# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 20 19:45:30 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 2-[5-methoxy-2-(quinolin-3-yl)pyrimidin-4-yl]-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cnc(nc1c2[nH]c3CCNC(=O)c3c2)c4cnc5ccccc5c4
#
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
 0YO  0YO  2-[5-methoxy-2-(quinolin-3-yl)pyrimidin-4-yl]-1,5,6,7-tetrahydro-4H-pyrrolo[3,2-c]pyridin-4-one  ligand  45  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0YO
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
 0YO  C1   C  CR6   0   0.386  -1.3588   1.0342  -0.0621
 0YO  C2   C  CR16  0  -0.147  -0.4229   3.0929  -0.0437
 0YO  C3   C  CR6   0   0.327   0.8497   2.5430  -0.0993
 0YO  C7   C  CR16  0  -0.226  -3.8260   0.7381   0.0470
 0YO  C8   C  CR66  0   0.104  -4.9547  -0.1037   0.0663
 0YO  C9   C  CR66  0   0.206  -4.7388  -1.5018  -0.0096
 0YO  C10  C  CR16  0  -0.291  -5.8514  -2.3708   0.0090
 0YO  C11  C  CR16  0  -0.256  -7.1201  -1.8635   0.0992
 0YO  C12  C  CR16  0  -0.255  -7.3360  -0.4708   0.1744
 0YO  C13  C  CR16  0  -0.309  -6.2751   0.3929   0.1580
 0YO  C14  C  CR5   0   0.307   2.1644   0.3807  -0.1882
 0YO  C15  C  CR15  0  -0.373   2.3046  -0.9928  -0.2157
 0YO  C16  C  CR5   0   0.366   4.3495  -0.0482  -0.2421
 0YO  C19  C  CH2   0  -0.286   6.4113  -1.2047   0.2754
 0YO  C20  C  CH2   0  -0.528   5.8262   0.0719  -0.3187
 0YO  C21  C  CH3   0  -0.441   1.9155   4.6666  -0.0870
 0YO  C17  C  CR5   0  -0.144   3.6859  -1.2613  -0.2451
 0YO  C18  C  C     0   0.476   4.4098  -2.5275  -0.3403
 0YO  O1   O  O     0  -0.492   3.8579  -3.6062  -0.5263
 0YO  N5   N  NH1   0  -0.649   5.7559  -2.3934  -0.2499
 0YO  N4   N  NR15  0  -0.713   3.4323   0.9259  -0.2112
 0YO  C4   C  CR6   0   0.141   0.9291   1.1368  -0.1338
 0YO  N2   N  N     0  -0.454  -0.1888   0.4189  -0.1149
 0YO  N1   N  N     0  -0.422  -1.5198   2.3490  -0.0249
 0YO  C5   C  CR6   0  -0.092  -2.5707   0.1930  -0.0415
 0YO  N3   N  N     0  -0.425  -3.4937  -2.0300  -0.0996
 0YO  C6   C  CR16  0  -0.097  -2.4720  -1.2209  -0.1135
 0YO  O2   O  O2    0  -0.485   1.9877   3.2485  -0.1205
 0YO  H1   H  HCR6  0   0.294  -0.5698   4.1662  -0.0139
 0YO  H2   H  HCR6  0   0.265  -3.9567   1.8117   0.1031
 0YO  H3   H  HCR6  0   0.263  -5.6782  -3.4378  -0.0487
 0YO  H4   H  HCR6  0   0.266  -7.9686  -2.5347   0.1127
 0YO  H5   H  HCR6  0   0.265  -8.3463  -0.0904   0.2457
 0YO  H6   H  HCR6  0   0.264  -6.4313   1.4632   0.2144
 0YO  H7   H  HCR5  0   0.264   1.4978  -1.7071  -0.2070
 0YO  H8   H  HCH2  0   0.266   7.4713  -1.2755   0.0413
