# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 14:06:57 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: 4-azanyl-6-[1-(pyridin-3-ylmethyl)pyrazol-4-yl]pyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc(c2cnn(Cc3cccnc3)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
 Q0E  Q0E  4-azanyl-6-[1-(pyridin-3-ylmethyl)pyrazol-4-yl]pyrimidine-5-carbonitrile  ligand  32  21  .  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_Q0E
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
 Q0E  C10  C  CR5   0  -0.212  20.2666  15.3104  34.3052
 Q0E  N12  N  NR5   0  -0.271  20.8552  14.8653  36.3599
 Q0E  C15  C  CH2   0  -0.398  21.2007  14.2001  37.6009
 Q0E  C17  C  CR16  0  -0.093  23.3076  14.8809  38.7931
 Q0E  C20  C  CR16  0  -0.315  24.8635  13.3417  37.2016
 Q0E  C21  C  CR16  0  -0.171  23.4967  13.3492  36.9840
 Q0E  C02  C  CR6   0   0.549  19.1775  14.2565  30.8405
 Q0E  N03  N  N     0  -0.448  18.8305  15.4597  30.3718
 Q0E  C04  C  CR16  0   0.069  18.9974  16.4839  31.1819
 Q0E  N05  N  N     0  -0.462  19.4434  16.4730  32.4263
 Q0E  C06  C  CR6   0   0.325  19.7883  15.2879  32.9372
 Q0E  C07  C  CR6   0  -0.171  19.6932  14.1295  32.1583
 Q0E  C08  C  CSP   0  -0.019  20.1203  12.8606  32.6105
 Q0E  N09  N  NS    0  -0.239  20.4642  11.8087  32.9385
 Q0E  C11  C  CR15  0   0.049  20.3951  14.2969  35.2423
 Q0E  N13  N  N     0  -0.261  21.0533  16.1788  36.2301
 Q0E  C14  C  CR15  0  -0.032  20.6910  16.4651  35.0020
 Q0E  C16  C  CR6   0   0.032  22.6896  14.1380  37.7959
 Q0E  N18  N  N     0  -0.397  24.6168  14.8793  39.0129
 Q0E  C19  C  CR16  0  -0.064  25.3746  14.1240  38.2287
 Q0E  H1   H  HCH2  0   0.295  20.7240  14.7344  38.4226
 Q0E  H2   H  HCH2  0   0.295  20.7709  13.1994  37.5620
 Q0E  H3   H  HCR6  0   0.264  22.7076  15.5063  39.4473
 Q0E  H4   H  HCR6  0   0.274  25.5244  12.7410  36.5923
 Q0E  H5   H  HCR6  0   0.276  23.0643  12.7469  36.1930
 Q0E  H6   H  HNH2  0   0.414  18.6625  13.3555  29.1050
 Q0E  H7   H  HNH2  0   0.422  19.2359  12.2691  30.3113
 Q0E  H8   H  HCR6  0   0.267  18.7289  17.4559  30.7807
 Q0E  H9   H  HCR5  0   0.305  20.1710  13.2439  35.2105
 Q0E  H10  H  HCR5  0   0.269  20.7451  17.4766  34.6310
 Q0E  H11  H  HCR6  0   0.266  26.4410  14.1385  38.4245
 Q0E  N01  N  NH2   0  -0.816  19.0301  13.2132  30.0312

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
 Q0E  N01  C02  single    1.329  0.020  1.329
 Q0E  N03  C02  aromatic  1.337  0.020  1.337
 Q0E  N03  C04  aromatic  1.317  0.020  1.317
 Q0E  C02  C07  aromatic  1.421  0.020  1.421
 Q0E  C04  N05  aromatic  1.322  0.020  1.322
 Q0E  C07  C08  single    1.413  0.020  1.413
 Q0E  C07  C06  aromatic  1.399  0.020  1.399
 Q0E  N05  C06  aromatic  1.336  0.020  1.336
 Q0E  C08  N09  triple    1.154  0.020  1.154
 Q0E  C06  C10  single    1.449  0.020  1.449
 Q0E  C10  C14  aromatic  1.414  0.020  1.414
 Q0E  C10  C11  aromatic  1.386  0.020  1.386
 Q0E  C14  N13  aromatic  1.312  0.020  1.312
