.417  0.020  1.417
 YSG  N3   C19  single    1.427  0.020  1.427
 YSG  N3   C18  single    1.356  0.020  1.356
 YSG  C19  C23  aromatic  1.386  0.020  1.386
 YSG  C19  C20  aromatic  1.383  0.020  1.383
 YSG  C23  N4   aromatic  1.324  0.020  1.324
 YSG  C13  C18  double    1.360  0.020  1.360
 YSG  C13  C14  single    1.468  0.020  1.468
 YSG  C20  C21  aromatic  1.386  0.020  1.386
 YSG  N4   C22  aromatic  1.329  0.020  1.329
 YSG  C16  C14  double    1.350  0.020  1.350
 YSG  C16  N2   single    1.357  0.020  1.357
 YSG  C22  C21  aromatic  1.387  0.020  1.387
 YSG  C14  C15  single    1.457  0.020  1.457
 YSG  N2   C17  single    1.370  0.020  1.370
 YSG  C15  O3   double    1.216  0.020  1.216
 YSG  C15  N1   single    1.385  0.020  1.385
 YSG  C17  N1   single    1.372  0.020  1.372
 YSG  C17  O4   double    1.211  0.020  1.211
 YSG  N1   H12  single    0.860  0.020  1.020
 YSG  C4   H1   single    0.930  0.020  1.080
 YSG  C6   H2   single    0.930  0.020  1.080
 YSG  C8   H3   single    0.970  0.020  1.090
 YSG  C8   H4   single    0.970  0.020  1.090
 YSG  C10  H8   single    0.970  0.020  1.090
 YSG  C10  H7   single    0.970  0.020  1.090
 YSG  C10  H9   single    0.970  0.020  1.090
 YSG  C11  H10  single    0.930  0.020  1.080
 YSG  C12  H11  single    0.930  0.020  1.080
 YSG  C16  H13  single    0.930  0.020  1.080
 YSG  C18  H15  single    0.930  0.020  1.080
 YSG  C20  H16  single    0.930  0.020  1.080
 YSG  C21  H17  single    0.930  0.020  1.080
 YSG  C22  H18  single    0.930  0.020  1.080
 YSG  C23  H19  single    0.930  0.020  1.080
 YSG  C9   H5   single    0.970  0.020  1.090
 YSG  C9   H6   single    0.970  0.020  1.090
 YSG  N2   H14  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
 YSG  H12  N1   C17  115.58  3.000
 YSG  H12  N1   C15  116.38  3.000
 YSG  C17  N1   C15  128.04  3.000
 YSG  C3   C2   C12  121.00  3.000
 YSG  C12  C2   C1   120.05  3.000
 YSG  C3   C2   C1   118.90  3.000
 YSG  C19  N3   C18  118.10  3.000
 YSG  C18  N3   C1   124.54  3.000
 YSG  C19  N3   C1   117.36  3.000
 YSG  H1   C4   C3   120.78  3.000
 YSG  H1   C4   C5   120.34  3.000
 YSG  C3   C4   C5   118.87  3.000
 YSG  CL1  C5   C6   118.86  3.000
 YSG  CL1  C5   C4   118.94  3.000
 YSG  C6   C5   C4   122.19  3.000
 YSG  H2   C6   C7   120.00  3.000
 YSG  H2   C6   C5   121.29  3.000
 YSG  C7   C6   C5   118.71  3.000
 YSG  H4   C8   H3   107.70  3.000
 YSG  H4   C8   O2   110.16  3.000
 YSG  H3   C8   O2   110.18  3.000
 YSG  H4   C8   C9   109.97  3.000
 YSG  H3   C8   C9   110.52  3.000
 YSG  O2   C8   C9   108.32  3.000
 YSG  O1   C1   N3   119.68  3.000
 YSG  N3   C1   C2   114.34  3.000
 YSG  O1   C1   C2   125.98  3.000
 YSG  H9   C10  H7   107.83  3.000
 YSG  H9   C10  H8   107.63  3.000
 YSG  H7   C10  H8   107.52  3.000
 YSG  H9   C10  C9   110.98  3.000
 YSG  H7   C10  C9   111.87  3.000
