# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 06:20:12 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 2,6-dimethyl-3-(1-pyrimidin-2-ylpiperidin-4-yl)-1~{H}-pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CC(=O)C(=C(C)N1)C2CCN(CC2)c3ncccn3
#
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
 9W8  9W8  2,6-dimethyl-3-(1-pyrimidin-2-ylpiperidin-4-yl)-1~{H}-pyridin-4-one  ligand  41  21  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9W8
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
 9W8  C13  C  CR6   0   0.623   3.2274   0.0741   0.0441
 9W8  C15  C  CR16  0  -0.014   5.1313  -0.6118   1.0736
 9W8  C17  C  CR16  0  -0.013   4.9396  -0.6553  -1.2574
 9W8  C20  C  CH3   0  -0.754  -2.7417  -2.0793  -1.2863
 9W8  C02  C  CR6   0   0.377  -4.4920   1.0377  -0.3733
 9W8  C03  C  CR16  0  -0.526  -3.5992   1.7134   0.3880
 9W8  C04  C  CR6   0   0.433  -2.2798   1.2032   0.6805
 9W8  O05  O  O     0  -0.516  -1.5031   1.8589   1.3908
 9W8  C06  C  CR6   0  -0.145  -1.9539  -0.0907   0.0971
 9W8  C07  C  CH1   0  -0.334  -0.6038  -0.7800   0.2375
 9W8  C08  C  CH2   0  -0.419   0.2583  -0.4997   1.4863
 9W8  C09  C  CH2   0  -0.320   1.2505   0.6579   1.3842
 9W8  N10  N  NT    0  -0.477   1.9858   0.6046   0.1330
 9W8  C11  C  CH2   0  -0.317   1.1003   0.6348  -1.0163
 9W8  C12  C  CH2   0  -0.430   0.2499  -0.6263  -1.0393
 9W8  N14  N  N     0  -0.468   3.9047  -0.1353   1.1834
 9W8  C16  C  CR16  0  -0.402   5.7284  -0.8978  -0.1442
 9W8  N18  N  N     0  -0.470   3.7084  -0.1840  -1.1817
 9W8  C19  C  CR6   0   0.333  -2.9136  -0.7362  -0.6439
 9W8  N21  N  NR16  0  -0.694  -4.1290  -0.1691  -0.8668
 9W8  H1   H  HCR6  0   0.265   5.6659  -0.7779   2.0033
 9W8  H2   H  HCR6  0   0.265   5.3157  -0.8554  -2.2556
 9W8  H3   H  HCH3  0   0.266  -3.7002  -2.4946  -1.5937
 9W8  H4   H  HCH3  0   0.272  -2.1065  -2.0182  -2.1708
 9W8  H5   H  HCH3  0   0.271  -2.2827  -2.7960  -0.6082
 9W8  H6   H  HCH3  0   0.264  -6.6202   0.8037  -0.4194
 9W8  H7   H  HCH3  0   0.266  -6.0663   2.4699  -0.2227
 9W8  H8   H  HCH3  0   0.266  -5.9557   1.6774  -1.7956
 9W8  H9   H  HCR6  0   0.252  -3.8752   2.6769   0.7965
 9W8  H11  H  HCH1  0   0.252  -0.8334  -1.8444   0.3193
 9W8  H12  H  HCH2  0   0.235  -0.3667  -0.3658   2.3696
 9W8  H13  H  HCH2  0   0.223   0.8398  -1.4101   1.6636
 9W8  H14  H  HCH2  0   0.254   0.7237   1.6073   1.4190
 9W8  H15  H  HCH2  0   0.253   1.9449   0.6251   2.2189
 9W8  H16  H  HCH2  0   0.242   0.4681   1.5232  -0.9310
 9W8  H17  H  HCH2  0   0.262   1.6771   0.7321  -1.9316
 9W8  H18  H  HCH2  0   0.231   0.9197  -1.4875  -1.1297
 9W8  H19  H  HCH2  0   0.240  -0.3802  -0.6279  -1.9312
 9W8  H20  H  HCR6  0   0.267   6.7313  -1.2895  -0.2194
 9W8  H10  H  HNR6  0   0.419  -4.7885  -0.6717  -1.4419
 9W8  C01  C  CH3   0  -0.730  -5.8587   1.5254  -0.7191

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
 9W8  O05  C04  double    1.240  0.020  1.240
 9W8  C11  N10  single    1.451  0.020  1.451
 9W8  C11  C12  single    1.521  0.020  1.521
 9W8  C09  N10  single    1.452  0.020  1.452
