# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 04:00:42 2022
#   Inital geometry file: a 123 line input string
#   Ligand name: (7~{R},8~{R},9~{R})-7-(2-methoxyethoxy)-2,3-dimethyl-9-phenyl-7,8,9,10-tetrahydroimidazo[1,2-h][1,7]naphthyridin-8-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCO[C@H]1[C@H](O)[C@H](Nc2c1ccn3c(C)c(C)nc23)c4ccccc4
#
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
 8CE  8CE  "Soraprazan"
  ligand  52  27  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8CE
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
 8CE  C02  C  CR16  0  -0.004  38.4303  -39.3610  -70.8433
 8CE  C03  C  CR16  0  -0.454  39.5232  -38.9470  -71.5284
 8CE  C04  C  CR6   0   0.081  40.8150  -38.9321  -70.9390
 8CE  C05  C  CR6   0   0.218  40.9650  -39.3431  -69.6352
 8CE  C06  C  CR56  0   0.445  39.8154  -39.7779  -68.9240
 8CE  C07  C  CR5   0   0.243  37.6761  -40.2412  -68.6361
 8CE  C08  C  CH1   0   0.040  42.0130  -38.4914  -71.7433
 8CE  C09  C  CR6   0   0.085  44.5688  -38.9627  -68.9052
 8CE  C10  C  CR5   0   0.081  38.4079  -40.5102  -67.5007
 8CE  C11  C  CH1   0   0.041  43.1831  -38.1550  -70.8261
 8CE  C18  C  CH2   0  -0.198  41.3163  -36.3377  -74.6463
 8CE  C19  C  CH3   0  -0.400  39.1596  -35.7666  -73.8350
 8CE  C20  C  CH3   0  -0.749  36.2363  -40.3740  -68.9650
 8CE  C21  C  CH3   0  -0.746  37.9094  -41.0420  -66.2023
 8CE  C22  C  CH1   0  -0.155  43.3723  -39.2597  -69.7708
 8CE  C23  C  CR16  0  -0.311  45.7622  -39.6484  -69.1052
 8CE  C24  C  CR16  0  -0.238  46.8870  -39.3499  -68.3466
 8CE  C25  C  CR16  0  -0.262  46.8278  -38.3591  -67.3769
 8CE  C26  C  CR16  0  -0.238  45.6395  -37.6686  -67.1709
 8CE  C27  C  CR16  0  -0.288  44.5177  -37.9676  -67.9303
 8CE  N01  N  N     0  -0.492  39.7244  -40.2215  -67.6866
 8CE  N02  N  N     0  -0.547  38.5934  -39.7712  -69.5458
 8CE  N03  N  NH1   0  -0.701  42.1666  -39.3337  -68.9767
 8CE  O01  O  OH1   0  -0.659  44.3252  -38.0086  -71.6241
 8CE  O02  O  O2    0  -0.496  41.6586  -37.3736  -72.5225
 8CE  O03  O  O2    0  -0.487  39.9267  -36.5630  -74.7051
 8CE  H1   H  HCR6  0   0.295  37.4320  -39.3910  -71.2516
 8CE  H2   H  HCR6  0   0.266  39.3965  -38.6221  -72.5517
 8CE  H3   H  HCH1  0   0.232  42.3222  -39.3202  -72.3989
 8CE  H4   H  HCH1  0   0.222  42.9373  -37.2250  -70.2920
 8CE  H5   H  HCH2  0   0.207  41.8359  -38.3902  -74.3155
 8CE  H6   H  HCH2  0   0.205  43.1308  -37.2358  -73.9895
 8CE  H7   H  HCH2  0   0.227  41.7069  -36.3470  -75.6690
 8CE  H8   H  HCH2  0   0.210  41.5431  -35.3479  -74.2305
 8CE  H9   H  HCH3  0   0.225  38.1095  -35.9880  -74.0257
 8CE  H10  H  HCH3  0   0.207  39.3653  -35.9676  -72.7801
 8CE  H11  H  HCH3  0   0.206  39.3179  -34.6964  -74.0135
 8CE  H12  H  HCH3  0   0.249  36.0676  -41.0589  -69.7994
 8CE  H13  H  HCH3  0   0.264  35.6872  -40.7609  -68.1090
 8CE  H14  H  HCH3  0   0.250  35.7876  -39.4149  -69.2349
 8CE  H15  H  HCH3  0   0.243  38.0807  -40.3303  -65.3929
