# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jun 10 00:57:07 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 1-[1-[[5-(3-chloranylphenoxy)pyridin-3-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(C2CCN(CC2)Cc3cncc(Oc4cccc(Cl)c4)c3)C(=O)NC1=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
 ZUI  ZUI  1-[1-[[5-(3-chloranylphenoxy)pyridin-3-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione  ligand  53  30  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZUI
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
 ZUI  O2   O   O     0  -0.460  -8.7193   0.2264   0.3398
 ZUI  C21  C   CR6   0   0.554  -7.5313   0.1074   0.0952
 ZUI  C1   C   CR6   0  -0.180  -6.8895  -1.1090  -0.3528
 ZUI  C    C   CH3   0  -0.706  -7.7170  -2.3365  -0.5484
 ZUI  N3   N   NR16  0  -0.731  -6.6715   1.1802   0.2344
 ZUI  C20  C   CR6   0   0.736  -5.3188   1.2228   0.0033
 ZUI  O1   O   O     0  -0.486  -4.6825   2.2463   0.1599
 ZUI  N    N   NR6   0  -0.547  -4.7712   0.0321  -0.4077
 ZUI  C2   C   CR16  0   0.053  -5.5629  -1.0731  -0.5748
 ZUI  C3   C   CH1   0  -0.092  -3.3302  -0.0781  -0.6924
 ZUI  C19  C   CH2   0  -0.433  -2.8819   0.7526  -1.8878
 ZUI  C18  C   CH2   0  -0.289  -1.4111   0.4764  -2.1638
 ZUI  N1   N   NT    0  -0.418  -0.5997   0.7584  -0.9938
 ZUI  C5   C   CH2   0  -0.290  -0.9924  -0.0708   0.1313
 ZUI  C4   C   CH2   0  -0.431  -2.4421   0.1830   0.5176
 ZUI  C6   C   CH2   0  -0.317   0.8133   0.6485  -1.2754
 ZUI  C7   C   CR6   0   0.007   1.6658   1.3321  -0.2388
 ZUI  C17  C   CR16  0  -0.294   2.9091   0.8159   0.1051
 ZUI  C10  C   CR6   0   0.297   3.6871   1.5067   1.0209
 ZUI  C9   C   CR16  0  -0.137   3.1917   2.6871   1.5687
 ZUI  N2   N   N     0  -0.386   2.0054   3.1734   1.2464
 ZUI  C8   C   CR16  0  -0.102   1.2601   2.5162   0.3656
 ZUI  O    O   O2    0  -0.510   4.9211   1.1167   1.4355
 ZUI  C11  C   CR6   0   0.298   5.4292  -0.0719   0.9771
 ZUI  C16  C   CR16  0  -0.261   6.2587  -0.0573  -0.1336
 ZUI  C15  C   CR6   0  -0.034   6.8038  -1.2575  -0.5624
 ZUI  CL   CL  CL    0  -0.118   7.8488  -1.2571  -1.9427
 ZUI  C14  C   CR16  0  -0.216   6.5310  -2.4522   0.0856
 ZUI  C13  C   CR16  0  -0.258   5.6941  -2.4358   1.1924
 ZUI  C12  C   CR16  0  -0.291   5.1347  -1.2501   1.6454
 ZUI  H3   H   HCH3  0   0.246  -8.1948  -2.6476   0.3817
 ZUI  H1   H   HCH3  0   0.246  -8.5096  -2.1691  -1.2787
 ZUI  H2   H   HCH3  0   0.246  -7.1063  -3.1652  -0.9032
 ZUI  H    H   HNR6  0   0.423  -7.0800   2.0541   0.5423
 ZUI  H4   H   HCR6  0   0.311  -5.0407  -1.9579  -0.9125
 ZUI  H5   H   HCH1  0   0.256  -3.1908  -1.1283  -0.9624