 9W8  C09  C08  single    1.528  0.020  1.528
 9W8  C04  C03  single    1.445  0.020  1.445
 9W8  C04  C06  single    1.456  0.020  1.456
 9W8  N10  C13  single    1.353  0.020  1.353
 9W8  C07  C12  single    1.544  0.020  1.544
 9W8  C07  C08  single    1.543  0.020  1.543
 9W8  C07  C06  single    1.522  0.020  1.522
 9W8  C03  C02  double    1.354  0.020  1.354
 9W8  C13  N18  aromatic  1.342  0.020  1.342
 9W8  C13  N14  aromatic  1.342  0.020  1.342
 9W8  N18  C17  aromatic  1.321  0.020  1.321
 9W8  C06  C19  double    1.374  0.020  1.374
 9W8  N14  C15  aromatic  1.320  0.020  1.320
 9W8  C17  C16  aromatic  1.386  0.020  1.386
 9W8  C02  C01  single    1.492  0.020  1.492
 9W8  C02  N21  single    1.353  0.020  1.353
 9W8  C19  N21  single    1.360  0.020  1.360
 9W8  C19  C20  single    1.499  0.020  1.499
 9W8  C15  C16  aromatic  1.386  0.020  1.386
 9W8  C15  H1   single    0.930  0.020  1.080
 9W8  C17  H2   single    0.930  0.020  1.080
 9W8  C20  H3   single    0.970  0.020  1.090
 9W8  C20  H4   single    0.970  0.020  1.090
 9W8  C20  H5   single    0.970  0.020  1.090
 9W8  C01  H6   single    0.970  0.020  1.090
 9W8  C01  H7   single    0.970  0.020  1.090
 9W8  C01  H8   single    0.970  0.020  1.090
 9W8  C03  H9   single    0.930  0.020  1.080
 9W8  C07  H11  single    0.970  0.020  1.090
 9W8  C08  H12  single    0.970  0.020  1.090
 9W8  C08  H13  single    0.970  0.020  1.090
 9W8  C09  H14  single    0.970  0.020  1.090
 9W8  C09  H15  single    0.970  0.020  1.090
 9W8  C11  H16  single    0.970  0.020  1.090
 9W8  C11  H17  single    0.970  0.020  1.090
 9W8  C12  H18  single    0.970  0.020  1.090
 9W8  C12  H19  single    0.970  0.020  1.090
 9W8  C16  H20  single    0.930  0.020  1.080
 9W8  N21  H10  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
 9W8  N18  C13  N14  124.38  3.000
 9W8  N14  C13  N10  117.95  3.000
 9W8  N18  C13  N10  117.66  3.000
 9W8  H1   C15  C16  120.59  3.000
 9W8  H1   C15  N14  116.20  3.000
 9W8  C16  C15  N14  123.21  3.000
 9W8  H2   C17  N18  116.21  3.000
 9W8  H2   C17  C16  120.62  3.000
 9W8  N18  C17  C16  123.17  3.000
 9W8  H5   C20  H4   107.25  3.000
 9W8  H5   C20  H3   107.21  3.000
 9W8  H4   C20  H3   107.76  3.000
 9W8  H5   C20  C19  111.81  3.000
 9W8  H4   C20  C19  111.36  3.000
 9W8  H3   C20  C19  111.22  3.000
 9W8  N21  C02  C03  118.24  3.000
 9W8  N21  C02  C01  116.92  3.000
 9W8  C03  C02  C01  124.84  3.000
 9W8  H9   C03  C04  118.09  3.000
 9W8  H9   C03  C02  119.23  3.000
 9W8  C04  C03  C02  122.68  3.000
 9W8  C06  C04  O05  124.00  3.000
 9W8  C06  C04  C03  115.92  3.000
 9W8  O05  C04  C03  120.08  3.000
 9W8  C19  C06  C07  117.17  3.000
 9W8  C19  C06  C04  118.51  3.000
 9W8  C07  C06  C04  124.32  3.000
 9W8  H11  C07  C12  105.98  3.000
 9W8  H11  C07  C08  103.53  3.000
 9W8  C12  C07  C08  110.02  3.000
 9W8  H11  C07  C06  105.18  3.000
 9W8  C08  C07  C06  119.20  3.000
 9W8  C12  C07  C06  111.66  3.000
 9W8  H13  C08  H12  105.98  3.000
 9W8  H13  C08  C09  107.21  3.000
 9W8  H12  C08  C09  109.47  3.000
 9W8  H13  C08  C07  106.07  3.000