 8CE  H16  H  HCH3  0   0.241  36.8423  -41.2539  -66.2366
 8CE  H17  H  HCH3  0   0.243  38.4234  -41.9660  -65.9335
 8CE  H18  H  HCH1  0   0.254  43.5547  -40.2058  -70.3037
 8CE  H19  H  HCR6  0   0.252  45.8121  -40.4302  -69.8539
 8CE  H20  H  HCR6  0   0.255  47.8075  -39.8947  -68.5116
 8CE  H21  H  HCR6  0   0.255  47.7017  -38.1263  -66.7822
 8CE  H22  H  HCR6  0   0.255  45.5860  -36.8951  -66.4155
 8CE  H23  H  HCR6  0   0.252  43.5946  -37.4266  -67.7608
 8CE  H24  H  HNH1  0   0.382  42.2120  -39.9316  -68.1644
 8CE  H25  H  HOH1  0   0.457  45.0112  -37.5710  -71.1094
 8CE  C17  C  CH2   0  -0.163  42.0539  -37.4085  -73.8746

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
 8CE  O03  C18  single    1.409  0.020  1.409
 8CE  O03  C19  single    1.407  0.020  1.407
 8CE  C18  C17  single    1.512  0.020  1.512
 8CE  C17  O02  single    1.409  0.020  1.409
 8CE  O02  C08  single    1.408  0.020  1.408
 8CE  C08  C04  single    1.509  0.020  1.509
 8CE  C08  C11  single    1.524  0.020  1.524
 8CE  O01  C11  single    1.401  0.020  1.401
 8CE  C03  C04  aromatic  1.420  0.020  1.420
 8CE  C03  C02  aromatic  1.355  0.020  1.355
 8CE  C04  C05  aromatic  1.375  0.020  1.375
 8CE  C11  C22  single    1.539  0.020  1.539
 8CE  C02  N02  aromatic  1.371  0.020  1.371
 8CE  C22  N03  single    1.446  0.020  1.446
 8CE  C22  C09  single    1.506  0.020  1.506
 8CE  C05  N03  single    1.370  0.020  1.370
 8CE  C05  C06  aromatic  1.420  0.020  1.420
 8CE  N02  C06  aromatic  1.371  0.020  1.371
 8CE  N02  C07  aromatic  1.375  0.020  1.375
 8CE  C06  N01  aromatic  1.318  0.020  1.318
 8CE  C27  C09  aromatic  1.394  0.020  1.394
 8CE  C27  C26  aromatic  1.387  0.020  1.387
 8CE  C09  C23  aromatic  1.391  0.020  1.391
 8CE  C20  C07  single    1.483  0.020  1.483
 8CE  C07  C10  aromatic  1.377  0.020  1.377
 8CE  C26  C25  aromatic  1.390  0.020  1.390
 8CE  C23  C24  aromatic  1.389  0.020  1.389
 8CE  N01  C10  aromatic  1.361  0.020  1.361
 8CE  C10  C21  single    1.489  0.020  1.489
 8CE  C25  C24  aromatic  1.388  0.020  1.388
 8CE  C02  H1   single    0.930  0.020  1.080
 8CE  C03  H2   single    0.930  0.020  1.080
 8CE  C08  H3   single    0.970  0.020  1.090
 8CE  C11  H4   single    0.970  0.020  1.090
 8CE  C17  H5   single    0.970  0.020  1.090
 8CE  C17  H6   single    0.970  0.020  1.090
 8CE  C18  H7   single    0.970  0.020  1.090
 8CE  C18  H8   single    0.970  0.020  1.090
 8CE  C19  H9   single    0.970  0.020  1.090
 8CE  C19  H10  single    0.970  0.020  1.090
 8CE  C19  H11  single    0.970  0.020  1.090
 8CE  C20  H12  single    0.970  0.020  1.090
 8CE  C20  H13  single    0.970  0.020  1.090
 8CE  C20  H14  single    0.970  0.020  1.090
 8CE  C21  H15  single    0.970  0.020  1.090
 8CE  C21  H16  single    0.970  0.020  1.090
 8CE  C21  H17  single    0.970  0.020  1.090
 8CE  C22  H18  single    0.970  0.020  1.090
 8CE  C23  H19  single    0.930  0.020  1.080
 8CE  C24  H20  single    0.930  0.020  1.080