 ZUI  H22  H   HCH2  0   0.246  -3.4695   0.4896  -2.7702
 ZUI  H21  H   HCH2  0   0.244  -3.0210   1.8163  -1.6953
 ZUI  H20  H   HCH2  0   0.196  -1.2917  -0.5695  -2.4987
 ZUI  H19  H   HCH2  0   0.247  -1.0741   1.1091  -2.9878
 ZUI  H8   H   HCH2  0   0.200  -0.8484  -1.1426  -0.0962
 ZUI  H9   H   HCH2  0   0.249  -0.3517   0.1548   0.9855
 ZUI  H6   H   HCH2  0   0.245  -2.5464   1.2105   0.8637
 ZUI  H7   H   HCH2  0   0.245  -2.7215  -0.4802   1.3392
 ZUI  H10  H   HCH2  0   0.220   1.1418  -0.3987  -1.3840
 ZUI  H11  H   HCH2  0   0.264   1.0079   1.1240  -2.2416
 ZUI  H18  H   HCR6  0   0.286   3.2454  -0.1113  -0.3435
 ZUI  H13  H   HCR6  0   0.272   3.7852   3.2402   2.2895
 ZUI  H12  H   HCR6  0   0.256   0.2887   2.9357   0.1310
 ZUI  H17  H   HCR6  0   0.297   6.4782   0.8718  -0.6433
 ZUI  H16  H   HCR6  0   0.286   6.9659  -3.3791  -0.2614
 ZUI  H15  H   HCR6  0   0.278   5.4782  -3.3619   1.7077
 ZUI  H14  H   HCR6  0   0.283   4.4849  -1.2405   2.5108

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
 ZUI  O2   C21  double    1.219  0.020  1.219
 ZUI  C21  N3   single    1.382  0.020  1.382
 ZUI  C21  C1   single    1.446  0.020  1.446
 ZUI  N3   C20  single    1.373  0.020  1.373
 ZUI  C    C1   single    1.493  0.020  1.493
 ZUI  C1   C2   double    1.346  0.020  1.346
 ZUI  C20  O1   double    1.215  0.020  1.215
 ZUI  C20  N    single    1.374  0.020  1.374
 ZUI  C2   N    single    1.370  0.020  1.370
 ZUI  N    C3   single    1.473  0.020  1.473
 ZUI  C19  C3   single    1.523  0.020  1.523
 ZUI  C19  C18  single    1.522  0.020  1.522
 ZUI  C3   C4   single    1.524  0.020  1.524
 ZUI  C18  N1   single    1.451  0.020  1.451
 ZUI  N2   C8   aromatic  1.328  0.020  1.328
 ZUI  N2   C9   aromatic  1.322  0.020  1.322
 ZUI  C8   C7   aromatic  1.390  0.020  1.390
 ZUI  C9   C10  aromatic  1.392  0.020  1.392
 ZUI  C4   C5   single    1.522  0.020  1.522
 ZUI  CL   C15  single    1.731  0.020  1.731
 ZUI  N1   C5   single    1.452  0.020  1.452
 ZUI  N1   C6   single    1.445  0.020  1.445
 ZUI  C7   C6   single    1.506  0.020  1.506
 ZUI  C7   C17  aromatic  1.389  0.020  1.389
 ZUI  C10  C17  aromatic  1.386  0.020  1.386
 ZUI  C10  O    single    1.359  0.020  1.359
 ZUI  C16  C15  aromatic  1.386  0.020  1.386
 ZUI  C16  C11  aromatic  1.386  0.020  1.386
 ZUI  C15  C14  aromatic  1.386  0.020  1.386
 ZUI  O    C11  single    1.371  0.020  1.371
 ZUI  C11  C12  aromatic  1.386  0.020  1.386
 ZUI  C14  C13  aromatic  1.388  0.020  1.388
 ZUI  C12  C13  aromatic  1.387  0.020  1.387
 ZUI  C    H3   single    0.970  0.020  1.090
