# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 17:57:08 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: 4-azanyl-6-[1-(2-morpholin-4-ylethyl)pyrazol-4-yl]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc(c2cnn(CCN3CCOCC3)c2)c1C#N
#
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
 Q0N  Q0N  4-azanyl-6-[1-(2-morpholin-4-ylethyl)pyrazol-4-yl]pyrimidine-5-carbonitrile  ligand  39  22  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Q0N
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
 Q0N  C10  C  CR5   0  -0.214  19.8089  15.4258  35.1475
 Q0N  N12  N  NR5   0  -0.261  19.9819  15.0849  37.2993
 Q0N  C15  C  CH2   0  -0.334  20.3073  14.5398  38.5990
 Q0N  C21  C  CH2   0  -0.152  23.8378  12.6895  36.9940
 Q0N  C22  C  CH2   0  -0.367  23.0197  13.0743  38.2249
 Q0N  C02  C  CR6   0   0.549  20.0980  14.3386  31.5299
 Q0N  N03  N  N     0  -0.450  19.5908  15.4358  30.9590
 Q0N  C04  C  CR16  0   0.069  19.2159  16.4041  31.7688
 Q0N  N05  N  N     0  -0.468  19.2730  16.4299  33.0879
 Q0N  C06  C  CR6   0   0.338  19.7710  15.3511  33.7015
 Q0N  C07  C  CR6   0  -0.171  20.2110  14.2582  32.9443
 Q0N  C08  C  CSP   0  -0.012  20.7724  13.0950  33.5147
 Q0N  N09  N  NS    0  -0.249  21.2413  12.1262  33.9328
 Q0N  C11  C  CR15  0   0.044  20.1604  14.4954  36.1168
 Q0N  N13  N  N     0  -0.270  19.5602  16.3479  37.1895
 Q0N  C14  C  CR15  0  -0.035  19.4427  16.5658  35.9017
 Q0N  C16  C  CH2   0  -0.275  21.7021  14.9455  39.0544
 Q0N  N17  N  NT    0  -0.418  22.7360  14.4918  38.1564
 Q0N  C18  C  CH2   0  -0.283  23.9634  15.2658  38.2948
 Q0N  C19  C  CH2   0  -0.220  25.1453  14.4864  37.7129
 Q0N  O20  O  O2    0  -0.482  24.7405  13.7103  36.6121
 Q0N  H1   H  HCH2  0   0.283  19.5668  14.9007  39.3113
 Q0N  H2   H  HCH2  0   0.270  20.2004  13.4571  38.5418
 Q0N  H3   H  HCH2  0   0.219  23.1715  12.5266  36.1437
 Q0N  H4   H  HCH2  0   0.201  24.3689  11.7488  37.1880
 Q0N  H5   H  HCH2  0   0.258  22.0958  12.4941  38.2133
 Q0N  H6   H  HCH2  0   0.218  23.5394  12.7992  39.1570
 Q0N  H7   H  HNH2  0   0.414  20.3864  13.4598  29.7324
 Q0N  H8   H  HNH2  0   0.422  20.8797  12.4908  31.0674
 Q0N  H9   H  HCR6  0   0.266  18.8076  17.2897  31.2925
 Q0N  H10  H  HCR5  0   0.298  20.4996  13.4754  36.0598
 Q0N  H11  H  HCR5  0   0.267  19.1003  17.5193  35.5318
 Q0N  H12  H  HCH2  0   0.251  21.7428  16.0363  39.1048
 Q0N  H13  H  HCH2  0   0.218  21.8424  14.5808  40.0845
 Q0N  H15  H  HCH2  0   0.232  23.8345  16.2221  37.7797
 Q0N  H16  H  HCH2  0   0.204  24.1962  15.4973  39.3458
 Q0N  H17  H  HCH2  0   0.209  25.6045  13.8579  38.4870
 Q0N  H18  H  HCH2  0   0.248  25.9165  15.1769  37.3693
 Q0N  N01  N  NH2   0  -0.817  20.4833  13.3510  30.7283

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
 Q0N  N01  C02  single    1.329  0.020  1.329
 Q0N  N03  C02  aromatic  1.337  0.020  1.337
 Q0N  N03  C04  aromatic  1.317  0.020  1.317
 Q0N  C02  C07  aromatic  1.421  0.020  1.421
 Q0N  C04  N05  aromatic  1.321  0.020  1.321
 Q0N  C07  C08  single    1.412  0.020  1.412
 Q0N  C07  C06  aromatic  1.401  0.020  1.401
 Q0N  N05  C06  aromatic  1.337  0.020  1.337
 Q0N  C08  N09  triple    1.155  0.020  1.155
 Q0N  C06  C10  single    1.448  0.020  1.448
 Q0N  C10  C14  aromatic  1.415  0.020  1.415