 8CE  C25  H21  single    0.930  0.020  1.080
 8CE  C26  H22  single    0.930  0.020  1.080
 8CE  C27  H23  single    0.930  0.020  1.080
 8CE  N03  H24  single    0.890  0.020  1.040
 8CE  O01  H25  single    0.850  0.020  0.980

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
 8CE  H1   C02  N02  117.40  3.000
 8CE  H1   C02  C03  124.29  3.000
 8CE  N02  C02  C03  118.31  3.000
 8CE  H2   C03  C04  119.76  3.000
 8CE  H2   C03  C02  118.42  3.000
 8CE  C04  C03  C02  121.82  3.000
 8CE  C08  C04  C05  120.40  3.000
 8CE  C05  C04  C03  119.31  3.000
 8CE  C08  C04  C03  120.28  3.000
 8CE  N03  C05  C06  118.12  3.000
 8CE  C06  C05  C04  118.56  3.000
 8CE  N03  C05  C04  123.31  3.000
 8CE  N02  C06  N01  111.47  3.000
 8CE  N01  C06  C05  129.00  3.000
 8CE  N02  C06  C05  119.53  3.000
 8CE  N02  C07  C20  122.12  3.000
 8CE  C20  C07  C10  132.94  3.000
 8CE  N02  C07  C10  104.94  3.000
 8CE  H3   C08  O02  109.81  3.000
 8CE  H3   C08  C11  107.99  3.000
 8CE  O02  C08  C11  110.55  3.000
 8CE  H3   C08  C04  108.69  3.000
 8CE  C11  C08  C04  110.68  3.000
 8CE  O02  C08  C04  109.09  3.000
 8CE  C27  C09  C23  118.94  3.000
 8CE  C23  C09  C22  120.11  3.000
 8CE  C27  C09  C22  120.90  3.000
 8CE  N01  C10  C21  121.25  3.000
 8CE  C21  C10  C07  127.64  3.000
 8CE  N01  C10  C07  111.11  3.000
 8CE  H4   C11  O01  111.74  3.000
 8CE  H4   C11  C22  107.53  3.000
 8CE  O01  C11  C22  111.42  3.000
 8CE  H4   C11  C08  107.89  3.000
 8CE  C22  C11  C08  110.39  3.000
 8CE  O01  C11  C08  107.82  3.000
 8CE  H8   C18  H7   106.73  3.000
 8CE  H8   C18  O03  111.34  3.000
 8CE  H7   C18  O03  108.15  3.000
 8CE  H8   C18  C17  110.16  3.000
 8CE  H7   C18  C17  107.26  3.000
 8CE  O03  C18  C17  112.91  3.000
 8CE  H11  C19  H10  108.01  3.000
 8CE  H11  C19  H9   107.99  3.000
 8CE  H10  C19  H9   108.22  3.000
 8CE  H11  C19  O03  111.90  3.000
 8CE  H10  C19  O03  112.96  3.000
 8CE  H9   C19  O03  107.59  3.000
 8CE  H14  C20  H13  107.41  3.000
 8CE  H14  C20  H12  107.35  3.000
 8CE  H13  C20  H12  107.45  3.000
 8CE  H14  C20  C07  112.02  3.000
 8CE  H13  C20  C07  110.33  3.000
 8CE  H12  C20  C07  112.05  3.000
 8CE  H17  C21  H16  107.74  3.000
 8CE  H17  C21  H15  107.20  3.000
 8CE  H16  C21  H15  107.71  3.000
 8CE  H17  C21  C10  111.08  3.000
 8CE  H16  C21  C10  111.73  3.000
 8CE  H15  C21  C10  111.18  3.000
 8CE  H18  C22  N03  111.11  3.000
 8CE  H18  C22  C11  107.77  3.000
 8CE  N03  C22  C11  108.10  3.000
 8CE  H18  C22  C09  108.42  3.000
 8CE  N03  C22  C09  110.91  3.000
 8CE  C11  C22  C09  110.49  3.000
 8CE  H19  C23  C24  119.68  3.000
 8CE  H19  C23  C09  119.64  3.000
 8CE  C24  C23  C09  120.68  3.000
 8CE  H20  C24  C25  120.15  3.000
 8CE  H20  C24  C23  119.81  3.000
 8CE  C25  C24  C23  120.04  3.000
 8CE  H21  C25  C26  120.14  3.000
 8CE  H21  C25  C24  120.20  3.000
 8CE  C26  C25  C24  119.66  3.000
 8CE  H22  C26  C27  119.74  3.000