 ZUI  C    H1   single    0.970  0.020  1.090
 ZUI  C    H2   single    0.970  0.020  1.090
 ZUI  N3   H    single    0.860  0.020  1.020
 ZUI  C2   H4   single    0.930  0.020  1.080
 ZUI  C3   H5   single    0.970  0.020  1.090
 ZUI  C19  H22  single    0.970  0.020  1.090
 ZUI  C19  H21  single    0.970  0.020  1.090
 ZUI  C18  H20  single    0.970  0.020  1.090
 ZUI  C18  H19  single    0.970  0.020  1.090
 ZUI  C5   H8   single    0.970  0.020  1.090
 ZUI  C5   H9   single    0.970  0.020  1.090
 ZUI  C4   H6   single    0.970  0.020  1.090
 ZUI  C4   H7   single    0.970  0.020  1.090
 ZUI  C6   H10  single    0.970  0.020  1.090
 ZUI  C6   H11  single    0.970  0.020  1.090
 ZUI  C17  H18  single    0.930  0.020  1.080
 ZUI  C9   H13  single    0.930  0.020  1.080
 ZUI  C8   H12  single    0.930  0.020  1.080
 ZUI  C16  H17  single    0.930  0.020  1.080
 ZUI  C14  H16  single    0.930  0.020  1.080
 ZUI  C13  H15  single    0.930  0.020  1.080
 ZUI  C12  H14  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
 ZUI  N3   C21  C1   114.08  3.000
 ZUI  C1   C21  O2   125.23  3.000
 ZUI  N3   C21  O2   120.69  3.000
 ZUI  C2   C1   C    123.14  3.000
 ZUI  C2   C1   C21  117.78  3.000
 ZUI  C    C1   C21  119.08  3.000
 ZUI  H2   C    H1   107.83  3.000
 ZUI  H2   C    H3   107.85  3.000
 ZUI  H1   C    H3   107.24  3.000
 ZUI  H2   C    C1   110.95  3.000
 ZUI  H1   C    C1   111.36  3.000
 ZUI  H3   C    C1   111.44  3.000
 ZUI  H    N3   C20  114.95  3.000
 ZUI  H    N3   C21  116.73  3.000
 ZUI  C20  N3   C21  128.32  3.000
 ZUI  N    C20  O1   124.05  3.000
 ZUI  N    C20  N3   114.61  3.000
 ZUI  O1   C20  N3   121.35  3.000
 ZUI  C3   N    C2   118.79  3.000
 ZUI  C3   N    C20  120.85  3.000
 ZUI  C2   N    C20  120.36  3.000
 ZUI  H4   C2   N    114.78  3.000
 ZUI  H4   C2   C1   120.39  3.000
 ZUI  N    C2   C1   124.84  3.000
 ZUI  H5   C3   C4   106.65  3.000
 ZUI  H5   C3   C19  107.01  3.000
 ZUI  C4   C3   C19  111.00  3.000
 ZUI  H5   C3   N    104.14  3.000
 ZUI  C4   C3   N    113.83  3.000
 ZUI  C19  C3   N    113.50  3.000
 ZUI  H21  C19  H22  108.00  3.000
 ZUI  H21  C19  C18  109.42  3.000
 ZUI  H22  C19  C18  109.25  3.000
 ZUI  H21  C19  C3   110.86  3.000
 ZUI  H22  C19  C3   110.15  3.000
 ZUI  C18  C19  C3   109.13  3.000
 ZUI  H19  C18  H20  106.64  3.000
 ZUI  H19  C18  N1   108.85  3.000
 ZUI  H20  C18  N1   111.59  3.000
 ZUI  H19  C18  C19  109.26  3.000
 ZUI  H20  C18  C19  109.35  3.000
 ZUI  N1   C18  C19  111.03  3.000
 ZUI  C6   N1   C5   111.84  3.000
 ZUI  C6   N1   C18  112.01  3.000