 0YO  H9   H  HCH2  0   0.271   6.1378   0.1920  -1.3610
 0YO  H10  H  HCH2  0   0.276   6.1993   0.9362   0.2318
 0YO  H11  H  HCH3  0   0.241   1.4368   5.0204   0.8284
 0YO  H12  H  HCH3  0   0.270   2.9406   5.0236  -0.1139
 0YO  H13  H  HCH3  0   0.241   1.3766   5.0592  -0.9518
 0YO  H14  H  HNR5  0   0.423   3.6328   1.9137  -0.2007
 0YO  H15  H  HCR6  0   0.267  -1.4906  -1.6757  -0.1866
 0YO  H16  H  HCH2  0   0.242   6.3190  -1.1673   1.3661
 0YO  H17  H  HNH1  0   0.397   6.2886  -3.2499  -0.2289

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
 0YO  C19  N5   single    1.455  0.020  1.455
 0YO  C19  C20  single    1.525  0.020  1.525
 0YO  N5   C18  single    1.356  0.020  1.356
 0YO  C20  C16  single    1.483  0.020  1.483
 0YO  C18  O1   double    1.226  0.020  1.226
 0YO  C18  C17  single    1.462  0.020  1.462
 0YO  C16  C17  aromatic  1.383  0.020  1.383
 0YO  C16  N4   aromatic  1.338  0.020  1.338
 0YO  C17  C15  aromatic  1.407  0.020  1.407
 0YO  N4   C14  aromatic  1.380  0.020  1.380
 0YO  C15  C14  aromatic  1.381  0.020  1.381
 0YO  C14  C4   single    1.449  0.020  1.449
 0YO  C13  C12  aromatic  1.368  0.020  1.368
 0YO  C13  C8   aromatic  1.414  0.020  1.414
 0YO  C4   N2   aromatic  1.329  0.020  1.329
 0YO  C4   C3   aromatic  1.409  0.020  1.409
 0YO  N2   C1   aromatic  1.323  0.020  1.323
 0YO  C12  C11  aromatic  1.411  0.020  1.411
 0YO  C7   C8   aromatic  1.408  0.020  1.408
 0YO  C7   C5   aromatic  1.371  0.020  1.371
 0YO  C8   C9   aromatic  1.417  0.020  1.417
 0YO  O2   C3   single    1.339  0.020  1.339
 0YO  O2   C21  single    1.420  0.020  1.420
 0YO  C3   C2   aromatic  1.388  0.020  1.388
 0YO  C1   C5   single    1.475  0.020  1.475
 0YO  C1   N1   aromatic  1.325  0.020  1.325
 0YO  C11  C10  aromatic  1.369  0.020  1.369
 0YO  C5   C6   aromatic  1.419  0.020  1.419
 0YO  C9   C10  aromatic  1.412  0.020  1.412
 0YO  C9   N3   aromatic  1.355  0.020  1.355
 0YO  C2   N1   aromatic  1.326  0.020  1.326
 0YO  C6   N3   aromatic  1.303  0.020  1.303
 0YO  C2   H1   single    0.930  0.020  1.080
 0YO  C7   H2   single    0.930  0.020  1.080
 0YO  C10  H3   single    0.930  0.020  1.080
 0YO  C11  H4   single    0.930  0.020  1.080
 0YO  C12  H5   single    0.930  0.020  1.080
 0YO  C13  H6   single    0.930  0.020  1.080
 0YO  C15  H7   single    0.930  0.020  1.080
 0YO  C19  H8   single    0.970  0.020  1.090
 0YO  C20  H9   single    0.970  0.020  1.090
 0YO  C20  H10  single    0.970  0.020  1.090
 0YO  C21  H11  single    0.970  0.020  1.090