 Q0N  C10  C11  aromatic  1.389  0.020  1.389
 Q0N  C14  N13  aromatic  1.311  0.020  1.311
 Q0N  C11  N12  aromatic  1.333  0.020  1.333
 Q0N  N13  N12  aromatic  1.336  0.020  1.336
 Q0N  N12  C15  single    1.446  0.020  1.446
 Q0N  C21  O20  single    1.415  0.020  1.415
 Q0N  C21  C22  single    1.527  0.020  1.527
 Q0N  O20  C19  single    1.406  0.020  1.406
 Q0N  C22  N17  single    1.447  0.020  1.447
 Q0N  C15  C16  single    1.522  0.020  1.522
 Q0N  N17  C18  single    1.458  0.020  1.458
 Q0N  N17  C16  single    1.443  0.020  1.443
 Q0N  C18  C19  single    1.531  0.020  1.531
 Q0N  C15  H1   single    0.970  0.020  1.090
 Q0N  C15  H2   single    0.970  0.020  1.090
 Q0N  C21  H3   single    0.970  0.020  1.090
 Q0N  C21  H4   single    0.970  0.020  1.090
 Q0N  C22  H5   single    0.970  0.020  1.090
 Q0N  C22  H6   single    0.970  0.020  1.090
 Q0N  N01  H7   single    0.860  0.020  1.020
 Q0N  N01  H8   single    0.860  0.020  1.020
 Q0N  C04  H9   single    0.930  0.020  1.080
 Q0N  C11  H10  single    0.930  0.020  1.080
 Q0N  C14  H11  single    0.930  0.020  1.080
 Q0N  C16  H12  single    0.970  0.020  1.090
 Q0N  C16  H13  single    0.970  0.020  1.090
 Q0N  C18  H15  single    0.970  0.020  1.090
 Q0N  C18  H16  single    0.970  0.020  1.090
 Q0N  C19  H17  single    0.970  0.020  1.090
 Q0N  C19  H18  single    0.970  0.020  1.090

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
 Q0N  C14  C10  C11  103.49  3.000
 Q0N  C11  C10  C06  131.97  3.000
 Q0N  C14  C10  C06  124.53  3.000
 Q0N  N13  N12  C11  112.79  3.000
 Q0N  N13  N12  C15  120.08  3.000
 Q0N  C11  N12  C15  126.88  3.000
 Q0N  H2   C15  H1   107.28  3.000
 Q0N  H2   C15  C16  111.75  3.000
 Q0N  H1   C15  C16  109.82  3.000
 Q0N  H2   C15  N12  107.77  3.000
 Q0N  H1   C15  N12  108.05  3.000
 Q0N  C16  C15  N12  111.99  3.000
 Q0N  H4   C21  H3   107.76  3.000
 Q0N  H4   C21  O20  110.94  3.000
 Q0N  H3   C21  O20  106.65  3.000
 Q0N  H4   C21  C22  109.43  3.000
 Q0N  H3   C21  C22  109.76  3.000
 Q0N  O20  C21  C22  112.18  3.000
 Q0N  H6   C22  H5   106.00  3.000
 Q0N  H6   C22  N17  112.15  3.000
 Q0N  H5   C22  N17  110.76  3.000
 Q0N  H6   C22  C21  111.47  3.000
 Q0N  H5   C22  C21  108.13  3.000
 Q0N  N17  C22  C21  108.28  3.000
 Q0N  C07  C02  N03  120.11  3.000
 Q0N  C07  C02  N01  122.35  3.000
 Q0N  N03  C02  N01  117.53  3.000
 Q0N  C04  N03  C02  116.68  3.000
 Q0N  H9   C04  N05  116.02  3.000
 Q0N  H9   C04  N03  115.94  3.000
 Q0N  N05  C04  N03  128.05  3.000
 Q0N  C06  N05  C04  117.30  3.000
 Q0N  C07  C06  N05  119.90  3.000
 Q0N  N05  C06  C10  115.23  3.000
 Q0N  C07  C06  C10  124.88  3.000
 Q0N  C08  C07  C06  123.33  3.000
 Q0N  C06  C07  C02  117.97  3.000
 Q0N  C08  C07  C02  118.70  3.000
 Q0N  N09  C08  C07  180.00  3.000
 Q0N  H10  C11  N12  120.54  3.000
 Q0N  H10  C11  C10  132.66  3.000
 Q0N  N12  C11  C10  106.79  3.000
 Q0N  C14  N13  N12  105.43  3.000
 Q0N  H11  C14  N13  120.81  3.000
 Q0N  H11  C14  C10  127.70  3.000
 Q0N  N13  C14  C10  111.49  3.000
 Q0N  H13  C16  H12  106.41  3.000
 Q0N  H13  C16  N17  112.75  3.000
 Q0N  H12  C16  N17  108.42  3.000
 Q0N  H13  C16  C15  107.95  3.000
 Q0N  H12  C16  C15  108.30  3.000
 Q0N  N17  C16  C15  112.74  3.000
 Q0N  C18  N17  C16  112.17  3.000
 Q0N  C16  N17  C22  114.77  3.000