 ZUI  C5   N1   C18  111.25  3.000
 ZUI  H9   C5   H8   106.57  3.000
 ZUI  H9   C5   C4   109.03  3.000
 ZUI  H8   C5   C4   109.77  3.000
 ZUI  H9   C5   N1   109.25  3.000
 ZUI  H8   C5   N1   111.05  3.000
 ZUI  C4   C5   N1   111.05  3.000
 ZUI  H7   C4   H6   108.02  3.000
 ZUI  H7   C4   C5   109.48  3.000
 ZUI  H6   C4   C5   109.22  3.000
 ZUI  H7   C4   C3   110.14  3.000
 ZUI  H6   C4   C3   110.99  3.000
 ZUI  C5   C4   C3   108.98  3.000
 ZUI  H11  C6   H10  105.82  3.000
 ZUI  H11  C6   C7   108.05  3.000
 ZUI  H10  C6   C7   109.28  3.000
 ZUI  H11  C6   N1   108.23  3.000
 ZUI  H10  C6   N1   112.50  3.000
 ZUI  C7   C6   N1   112.64  3.000
 ZUI  C8   C7   C17  118.04  3.000
 ZUI  C17  C7   C6   120.55  3.000
 ZUI  C8   C7   C6   121.38  3.000
 ZUI  H18  C17  C10  121.73  3.000
 ZUI  H18  C17  C7   119.55  3.000
 ZUI  C10  C17  C7   118.73  3.000
 ZUI  O    C10  C9   116.51  3.000
 ZUI  O    C10  C17  124.62  3.000
 ZUI  C9   C10  C17  118.87  3.000
 ZUI  H13  C9   N2   117.72  3.000
 ZUI  H13  C9   C10  119.92  3.000
 ZUI  N2   C9   C10  122.36  3.000
 ZUI  C8   N2   C9   118.90  3.000
 ZUI  H12  C8   N2   117.07  3.000
 ZUI  H12  C8   C7   119.82  3.000
 ZUI  N2   C8   C7   123.11  3.000
 ZUI  C11  O    C10  118.89  3.000
 ZUI  C12  C11  C16  121.49  3.000
 ZUI  C12  C11  O    119.79  3.000
 ZUI  C16  C11  O    118.71  3.000
 ZUI  H17  C16  C15  121.19  3.000
 ZUI  H17  C16  C11  120.51  3.000
 ZUI  C15  C16  C11  118.29  3.000
 ZUI  C14  C15  CL   119.45  3.000
 ZUI  C14  C15  C16  121.62  3.000
 ZUI  CL   C15  C16  118.93  3.000
 ZUI  H16  C14  C13  120.58  3.000
 ZUI  H16  C14  C15  120.65  3.000
 ZUI  C13  C14  C15  118.77  3.000
 ZUI  H15  C13  C12  119.73  3.000
 ZUI  H15  C13  C14  119.36  3.000
 ZUI  C12  C13  C14  120.92  3.000
 ZUI  H14  C12  C13  120.72  3.000
 ZUI  H14  C12  C11  120.37  3.000
 ZUI  C13  C12  C11  118.91  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
 ZUI  CONST_01  C9   N2   C8   C7     0.00   0.0  0
 ZUI  CONST_02  C9   C10  C17  C7     0.00   0.0  0
 ZUI  CONST_03  N2   C8   C7   C17    0.00   0.0  0
 ZUI  CONST_04  N2   C9   C10  C17    0.00   0.0  0
 ZUI  CONST_05  C8   N2   C9   C10    0.00   0.0  0
 ZUI  CONST_06  C8   C7   C17  C10    0.00   0.0  0
 ZUI  CONST_07  C14  C15  C16  C11    0.00   0.0  0
 ZUI  CONST_08  C14  C13  C12  C11    0.00   0.0  0
 ZUI  CONST_09  C13  C14  C15  C16    0.00   0.0  0
 ZUI  CONST_10  C13  C12  C11  C16    0.00   0.0  0
 ZUI  CONST_11  C12  C11  C16  C15    0.00   0.0  0
 ZUI  CONST_12  C12  C13  C14  C15    0.00   0.0  0
 ZUI  CONST_13  N    C20  N3   C21    0.00   0.0  0