 8CE  H22  C26  C25  120.05  3.000
 8CE  C27  C26  C25  120.21  3.000
 8CE  H23  C27  C26  119.72  3.000
 8CE  H23  C27  C09  119.81  3.000
 8CE  C26  C27  C09  120.47  3.000
 8CE  C10  N01  C06  105.46  3.000
 8CE  C07  N02  C06  107.03  3.000
 8CE  C07  N02  C02  130.49  3.000
 8CE  C06  N02  C02  122.47  3.000
 8CE  H24  N03  C22  115.77  3.000
 8CE  H24  N03  C05  114.96  3.000
 8CE  C22  N03  C05  117.89  3.000
 8CE  H25  O01  C11  108.90  3.000
 8CE  C17  O02  C08  116.15  3.000
 8CE  C19  O03  C18  114.92  3.000
 8CE  H6   C17  H5   107.08  3.000
 8CE  H6   C17  O02  111.85  3.000
 8CE  H5   C17  O02  110.60  3.000
 8CE  H6   C17  C18  108.30  3.000
 8CE  H5   C17  C18  109.35  3.000
 8CE  O02  C17  C18  109.59  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
 8CE  CONST_01  C05  C04  C03  C02     0.00   0.0  0
 8CE  CONST_02  C05  C06  N02  C02     0.00   0.0  0
 8CE  CONST_03  N01  C06  N02  C02   180.00   0.0  0
 8CE  CONST_04  C10  C07  N02  C02   180.00   0.0  0
 8CE  CONST_05  C06  C05  C04  C03     0.00   0.0  0
 8CE  CONST_06  C06  N02  C02  C03     0.00   0.0  0
 8CE  CONST_07  C07  N02  C02  C03   180.00   0.0  0
 8CE  CONST_08  N02  C02  C03  C04     0.00   0.0  0
 8CE  CONST_09  N02  C06  C05  C04     0.00   0.0  0
 8CE  CONST_10  N01  C06  C05  C04   180.00   0.0  0
 8CE  CONST_11  C07  N02  C06  C05   180.00   0.0  0
 8CE  CONST_12  C10  N01  C06  C05   180.00   0.0  0
 8CE  CONST_13  C10  C07  N02  C06     0.00   0.0  0
 8CE  CONST_14  C07  C10  N01  C06     0.00   0.0  0
 8CE  CONST_15  N01  C06  N02  C07     0.00   0.0  0
 8CE  CONST_16  C25  C26  C27  C09     0.00   0.0  0
 8CE  CONST_17  C25  C24  C23  C09     0.00   0.0  0
 8CE  CONST_18  N02  C06  N01  C10     0.00   0.0  0
 8CE  CONST_19  C26  C27  C09  C23     0.00   0.0  0
 8CE  CONST_20  C26  C25  C24  C23     0.00   0.0  0
 8CE  CONST_21  C27  C09  C23  C24     0.00   0.0  0
 8CE  CONST_22  C27  C26  C25  C24     0.00   0.0  0
 8CE  CONST_23  N02  C07  C10  N01     0.00   0.0  0
 8CE  CONST_24  C26  C27  C09  C22   180.00   0.0  0
 8CE  CONST_25  C24  C23  C09  C22   180.00   0.0  0
 8CE  CONST_26  C20  C07  N02  C02     0.00   0.0  0
 8CE  CONST_27  C20  C07  N02  C06   180.00   0.0  0
 8CE  CONST_28  C21  C10  N01  C06   180.00   0.0  0
 8CE  CONST_29  N01  C10  C07  C20   180.00   0.0  0
 8CE  CONST_30  N02  C07  C10  C21   180.00   0.0  0
 8CE  CONST_31  H1   C02  C03  C04   180.00   0.0  0
 8CE  CONST_32  H2   C03  C04  C05   180.00   0.0  0
 8CE  CONST_33  H1   C02  N02  C06   180.00   0.0  0
 8CE  CONST_34  H1   C02  N02  C07     0.00   0.0  0
 8CE  CONST_35  H2   C03  C04  C08     0.00   0.0  0
 8CE  CONST_36  H22  C26  C27  C09   180.00   0.0  0
 8CE  CONST_37  H20  C24  C23  C09   180.00   0.0  0
 8CE  CONST_38  H23  C27  C09  C22     0.00   0.0  0
 8CE  CONST_39  H19  C23  C09  C22     0.00   0.0  0
 8CE  CONST_40  H23  C27  C09  C23   180.00   0.0  0
 8CE  CONST_41  H21  C25  C24  C23   180.00   0.0  0
 8CE  CONST_42  H22  C26  C25  C24   180.00   0.0  0