 0YO  C21  H12  single    0.970  0.020  1.090
 0YO  C21  H13  single    0.970  0.020  1.090
 0YO  N4   H14  single    0.860  0.020  1.020
 0YO  C6   H15  single    0.930  0.020  1.080
 0YO  C19  H16  single    0.970  0.020  1.090
 0YO  N5   H17  single    0.890  0.020  1.040

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
 0YO  C5   C1   N1   117.74  3.000
 0YO  N1   C1   N2   124.75  3.000
 0YO  C5   C1   N2   117.51  3.000
 0YO  H1   C2   N1   116.32  3.000
 0YO  H1   C2   C3   121.19  3.000
 0YO  N1   C2   C3   122.49  3.000
 0YO  O2   C3   C4   118.53  3.000
 0YO  O2   C3   C2   124.84  3.000
 0YO  C4   C3   C2   116.63  3.000
 0YO  H2   C7   C5   120.52  3.000
 0YO  H2   C7   C8   119.69  3.000
 0YO  C5   C7   C8   119.79  3.000
 0YO  C13  C8   C9   119.50  3.000
 0YO  C9   C8   C7   117.85  3.000
 0YO  C13  C8   C7   122.65  3.000
 0YO  N3   C9   C10  119.01  3.000
 0YO  N3   C9   C8   121.87  3.000
 0YO  C10  C9   C8   119.12  3.000
 0YO  H3   C10  C11  121.13  3.000
 0YO  H3   C10  C9   118.68  3.000
 0YO  C11  C10  C9   120.20  3.000
 0YO  H4   C11  C12  119.44  3.000
 0YO  H4   C11  C10  119.84  3.000
 0YO  C12  C11  C10  120.72  3.000
 0YO  H5   C12  C13  120.20  3.000
 0YO  H5   C12  C11  119.55  3.000
 0YO  C13  C12  C11  120.24  3.000
 0YO  H6   C13  C12  120.76  3.000
 0YO  H6   C13  C8   119.02  3.000
 0YO  C12  C13  C8   120.22  3.000
 0YO  C4   C14  N4   125.27  3.000
 0YO  C4   C14  C15  127.31  3.000
 0YO  N4   C14  C15  107.41  3.000
 0YO  H7   C15  C17  127.48  3.000
 0YO  H7   C15  C14  125.67  3.000
 0YO  C17  C15  C14  106.85  3.000
 0YO  N4   C16  C17  108.04  3.000
 0YO  N4   C16  C20  128.64  3.000
 0YO  C17  C16  C20  123.27  3.000
 0YO  H16  C19  H8   107.38  3.000
 0YO  H16  C19  N5   110.45  3.000
 0YO  H8   C19  N5   107.93  3.000
 0YO  H16  C19  C20  109.09  3.000
 0YO  H8   C19  C20  110.16  3.000
 0YO  N5   C19  C20  111.74  3.000
 0YO  H10  C20  H9   107.23  3.000
 0YO  H10  C20  C19  109.61  3.000
 0YO  H9   C20  C19  110.71  3.000
 0YO  H10  C20  C16  112.25  3.000
 0YO  H9   C20  C16  109.97  3.000
 0YO  C19  C20  C16  107.10  3.000
 0YO  H13  C21  H12  109.15  3.000
 0YO  H13  C21  H11  109.33  3.000
 0YO  H12  C21  H11  109.15  3.000
 0YO  H13  C21  O2   111.43  3.000
 0YO  H12  C21  O2   106.24  3.000
 0YO  H11  C21  O2   111.45  3.000
 0YO  C18  C17  C16  121.49  3.000
 0YO  C16  C17  C15  107.67  3.000
 0YO  C18  C17  C15  130.75  3.000
 0YO  N5   C18  O1   122.97  3.000
 0YO  O1   C18  C17  123.31  3.000
 0YO  N5   C18  C17  113.69  3.000
 0YO  H17  N5   C18  116.20  3.000
 0YO  H17  N5   C19  116.63  3.000