 ZUI  CONST_14  C20  N3   C21  C1     0.00   0.0  0
 ZUI  CONST_15  C2   N    C20  N3     0.00   0.0  0
 ZUI  CONST_16  C3   N    C20  N3   180.00   0.0  0
 ZUI  CONST_17  N2   C8   C7   C6   180.00   0.0  0
 ZUI  CONST_18  C10  C17  C7   C6   180.00   0.0  0
 ZUI  CONST_19  O    C10  C17  C7   180.00   0.0  0
 ZUI  CONST_20  O    C10  C9   N2   180.00   0.0  0
 ZUI  CONST_21  C15  C16  C11  O    180.00   0.0  0
 ZUI  CONST_22  C13  C12  C11  O    180.00   0.0  0
 ZUI  CONST_23  CL   C15  C16  C11  180.00   0.0  0
 ZUI  CONST_24  C13  C14  C15  CL   180.00   0.0  0
 ZUI  CONST_25  C20  N3   C21  O2   180.00   0.0  0
 ZUI  CONST_26  O1   C20  N3   C21  180.00   0.0  0
 ZUI  CONST_27  C2   N    C20  O1   180.00   0.0  0
 ZUI  CONST_28  C3   N    C20  O1     0.00   0.0  0
 ZUI  CONST_29  H12  C8   C7   C17  180.00   0.0  0
 ZUI  CONST_30  H13  C9   C10  C17  180.00   0.0  0
 ZUI  CONST_31  H18  C17  C10  C9   180.00   0.0  0
 ZUI  CONST_32  H15  C13  C12  C11  180.00   0.0  0
 ZUI  CONST_33  H16  C14  C15  C16  180.00   0.0  0
 ZUI  CONST_34  H14  C12  C11  C16  180.00   0.0  0
 ZUI  CONST_35  H17  C16  C15  C14  180.00   0.0  0
 ZUI  CONST_36  H    N3   C21  C1   180.00   0.0  0
 ZUI  Var_01    N1   C18  C19  C3   -57.04  30.0  1
 ZUI  Var_02    N1   C5   C4   C3    57.31  30.0  1
 ZUI  Var_03    C5   N1   C18  C19   60.50  30.0  1
 ZUI  Var_04    C4   C5   N1   C18  -60.70  30.0  1
 ZUI  Var_05    C7   C6   N1   C18  162.28  30.0  3
 ZUI  Var_06    C8   C7   C6   N1   -36.26  30.0  2
 ZUI  Var_07    C16  C11  O    C10   94.76  30.0  2
 ZUI  Var_08    H3   C    C1   C21  -60.85  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ZUI  chir_01  C3  N  C19  C4  negativ

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
 ZUI  plan-1  O2   0.020
 ZUI  plan-1  C21  0.020
 ZUI  plan-1  C1   0.020
 ZUI  plan-1  C    0.020
 ZUI  plan-1  N3   0.020
 ZUI  plan-1  C20  0.020
 ZUI  plan-1  O1   0.020
 ZUI  plan-1  N    0.020
 ZUI  plan-1  C2   0.020
 ZUI  plan-1  C3   0.020
 ZUI  plan-1  H    0.020
 ZUI  plan-1  H4   0.020
 ZUI  plan-2  C6   0.020
 ZUI  plan-2  C7   0.020
 ZUI  plan-2  C17  0.020
 ZUI  plan-2  C10  0.020
 ZUI  plan-2  C9   0.020
 ZUI  plan-2  N2   0.020
 ZUI  plan-2  C8   0.020
 ZUI  plan-2  O    0.020
 ZUI  plan-2  H18  0.020
 ZUI  plan-2  H13  0.020
 ZUI  plan-2  H12  0.020
 ZUI  plan-3  O    0.020
 ZUI  plan-3  C11  0.020
 ZUI  plan-3  C16  0.020
 ZUI  plan-3  C15  0.020
 ZUI  plan-3  CL   0.020
 ZUI  plan-3  C14  0.020
 ZUI  plan-3  C13  0.020
 ZUI  plan-3  C12  0.020
 ZUI  plan-3  H17  0.020
 ZUI  plan-3  H16  0.020
 ZUI  plan-3  H15  0.020
 ZUI  plan-3  H14  0.020