 YSG  H8   C10  C9   110.82  3.000
 YSG  H10  C11  C7   120.55  3.000
 YSG  H10  C11  C3   119.27  3.000
 YSG  C7   C11  C3   120.18  3.000
 YSG  H11  C12  C13  118.38  3.000
 YSG  H11  C12  C2   118.85  3.000
 YSG  C13  C12  C2   122.77  3.000
 YSG  C18  C13  C14  121.31  3.000
 YSG  C14  C13  C12  121.89  3.000
 YSG  C18  C13  C12  116.79  3.000
 YSG  C16  C14  C15  117.94  3.000
 YSG  C15  C14  C13  120.02  3.000
 YSG  C16  C14  C13  122.02  3.000
 YSG  O3   C15  C14  125.34  3.000
 YSG  O3   C15  N1   120.23  3.000
 YSG  C14  C15  N1   114.43  3.000
 YSG  H13  C16  N2   114.91  3.000
 YSG  H13  C16  C14  122.24  3.000
 YSG  N2   C16  C14  122.85  3.000
 YSG  O4   C17  N2   123.48  3.000
 YSG  O4   C17  N1   123.22  3.000
 YSG  N2   C17  N1   113.30  3.000
 YSG  H15  C18  C13  123.04  3.000
 YSG  H15  C18  N3   115.46  3.000
 YSG  C13  C18  N3   121.50  3.000
 YSG  C23  C19  C20  119.45  3.000
 YSG  C20  C19  N3   120.73  3.000
 YSG  C23  C19  N3   119.81  3.000
 YSG  H16  C20  C21  121.39  3.000
 YSG  H16  C20  C19  120.66  3.000
 YSG  C21  C20  C19  117.94  3.000
 YSG  H17  C21  C22  120.43  3.000
 YSG  H17  C21  C20  121.03  3.000
 YSG  C22  C21  C20  118.55  3.000
 YSG  H18  C22  N4   116.48  3.000
 YSG  H18  C22  C21  120.14  3.000
 YSG  N4   C22  C21  123.38  3.000
 YSG  H19  C23  N4   117.36  3.000
 YSG  H19  C23  C19  120.00  3.000
 YSG  N4   C23  C19  122.63  3.000
 YSG  C11  C3   C4   119.90  3.000
 YSG  C4   C3   C2   119.23  3.000
 YSG  C11  C3   C2   120.86  3.000
 YSG  O2   C7   C11  124.20  3.000
 YSG  C11  C7   C6   120.14  3.000
 YSG  O2   C7   C6   115.66  3.000
 YSG  H6   C9   H5   106.24  3.000
 YSG  H6   C9   C10  109.75  3.000
 YSG  H5   C9   C10  110.49  3.000
 YSG  H6   C9   C8   106.82  3.000
 YSG  H5   C9   C8   109.66  3.000
 YSG  C10  C9   C8   113.56  3.000
 YSG  H14  N2   C17  117.28  3.000
 YSG  H14  N2   C16  119.28  3.000
 YSG  C17  N2   C16  123.42  3.000
 YSG  C23  N4   C22  118.05  3.000
 YSG  C7   O2   C8   119.47  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
 YSG  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 YSG  CONST_02  C7   C11  C3   C4      0.00   0.0  0
 YSG  CONST_03  C11  C7   C6   C5      0.00   0.0  0
 YSG  CONST_04  C11  C3   C4   C5      0.00   0.0  0
 YSG  CONST_05  C3   C11  C7   C6      0.00   0.0  0
 YSG  CONST_06  C3   C4   C5   C6      0.00   0.0  0
 YSG  CONST_07  C22  N4   C23  C19     0.00   0.0  0
 YSG  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 YSG  CONST_09  N4   C23  C19  C20     0.00   0.0  0
 YSG  CONST_10  N4   C22  C21  C20     0.00   0.0  0
 YSG  CONST_11  C23  C19  C20  C21     0.00   0.0  0
 YSG  CONST_12  C23  N4   C22  C21     0.00   0.0  0
 YSG  CONST_13  C7   C11  C3   C2    180.00   0.0  0
 YSG  CONST_14  C5   C4   C3   C2    180.00   0.0  0
 YSG  CONST_15  N4   C23  C19  N3    180.00   0.0  0