 Q0E  C11  N12  aromatic  1.336  0.020  1.336
 Q0E  N13  N12  aromatic  1.335  0.020  1.335
 Q0E  N12  C15  single    1.450  0.020  1.450
 Q0E  C21  C20  aromatic  1.384  0.020  1.384
 Q0E  C21  C16  aromatic  1.390  0.020  1.390
 Q0E  C20  C19  aromatic  1.389  0.020  1.389
 Q0E  C19  N18  aromatic  1.327  0.020  1.327
 Q0E  C16  C15  single    1.503  0.020  1.503
 Q0E  C16  C17  aromatic  1.389  0.020  1.389
 Q0E  N18  C17  aromatic  1.328  0.020  1.328
 Q0E  C15  H1   single    0.970  0.020  1.090
 Q0E  C15  H2   single    0.970  0.020  1.090
 Q0E  C17  H3   single    0.930  0.020  1.080
 Q0E  C20  H4   single    0.930  0.020  1.080
 Q0E  C21  H5   single    0.930  0.020  1.080
 Q0E  N01  H6   single    0.860  0.020  1.020
 Q0E  N01  H7   single    0.860  0.020  1.020
 Q0E  C04  H8   single    0.930  0.020  1.080
 Q0E  C11  H9   single    0.930  0.020  1.080
 Q0E  C14  H10  single    0.930  0.020  1.080
 Q0E  C19  H11  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
 Q0E  C14  C10  C11  103.65  3.000
 Q0E  C11  C10  C06  131.09  3.000
 Q0E  C14  C10  C06  125.24  3.000
 Q0E  N13  N12  C11  112.87  3.000
 Q0E  N13  N12  C15  119.96  3.000
 Q0E  C11  N12  C15  127.09  3.000
 Q0E  H2   C15  H1   107.73  3.000
 Q0E  H2   C15  C16  110.94  3.000
 Q0E  H1   C15  C16  110.84  3.000
 Q0E  H2   C15  N12  107.26  3.000
 Q0E  H1   C15  N12  108.44  3.000
 Q0E  C16  C15  N12  111.47  3.000
 Q0E  H3   C17  N18  116.48  3.000
 Q0E  H3   C17  C16  119.67  3.000
 Q0E  N18  C17  C16  123.86  3.000
 Q0E  H4   C20  C19  120.32  3.000
 Q0E  H4   C20  C21  121.21  3.000
 Q0E  C19  C20  C21  118.47  3.000
 Q0E  H5   C21  C16  120.64  3.000
 Q0E  H5   C21  C20  120.37  3.000
 Q0E  C16  C21  C20  118.98  3.000
 Q0E  C07  C02  N03  119.99  3.000
 Q0E  C07  C02  N01  122.35  3.000
 Q0E  N03  C02  N01  117.67  3.000
 Q0E  C04  N03  C02  116.84  3.000
 Q0E  H8   C04  N05  116.03  3.000
 Q0E  H8   C04  N03  115.97  3.000
 Q0E  N05  C04  N03  127.99  3.000
 Q0E  C06  N05  C04  117.03  3.000
 Q0E  C07  C06  N05  120.26  3.000
 Q0E  N05  C06  C10  115.62  3.000
 Q0E  C07  C06  C10  124.11  3.000
 Q0E  C08  C07  C06  123.00  3.000
 Q0E  C06  C07  C02  117.84  3.000
 Q0E  C08  C07  C02  119.13  3.000
 Q0E  N09  C08  C07  180.00  3.000
 Q0E  H9   C11  N12  120.83  3.000
 Q0E  H9   C11  C10  132.50  3.000
 Q0E  N12  C11  C10  106.64  3.000
 Q0E  C14  N13  N12  105.35  3.000
 Q0E  H10  C14  N13  120.84  3.000
 Q0E  H10  C14  C10  127.68  3.000
 Q0E  N13  C14  C10  111.47  3.000
 Q0E  C21  C16  C17  117.68  3.000
 Q0E  C17  C16  C15  120.79  3.000
 Q0E  C21  C16  C15  121.52  3.000
 Q0E  C19  N18  C17  117.78  3.000
 Q0E  H11  C19  N18  116.58  3.000
 Q0E  H11  C19  C20  120.21  3.000
 Q0E  N18  C19  C20  123.22  3.000
 Q0E  H7   N01  H6   117.62  3.000
 Q0E  H7   N01  C02  122.99  3.000
 Q0E  H6   N01  C02  119.34  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
 Q0E  CONST_01  C02  C07  C06  C10  180.00   0.0  0