 Q0N  C18  N17  C22  110.52  3.000
 Q0N  H16  C18  H15  106.89  3.000
 Q0N  H16  C18  C19  107.86  3.000
 Q0N  H15  C18  C19  110.93  3.000
 Q0N  H16  C18  N17  112.35  3.000
 Q0N  H15  C18  N17  108.68  3.000
 Q0N  C19  C18  N17  110.10  3.000
 Q0N  H18  C19  H17  106.79  3.000
 Q0N  H18  C19  O20  107.84  3.000
 Q0N  H17  C19  O20  110.88  3.000
 Q0N  H18  C19  C18  110.08  3.000
 Q0N  H17  C19  C18  110.27  3.000
 Q0N  O20  C19  C18  110.88  3.000
 Q0N  C19  O20  C21  111.74  3.000
 Q0N  H8   N01  H7   117.63  3.000
 Q0N  H8   N01  C02  123.12  3.000
 Q0N  H7   N01  C02  119.25  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
 Q0N  CONST_01  C02  C07  C06  C10  180.00   0.0  0
 Q0N  CONST_02  C04  N05  C06  C10  180.00   0.0  0
 Q0N  CONST_03  N12  N13  C14  C10    0.00   0.0  0
 Q0N  CONST_04  N13  N12  C11  C10    0.00   0.0  0
 Q0N  CONST_05  C06  C10  C11  N12  180.00   0.0  0
 Q0N  CONST_06  C14  C10  C11  N12    0.00   0.0  0
 Q0N  CONST_07  N05  C04  N03  C02    0.00   0.0  0
 Q0N  CONST_08  N05  C06  C07  C02    0.00   0.0  0
 Q0N  CONST_09  C06  C07  C02  N03    0.00   0.0  0
 Q0N  CONST_10  C06  N05  C04  N03    0.00   0.0  0
 Q0N  CONST_11  C07  C02  N03  C04    0.00   0.0  0
 Q0N  CONST_12  C07  C06  N05  C04    0.00   0.0  0
 Q0N  CONST_13  C14  C10  C06  N05    0.00   0.0  0
 Q0N  CONST_14  C11  C10  C06  N05  180.00   0.0  0
 Q0N  CONST_15  N13  C14  C10  C06  180.00   0.0  0
 Q0N  CONST_16  C14  C10  C06  C07  180.00   0.0  0
 Q0N  CONST_17  C11  C10  C06  C07    0.00   0.0  0
 Q0N  CONST_18  N13  C14  C10  C11    0.00   0.0  0
 Q0N  CONST_19  C14  N13  N12  C11    0.00   0.0  0
 Q0N  CONST_20  C08  C07  C06  C10    0.00   0.0  0
 Q0N  CONST_21  C15  N12  C11  C10  180.00   0.0  0
 Q0N  CONST_22  C14  N13  N12  C15  180.00   0.0  0
 Q0N  CONST_23  C04  N03  C02  N01  180.00   0.0  0
 Q0N  CONST_24  C06  C07  C02  N01  180.00   0.0  0
 Q0N  CONST_25  C08  C07  C02  N03  180.00   0.0  0
 Q0N  CONST_26  C08  C07  C06  N05  180.00   0.0  0
 Q0N  CONST_27  H11  C14  N13  N12  180.00   0.0  0
 Q0N  CONST_28  H9   C04  N03  C02  180.00   0.0  0
 Q0N  CONST_29  H10  C11  C10  C06    0.00   0.0  0
 Q0N  CONST_30  H7   N01  C02  N03    0.00   0.0  0
 Q0N  CONST_31  H8   N01  C02  N03  180.00   0.0  0
 Q0N  Var_01    C18  C19  O20  C21  -65.51  30.0  1
 Q0N  Var_02    C18  N17  C22  C21  -66.77  30.0  1
 Q0N  Var_03    C19  C18  N17  C22   31.17  30.0  1
 Q0N  Var_04    O20  C21  C22  N17   35.86  30.0  1
 Q0N  Var_05    O20  C19  C18  N17   33.44  30.0  1
 Q0N  Var_06    N17  C16  C15  N12  -60.25  30.0  3
 Q0N  Var_07    C22  N17  C16  C15  -74.11  30.0  2
 Q0N  Var_08    C16  C15  N12  C11   92.76  30.0  2

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
 Q0N  plan-1  C10  0.020
 Q0N  plan-1  N12  0.020
 Q0N  plan-1  C15  0.020
 Q0N  plan-1  C06  0.020
 Q0N  plan-1  C11  0.020
 Q0N  plan-1  N13  0.020
 Q0N  plan-1  C14  0.020
 Q0N  plan-1  H10  0.020
 Q0N  plan-1  H11  0.020
 Q0N  plan-2  C10  0.020
 Q0N  plan-2  C02  0.020
 Q0N  plan-2  N03  0.020
 Q0N  plan-2  C04  0.020
 Q0N  plan-2  N05  0.020
 Q0N  plan-2  C06  0.020
 Q0N  plan-2  C07  0.020
 Q0N  plan-2  C08  0.020
 Q0N  plan-2  N09  0.020
 Q0N  plan-2  H9   0.020
 Q0N  plan-2  N01  0.020
 Q0N  plan-3  C02  0.020
 Q0N  plan-3  H7   0.020
 Q0N  plan-3  H8   0.020
 Q0N  plan-3  N01  0.020