 0YO  C18  N5   C19  123.50  3.000
 0YO  H14  N4   C16  125.26  3.000
 0YO  H14  N4   C14  124.72  3.000
 0YO  C16  N4   C14  110.02  3.000
 0YO  N2   C4   C14  115.83  3.000
 0YO  N2   C4   C3   119.44  3.000
 0YO  C14  C4   C3   124.73  3.000
 0YO  C4   N2   C1   119.57  3.000
 0YO  C2   N1   C1   117.12  3.000
 0YO  C6   C5   C7   117.58  3.000
 0YO  C6   C5   C1   120.68  3.000
 0YO  C7   C5   C1   121.75  3.000
 0YO  C6   N3   C9   118.61  3.000
 0YO  H15  C6   N3   116.75  3.000
 0YO  H15  C6   C5   118.97  3.000
 0YO  N3   C6   C5   124.29  3.000
 0YO  C21  O2   C3   118.85  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
 0YO  CONST_01  C14  C4   N2   C1    180.00   0.0  0
 0YO  CONST_02  C3   C4   N2   C1      0.00   0.0  0
 0YO  CONST_03  C8   C7   C5   C1    180.00   0.0  0
 0YO  CONST_04  N3   C6   C5   C1    180.00   0.0  0
 0YO  CONST_05  C3   C2   N1   C1      0.00   0.0  0
 0YO  CONST_06  C14  C4   C3   C2    180.00   0.0  0
 0YO  CONST_07  N2   C4   C3   C2      0.00   0.0  0
 0YO  CONST_08  N2   C1   N1   C2      0.00   0.0  0
 0YO  CONST_09  C5   C1   N1   C2    180.00   0.0  0
 0YO  CONST_10  N4   C14  C4   C3      0.00   0.0  0
 0YO  CONST_11  C15  C14  C4   C3    180.00   0.0  0
 0YO  CONST_12  C12  C13  C8   C7    180.00   0.0  0
 0YO  CONST_13  C10  C9   C8   C7    180.00   0.0  0
 0YO  CONST_14  N3   C9   C8   C7      0.00   0.0  0
 0YO  CONST_15  N2   C1   C5   C7    180.00   0.0  0
 0YO  CONST_16  N1   C1   C5   C7      0.00   0.0  0
 0YO  CONST_17  N3   C6   C5   C7      0.00   0.0  0
 0YO  CONST_18  C11  C12  C13  C8      0.00   0.0  0
 0YO  CONST_19  C6   C5   C7   C8      0.00   0.0  0
 0YO  CONST_20  C11  C10  C9   C8      0.00   0.0  0
 0YO  CONST_21  C6   N3   C9   C8      0.00   0.0  0
 0YO  CONST_22  C12  C13  C8   C9      0.00   0.0  0
 0YO  CONST_23  C5   C7   C8   C9      0.00   0.0  0
 0YO  CONST_24  C12  C11  C10  C9      0.00   0.0  0
 0YO  CONST_25  C5   C6   N3   C9      0.00   0.0  0
 0YO  CONST_26  C13  C12  C11  C10     0.00   0.0  0
 0YO  CONST_27  C13  C8   C9   C10     0.00   0.0  0
 0YO  CONST_28  C6   N3   C9   C10   180.00   0.0  0
 0YO  CONST_29  N3   C9   C10  C11   180.00   0.0  0
 0YO  CONST_30  C5   C7   C8   C13   180.00   0.0  0
 0YO  CONST_31  N3   C9   C8   C13   180.00   0.0  0
 0YO  CONST_32  C17  C16  N4   C14     0.00   0.0  0
 0YO  CONST_33  C16  C17  C15  C14     0.00   0.0  0
 0YO  CONST_34  N4   C16  C17  C15     0.00   0.0  0
 0YO  CONST_35  C16  N4   C14  C15     0.00   0.0  0
 0YO  CONST_36  N2   C4   C14  C15     0.00   0.0  0