 YSG  CONST_16  C21  C20  C19  N3    180.00   0.0  0
 YSG  CONST_17  C16  N2   C17  N1      0.00   0.0  0
 YSG  CONST_18  C19  N3   C1   C2    180.00   0.0  0
 YSG  CONST_19  C18  N3   C1   C2      0.00   0.0  0
 YSG  CONST_20  C17  N1   C15  C14     0.00   0.0  0
 YSG  CONST_21  N2   C17  N1   C15     0.00   0.0  0
 YSG  CONST_22  O2   C7   C6   C5    180.00   0.0  0
 YSG  CONST_23  O2   C7   C11  C3    180.00   0.0  0
 YSG  CONST_24  CL1  C5   C4   C3    180.00   0.0  0
 YSG  CONST_25  CL1  C5   C6   C7    180.00   0.0  0
 YSG  CONST_26  O4   C17  N1   C15   180.00   0.0  0
 YSG  CONST_27  O4   C17  N2   C16   180.00   0.0  0
 YSG  CONST_28  O3   C15  N1   C17   180.00   0.0  0
 YSG  CONST_29  O1   C1   N3   C18   180.00   0.0  0
 YSG  CONST_30  O1   C1   N3   C19     0.00   0.0  0
 YSG  CONST_31  H10  C11  C3   C2      0.00   0.0  0
 YSG  CONST_32  H1   C4   C3   C2      0.00   0.0  0
 YSG  CONST_33  H19  C23  C19  N3      0.00   0.0  0
 YSG  CONST_34  H16  C20  C19  N3      0.00   0.0  0
 YSG  CONST_35  H2   C6   C5   C4    180.00   0.0  0
 YSG  CONST_36  H17  C21  C20  C19   180.00   0.0  0
 YSG  CONST_37  H18  C22  C21  C20   180.00   0.0  0
 YSG  CONST_38  H14  N2   C17  N1    180.00   0.0  0
 YSG  CONST_39  H12  N1   C15  C14   180.00   0.0  0
 YSG  Var_01    C1   C2   C3   C4   -134.64  30.0  2
 YSG  Var_02    C23  C19  N3   C1     85.77  30.0  2
 YSG  Var_03    C16  C14  C13  C12    44.62  30.0  2
 YSG  Var_04    C11  C7   O2   C8     -6.21  30.0  2
 YSG  Var_05    C9   C8   O2   C7   -171.84  30.0  3
 YSG  Var_06    O2   C8   C9   C10    63.17  30.0  3
 YSG  Var_07    H8   C10  C9   C8    175.77  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
 YSG  plan-1  C2   0.020
 YSG  plan-1  N3   0.020
 YSG  plan-1  C1   0.020
 YSG  plan-1  C12  0.020
 YSG  plan-1  C13  0.020
 YSG  plan-1  C14  0.020
 YSG  plan-1  C18  0.020
 YSG  plan-1  C19  0.020
 YSG  plan-1  C3   0.020
 YSG  plan-1  H11  0.020
 YSG  plan-1  H15  0.020
 YSG  plan-1  O1   0.020
 YSG  plan-2  C2   0.020
 YSG  plan-2  C4   0.020
 YSG  plan-2  C5   0.020
 YSG  plan-2  C6   0.020
 YSG  plan-2  C11  0.020
 YSG  plan-2  C3   0.020
 YSG  plan-2  C7   0.020
 YSG  plan-2  O2   0.020
 YSG  plan-2  CL1  0.020
 YSG  plan-2  H1   0.020
 YSG  plan-2  H2   0.020
 YSG  plan-2  H10  0.020
 YSG  plan-3  N1   0.020
 YSG  plan-3  C13  0.020
 YSG  plan-3  C14  0.020
 YSG  plan-3  C15  0.020
 YSG  plan-3  C16  0.020
 YSG  plan-3  C17  0.020
 YSG  plan-3  N2   0.020
 YSG  plan-3  O3   0.020
 YSG  plan-3  O4   0.020
 YSG  plan-3  H12  0.020
 YSG  plan-3  H13  0.020
 YSG  plan-3  H14  0.020
 YSG  plan-4  N3   0.020
 YSG  plan-4  C19  0.020
 YSG  plan-4  C20  0.020
 YSG  plan-4  C21  0.020
 YSG  plan-4  C22  0.020
 YSG  plan-4  C23  0.020
 YSG  plan-4  N4   0.020
 YSG  plan-4  H16  0.020
 YSG  plan-4  H17  0.020
 YSG  plan-4  H18  0.020
 YSG  plan-4  H19  0.020