 9W8  H12  C08  C07  110.96  3.000
 9W8  C09  C08  C07  116.51  3.000
 9W8  H15  C09  H14  108.17  3.000
 9W8  H15  C09  N10  109.71  3.000
 9W8  H14  C09  N10  107.77  3.000
 9W8  H15  C09  C08  109.93  3.000
 9W8  H14  C09  C08  110.18  3.000
 9W8  N10  C09  C08  111.01  3.000
 9W8  C11  N10  C09  111.88  3.000
 9W8  C09  N10  C13  122.38  3.000
 9W8  C11  N10  C13  121.07  3.000
 9W8  H17  C11  H16  107.45  3.000
 9W8  H17  C11  C12  111.00  3.000
 9W8  H16  C11  C12  110.58  3.000
 9W8  H17  C11  N10  110.19  3.000
 9W8  H16  C11  N10  107.93  3.000
 9W8  C12  C11  N10  109.63  3.000
 9W8  H19  C12  H18  106.52  3.000
 9W8  H19  C12  C11  109.64  3.000
 9W8  H18  C12  C11  108.14  3.000
 9W8  H19  C12  C07  110.88  3.000
 9W8  H18  C12  C07  109.17  3.000
 9W8  C11  C12  C07  112.28  3.000
 9W8  C15  N14  C13  117.04  3.000
 9W8  H20  C16  C17  122.44  3.000
 9W8  H20  C16  C15  122.44  3.000
 9W8  C17  C16  C15  115.12  3.000
 9W8  C17  N18  C13  117.08  3.000
 9W8  N21  C19  C06  121.13  3.000
 9W8  N21  C19  C20  113.96  3.000
 9W8  C06  C19  C20  124.91  3.000
 9W8  H10  N21  C19  118.03  3.000
 9W8  H10  N21  C02  118.46  3.000
 9W8  C19  N21  C02  123.50  3.000
 9W8  H8   C01  H7   108.21  3.000
 9W8  H8   C01  H6   107.52  3.000
 9W8  H7   C01  H6   108.42  3.000
 9W8  H8   C01  C02  110.83  3.000
 9W8  H7   C01  C02  110.68  3.000
 9W8  H6   C01  C02  111.06  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
 9W8  CONST_01  C16  C17  N18  C13     0.00   0.0  0
 9W8  CONST_02  C16  C15  N14  C13     0.00   0.0  0
 9W8  CONST_03  N18  C13  N14  C15     0.00   0.0  0
 9W8  CONST_04  N18  C17  C16  C15     0.00   0.0  0
 9W8  CONST_05  N14  C13  N18  C17     0.00   0.0  0
 9W8  CONST_06  N14  C15  C16  C17     0.00   0.0  0
 9W8  CONST_07  N10  C13  N14  C15   180.00   0.0  0
 9W8  CONST_08  N10  C13  N18  C17   180.00   0.0  0
 9W8  CONST_09  H2   C17  N18  C13   180.00   0.0  0
 9W8  CONST_10  H1   C15  N14  C13   180.00   0.0  0
 9W8  CONST_11  H20  C16  C15  N14   180.00   0.0  0
 9W8  Var_01    C12  C11  N10  C13    90.97  30.0  1
 9W8  Var_02    C08  C09  N10  C13   -98.11  30.0  1
 9W8  Var_03    N10  C11  C12  C07    59.14  30.0  1
 9W8  Var_04    N10  C09  C08  C07   -45.93  30.0  1
 9W8  Var_05    N18  C13  N10  C09   166.39  30.0  2
 9W8  Var_06    H6   C01  C02  C03  -124.20  30.0  3
 9W8  Var_07    H3   C20  C19  C06   165.29  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
 9W8  chir_01  C07  C12  C08  C06  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
 9W8  plan-1  C13  0.020
 9W8  plan-1  C15  0.020
 9W8  plan-1  C17  0.020
 9W8  plan-1  N10  0.020
 9W8  plan-1  N14  0.020
 9W8  plan-1  C16  0.020
 9W8  plan-1  N18  0.020
 9W8  plan-1  H1   0.020
 9W8  plan-1  H2   0.020
 9W8  plan-1  H20  0.020
 9W8  plan-2  C20  0.020
 9W8  plan-2  C02  0.020
 9W8  plan-2  C03  0.020
 9W8  plan-2  C04  0.020
 9W8  plan-2  O05  0.020
 9W8  plan-2  C06  0.020
 9W8  plan-2  C07  0.020
 9W8  plan-2  C19  0.020
 9W8  plan-2  N21  0.020
 9W8  plan-2  H9   0.020
 9W8  plan-2  H10  0.020
 9W8  plan-2  C01  0.020