 0YO  CONST_37  C4   C14  N4   C16   180.00   0.0  0
 0YO  CONST_38  N4   C14  C15  C17     0.00   0.0  0
 0YO  CONST_39  C4   C14  C15  C17   180.00   0.0  0
 0YO  CONST_40  N2   C4   C14  N4    180.00   0.0  0
 0YO  CONST_41  C5   C1   N2   C4    180.00   0.0  0
 0YO  CONST_42  N1   C1   N2   C4      0.00   0.0  0
 0YO  CONST_43  N1   C2   C3   C4      0.00   0.0  0
 0YO  CONST_44  C6   C5   C1   N2      0.00   0.0  0
 0YO  CONST_45  C6   C5   C1   N1    180.00   0.0  0
 0YO  CONST_47  O2   C3   C4   C14     0.00   0.0  0
 0YO  CONST_48  O2   C3   C4   N2    180.00   0.0  0
 0YO  CONST_49  O2   C3   C2   N1    180.00   0.0  0
 0YO  CONST_51  H2   C7   C5   C1      0.00   0.0  0
 0YO  CONST_52  H15  C6   C5   C1      0.00   0.0  0
 0YO  CONST_53  H1   C2   N1   C1    180.00   0.0  0
 0YO  CONST_54  H6   C13  C8   C7      0.00   0.0  0
 0YO  CONST_55  H5   C12  C13  C8    180.00   0.0  0
 0YO  CONST_56  H3   C10  C9   C8    180.00   0.0  0
 0YO  CONST_57  H4   C11  C10  C9    180.00   0.0  0
 0YO  CONST_58  H14  N4   C14  C15   180.00   0.0  0
 0YO  CONST_59  H7   C15  C17  C16   180.00   0.0  0
 0YO  CONST_60  H17  N5   C18  C17   180.00   0.0  0
 0YO  Var_01    N5   C18  C17  C15  -175.80  30.0  1
 0YO  Var_02    N5   C19  C20  C16    47.08  30.0  1
 0YO  Var_03    C17  C16  C20  C19   -27.19  30.0  1
 0YO  Var_04    C18  N5   C19  C20   -46.97  30.0  1
 0YO  Var_05    C4   C3   O2   C21   179.95  30.0  2
 0YO  Var_06    H11  C21  O2   C3     61.30  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
 0YO  plan-1  C1   0.020
 0YO  plan-1  C2   0.020
 0YO  plan-1  C3   0.020
 0YO  plan-1  C14  0.020
 0YO  plan-1  C4   0.020
 0YO  plan-1  N2   0.020
 0YO  plan-1  N1   0.020
 0YO  plan-1  C5   0.020
 0YO  plan-1  O2   0.020
 0YO  plan-1  H1   0.020
 0YO  plan-2  C14  0.020
 0YO  plan-2  C15  0.020
 0YO  plan-2  C16  0.020
 0YO  plan-2  C20  0.020
 0YO  plan-2  C17  0.020
 0YO  plan-2  C18  0.020
 0YO  plan-2  N4   0.020
 0YO  plan-2  C4   0.020
 0YO  plan-2  H7   0.020
 0YO  plan-2  H14  0.020
 0YO  plan-3  C1   0.020
 0YO  plan-3  C7   0.020
 0YO  plan-3  C8   0.020
 0YO  plan-3  C9   0.020
 0YO  plan-3  C10  0.020
 0YO  plan-3  C11  0.020
 0YO  plan-3  C12  0.020
 0YO  plan-3  C13  0.020
 0YO  plan-3  C5   0.020
 0YO  plan-3  N3   0.020
 0YO  plan-3  C6   0.020
 0YO  plan-3  H2   0.020
 0YO  plan-3  H3   0.020
 0YO  plan-3  H4   0.020
 0YO  plan-3  H5   0.020
 0YO  plan-3  H6   0.020
 0YO  plan-3  H15  0.020
 0YO  plan-4  C19  0.020
 0YO  plan-4  C17  0.020
 0YO  plan-4  C18  0.020
 0YO  plan-4  O1   0.020
 0YO  plan-4  N5   0.020
 0YO  plan-4  H17  0.020