 Q0E  CONST_02  C04  N05  C06  C10  180.00   0.0  0
 Q0E  CONST_03  N12  N13  C14  C10    0.00   0.0  0
 Q0E  CONST_04  N13  N12  C11  C10    0.00   0.0  0
 Q0E  CONST_05  C06  C10  C11  N12  180.00   0.0  0
 Q0E  CONST_06  C14  C10  C11  N12    0.00   0.0  0
 Q0E  CONST_07  C20  C21  C16  C17    0.00   0.0  0
 Q0E  CONST_08  C20  C19  N18  C17    0.00   0.0  0
 Q0E  CONST_09  N18  C19  C20  C21    0.00   0.0  0
 Q0E  CONST_10  N18  C17  C16  C21    0.00   0.0  0
 Q0E  CONST_11  N05  C04  N03  C02    0.00   0.0  0
 Q0E  CONST_12  N05  C06  C07  C02    0.00   0.0  0
 Q0E  CONST_13  C06  C07  C02  N03    0.00   0.0  0
 Q0E  CONST_14  C06  N05  C04  N03    0.00   0.0  0
 Q0E  CONST_15  C07  C02  N03  C04    0.00   0.0  0
 Q0E  CONST_16  C07  C06  N05  C04    0.00   0.0  0
 Q0E  CONST_19  N13  C14  C10  C06  180.00   0.0  0
 Q0E  CONST_22  N13  C14  C10  C11    0.00   0.0  0
 Q0E  CONST_23  C14  N13  N12  C11    0.00   0.0  0
 Q0E  CONST_24  C19  C20  C21  C16    0.00   0.0  0
 Q0E  CONST_25  C19  N18  C17  C16    0.00   0.0  0
 Q0E  CONST_26  C08  C07  C06  C10    0.00   0.0  0
 Q0E  CONST_27  C15  N12  C11  C10  180.00   0.0  0
 Q0E  CONST_28  C14  N13  N12  C15  180.00   0.0  0
 Q0E  CONST_29  C20  C21  C16  C15  180.00   0.0  0
 Q0E  CONST_30  N18  C17  C16  C15  180.00   0.0  0
 Q0E  CONST_31  C04  N03  C02  N01  180.00   0.0  0
 Q0E  CONST_32  C06  C07  C02  N01  180.00   0.0  0
 Q0E  CONST_33  C08  C07  C02  N03  180.00   0.0  0
 Q0E  CONST_34  C08  C07  C06  N05  180.00   0.0  0
 Q0E  CONST_35  H10  C14  N13  N12  180.00   0.0  0
 Q0E  CONST_36  H5   C21  C16  C17  180.00   0.0  0
 Q0E  CONST_37  H11  C19  N18  C17  180.00   0.0  0
 Q0E  CONST_38  H3   C17  C16  C21  180.00   0.0  0
 Q0E  CONST_39  H8   C04  N03  C02  180.00   0.0  0
 Q0E  CONST_40  H9   C11  C10  C06    0.00   0.0  0
 Q0E  CONST_41  H4   C20  C21  C16  180.00   0.0  0
 Q0E  CONST_42  H6   N01  C02  N03    0.00   0.0  0
 Q0E  CONST_43  H7   N01  C02  N03  180.00   0.0  0
 Q0E  Var_01    C21  C16  C15  N12  -68.36  30.0  2
 Q0E  Var_02    C16  C15  N12  C11  106.55  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
 Q0E  plan-1  C10  0.020
 Q0E  plan-1  N12  0.020
 Q0E  plan-1  C15  0.020
 Q0E  plan-1  C06  0.020
 Q0E  plan-1  C11  0.020
 Q0E  plan-1  N13  0.020
 Q0E  plan-1  C14  0.020
 Q0E  plan-1  H9   0.020
 Q0E  plan-1  H10  0.020
 Q0E  plan-2  C15  0.020
 Q0E  plan-2  C17  0.020
 Q0E  plan-2  C20  0.020
 Q0E  plan-2  C21  0.020
 Q0E  plan-2  C16  0.020
 Q0E  plan-2  N18  0.020
 Q0E  plan-2  C19  0.020
 Q0E  plan-2  H3   0.020
 Q0E  plan-2  H4   0.020
 Q0E  plan-2  H5   0.020
 Q0E  plan-2  H11  0.020
 Q0E  plan-3  C10  0.020
 Q0E  plan-3  C02  0.020
 Q0E  plan-3  N03  0.020
 Q0E  plan-3  C04  0.020
 Q0E  plan-3  N05  0.020
 Q0E  plan-3  C06  0.020
 Q0E  plan-3  C07  0.020
 Q0E  plan-3  C08  0.020
 Q0E  plan-3  N09  0.020
 Q0E  plan-3  H8   0.020
 Q0E  plan-3  N01  0.020
 Q0E  plan-4  C02  0.020
 Q0E  plan-4  H6   0.020
 Q0E  plan-4  H7   0.020
 Q0E  plan-4  N01  0.020