 8CE  CONST_43  H23  C27  C26  C25   180.00   0.0  0
 8CE  CONST_44  H19  C23  C24  C25   180.00   0.0  0
 8CE  CONST_45  H20  C24  C25  C26   180.00   0.0  0
 8CE  CONST_46  H19  C23  C09  C27   180.00   0.0  0
 8CE  CONST_47  H21  C25  C26  C27   180.00   0.0  0
 8CE  CONST_48  H2   C03  C02  N02   180.00   0.0  0
 8CE  Var_01    C08  C04  C03  C02   178.72  30.0  1
 8CE  Var_02    N03  C05  C04  C03  -178.48  30.0  1
 8CE  Var_03    C22  N03  C05  C04   -18.12  30.0  1
 8CE  Var_04    C08  C04  C05  C06  -178.62  30.0  1
 8CE  Var_05    C22  N03  C05  C06   163.02  30.0  1
 8CE  Var_06    N03  C05  C04  C08     2.53  30.0  1
 8CE  Var_07    N03  C05  C06  N01    -1.80  30.0  1
 8CE  Var_08    N03  C05  C06  N02   178.58  30.0  1
 8CE  Var_09    H24  N03  C05  C04  -160.20  30.0  1
 8CE  Var_10    H24  N03  C05  C06    20.94  30.0  1
 8CE  Var_11    H15  C21  C10  C07  -118.01  30.0  2
 8CE  Var_12    H16  C21  C10  C07     2.36  30.0  2
 8CE  Var_13    H17  C21  C10  C07   122.70  30.0  2
 8CE  Var_14    H12  C20  C07  C10  -119.43  30.0  2
 8CE  Var_15    H13  C20  C07  C10     0.25  30.0  2
 8CE  Var_16    H14  C20  C07  C10   119.85  30.0  2
 8CE  Var_17    H15  C21  C10  N01    61.82  30.0  2
 8CE  Var_18    H16  C21  C10  N01  -177.81  30.0  2
 8CE  Var_19    H17  C21  C10  N01   -57.46  30.0  2
 8CE  Var_20    H12  C20  C07  N02    60.41  30.0  2
 8CE  Var_21    H13  C20  C07  N02  -179.91  30.0  2
 8CE  Var_22    H14  C20  C07  N02   -60.30  30.0  2
 8CE  Var_23    C18  C17  O02  C08   165.77  30.0  3
 8CE  Var_24    H5   C17  O02  C08    45.15  30.0  3
 8CE  Var_25    H6   C17  O02  C08   -74.11  30.0  3
 8CE  Var_26    C19  O03  C18  C17   102.94  30.0  2
 8CE  Var_27    O03  C18  C17  O02   -65.26  30.0  1
 8CE  Var_28    H9   C19  O03  C18   176.23  30.0  3
 8CE  Var_29    H10  C19  O03  C18   -64.40  30.0  3
 8CE  Var_30    H11  C19  O03  C18    57.76  30.0  3
 8CE  Var_31    H7   C18  O03  C19  -138.53  30.0  3
 8CE  Var_32    H8   C18  O03  C19   -21.58  30.0  3
 8CE  Var_33    H7   C18  C17  O02   175.70  30.0  1
 8CE  Var_34    H8   C18  C17  O02    59.90  30.0  1
 8CE  Var_35    H5   C17  C18  O03    56.12  30.0  3
 8CE  Var_36    H6   C17  C18  O03   172.48  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
 8CE  chir_01  C08  O02  C04  C11  positiv
 8CE  chir_02  C11  O01  C08  C22  negativ
 8CE  chir_03  C22  N03  C11  C09  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
 8CE  plan-1  C09  0.020
 8CE  plan-1  C22  0.020
 8CE  plan-1  C23  0.020
 8CE  plan-1  C24  0.020
 8CE  plan-1  C25  0.020
 8CE  plan-1  C26  0.020
 8CE  plan-1  C27  0.020
 8CE  plan-1  H19  0.020
 8CE  plan-1  H20  0.020
 8CE  plan-1  H21  0.020
 8CE  plan-1  H22  0.020
 8CE  plan-1  H23  0.020
 8CE  plan-2  C02  0.020
 8CE  plan-2  C05  0.020
 8CE  plan-2  C06  0.020
 8CE  plan-2  C07  0.020
 8CE  plan-2  C10  0.020
 8CE  plan-2  C20  0.020
 8CE  plan-2  C21  0.020
 8CE  plan-2  N01  0.020
 8CE  plan-2  N02  0.020

