# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 12:46:45 2022
#   Inital geometry file: a 42 line input string
#   Ligand name: 4-azanylpyrimidine-5-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncncc1C#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
 Q4H  Q4H  4-azanylpyrimidine-5-carbonitrile  ligand  13  9  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_Q4H
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
 Q4H  N01  N  NS    0  -0.239  35.6934  11.2365  55.7919
 Q4H  C02  C  CSP   0   0.044  35.3158  12.2564  55.4081
 Q4H  C03  C  CR6   0  -0.170  34.8451  13.4990  54.9180
 Q4H  C04  C  CR16  0   0.005  34.8025  14.6211  55.7302
 Q4H  N05  N  N     0  -0.421  34.3683  15.7975  55.3073
 Q4H  C06  C  CR16  0   0.079  33.9705  15.8346  54.0389
 Q4H  N07  N  N     0  -0.439  33.9607  14.8479  53.1701
 Q4H  C08  C  CR6   0   0.546  34.3966  13.6497  53.5797
 Q4H  N09  N  NH2   0  -0.810  34.3876  12.6517  52.7051
 Q4H  H1   H  HCR6  0   0.295  35.1348  14.5505  56.7602
 Q4H  H2   H  HCR6  0   0.272  33.6111  16.7915  53.6755
 Q4H  H3   H  HNH2  0   0.416  34.0580  12.8158  51.7681
 Q4H  H4   H  HNH2  0   0.423  34.7002  11.7230  52.9337

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
 Q4H  N09  C08  single    1.327  0.020  1.327
 Q4H  N07  C08  aromatic  1.339  0.020  1.339
 Q4H  N07  C06  aromatic  1.315  0.020  1.315
 Q4H  C08  C03  aromatic  1.419  0.020  1.419
 Q4H  C06  N05  aromatic  1.330  0.020  1.330
 Q4H  C03  C02  single    1.416  0.020  1.416
 Q4H  C03  C04  aromatic  1.386  0.020  1.386
 Q4H  N05  C04  aromatic  1.323  0.020  1.323
 Q4H  C02  N01  triple    1.153  0.020  1.153
 Q4H  C04  H1   single    0.930  0.020  1.080
 Q4H  C06  H2   single    0.930  0.020  1.080
 Q4H  N09  H3   single    0.860  0.020  1.020
 Q4H  N09  H4   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
 Q4H  C03  C02  N01  180.00  3.000
 Q4H  C08  C03  C04  117.18  3.000
 Q4H  C04  C03  C02  121.18  3.000
 Q4H  C08  C03  C02  121.63  3.000
 Q4H  H1   C04  N05  117.51  3.000
 Q4H  H1   C04  C03  119.63  3.000
 Q4H  N05  C04  C03  122.86  3.000
 Q4H  C06  N05  C04  115.32  3.000
 Q4H  H2   C06  N07  115.98  3.000
 Q4H  H2   C06  N05  116.31  3.000
 Q4H  N07  C06  N05  127.71  3.000
 Q4H  C08  N07  C06  117.84  3.000
 Q4H  N09  C08  N07  117.97  3.000
 Q4H  N07  C08  C03  119.09  3.000
 Q4H  N09  C08  C03  122.94  3.000
 Q4H  H4   N09  H3   117.62  3.000
 Q4H  H4   N09  C08  122.84  3.000
 Q4H  H3   N09  C08  119.54  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
 Q4H  CONST_01  C06  N07  C08  C03    0.00  0.0  0
 Q4H  CONST_02  C06  N05  C04  C03    0.00  0.0  0
 Q4H  CONST_03  N07  C08  C03  C04    0.00  0.0  0
 Q4H  CONST_04  N07  C06  N05  C04    0.00  0.0  0
 Q4H  CONST_05  C08  N07  C06  N05    0.00  0.0  0
 Q4H  CONST_06  C08  C03  C04  N05    0.00  0.0  0
 Q4H  CONST_07  N07  C08  C03  C02  180.00  0.0  0
 Q4H  CONST_08  N05  C04  C03  C02  180.00  0.0  0
 Q4H  CONST_09  N09  C08  C03  C04  180.00  0.0  0
 Q4H  CONST_10  N09  C08  N07  C06  180.00  0.0  0
 Q4H  CONST_11  H2   C06  N05  C04  180.00  0.0  0
 Q4H  CONST_12  H1   C04  N05  C06  180.00  0.0  0
 Q4H  CONST_13  H3   N09  C08  C03  180.00  0.0  0
 Q4H  CONST_14  H4   N09  C08  C03    0.00  0.0  0

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
 Q4H  plan-1  N01  0.020
 Q4H  plan-1  C02  0.020
 Q4H  plan-1  C03  0.020
 Q4H  plan-1  C04  0.020
 Q4H  plan-1  N05  0.020
 Q4H  plan-1  C06  0.020
 Q4H  plan-1  N07  0.020
 Q4H  plan-1  C08  0.020
 Q4H  plan-1  N09  0.020
 Q4H  plan-1  H1   0.020
 Q4H  plan-1  H2   0.020
 Q4H  plan-2  C08  0.020
 Q4H  plan-2  N09  0.020
 Q4H  plan-2  H3   0.020
 Q4H  plan-2  H4   0.020

