# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 07:18:26 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1C=C(Cn2cnc3ccccc23)N=C4C=CC=CN14
#
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
 1OX  1OX  2-(1H-benzimidazol-1-ylmethyl)-4H-pyrido[1,2-a]pyrimidin-4-one  ligand  33  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1OX
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
 1OX  C1   C  CR16  0  -0.274   4.1749   2.2446  -0.0740
 1OX  C2   C  CR16  0  -0.280   3.2942   2.2041   1.0189
 1OX  C3   C  CR16  0  -0.325   4.2291   1.2125  -0.9925
 1OX  C4   C  CR16  0  -0.294   2.4436   1.1331   1.2248
 1OX  C5   C  CR15  0   0.108   2.3177  -1.7095  -0.9167
 1OX  C6   C  CR56  0   0.119   3.3813   0.1210  -0.8000
 1OX  C7   C  CR56  0   0.363   2.5108   0.0964   0.3013
 1OX  C8   C  CR16  0  -0.110  -3.1845   2.3179  -1.0846
 1OX  C9   C  CR16  0  -0.394  -1.9648   1.8064  -0.7760
 1OX  C10  C  CR16  0  -0.377  -4.3479   1.5683  -0.7945
 1OX  C11  C  CR16  0  -0.504  -1.6475  -1.9147   0.9923
 1OX  C12  C  CR16  0   0.050  -4.2257   0.3521  -0.2171
 1OX  C13  C  CR6   0   0.278  -0.5606  -1.1313   0.6993
 1OX  C14  C  CR66  0   0.583  -1.8385   0.5318  -0.1676
 1OX  C15  C  CR6   0   0.594  -2.9577  -1.4705   0.7034
 1OX  N17  N  N     0  -0.468   3.2301  -1.0272  -1.5443
 1OX  N18  N  N     0  -0.476  -0.6415   0.0667   0.1258
 1OX  N19  N  NR5   0  -0.502   1.8498  -1.1010   0.2039
 1OX  N20  N  N     0  -0.619  -2.9962  -0.1676   0.0953
 1OX  O21  O  O     0  -0.482  -4.0048  -2.0606   0.9077
 1OX  H1   H  HCR6  0   0.252   4.8202   3.1044  -0.1982
 1OX  H2   H  HCR6  0   0.255   3.2756   3.0345   1.7123
 1OX  H3   H  HCR6  0   0.254   4.9060   1.2454  -1.8366
 1OX  H4   H  HCR6  0   0.264   1.7558   1.1172   2.0599
 1OX  H5   H  HCR5  0   0.291   1.9462  -2.6792  -1.2168
 1OX  H7   H  HCR6  0   0.293  -1.0479   2.3419  -0.9756
 1OX  H8   H  HCR6  0   0.294  -5.3314   1.9495  -1.0244
 1OX  H9   H  HCR6  0   0.277  -1.5320  -2.8897   1.4460
 1OX  H11  H  HCR6  0   0.324  -5.0710  -0.2698   0.0281
 1OX  C16  C  CH2   0  -0.390   0.8213  -1.6052   1.0731
 1OX  H6   H  HCR6  0   0.294  -3.2688   3.2910  -1.5485
 1OX  H12  H  HCH2  0   0.302   1.0379  -1.2912   2.0970
 1OX  H13  H  HCH2  0   0.300   0.8600  -2.6941   1.0703

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
 1OX  C12  C10  double    1.352  0.020  1.352
 1OX  C12  N20  single    1.371  0.020  1.371
 1OX  C10  C8   single    1.414  0.020  1.414
 1OX  O21  C15  double    1.219  0.020  1.219
 1OX  C15  N20  single    1.438  0.020  1.438
 1OX  C15  C11  single    1.413  0.020  1.413
 1OX  N20  C14  single    1.378  0.020  1.378
 1OX  C8   C9   double    1.358  0.020  1.358
 1OX  C11  C13  double    1.372  0.020  1.372
 1OX  C14  C9   single    1.418  0.020  1.418
 1OX  C14  N18  double    1.317  0.020  1.317
 1OX  C13  N18  single    1.331  0.020  1.331
 1OX  C13  C16  single    1.508  0.020  1.508
 1OX  C16  N19  single    1.438  0.020  1.438
 1OX  C4   C7   aromatic  1.390  0.020  1.390
 1OX  C4   C2   aromatic  1.383  0.020  1.383
 1OX  N19  C7   aromatic  1.371  0.020  1.371
 1OX  N19  C5   aromatic  1.358  0.020  1.358
 1OX  C7   C6   aromatic  1.404  0.020  1.404
 1OX  C2   C1   aromatic  1.404  0.020  1.404
 1OX  C5   N17  aromatic  1.301  0.020  1.301
 1OX  C6   N17  aromatic  1.377  0.020  1.377
 1OX  C6   C3   aromatic  1.395  0.020  1.395
 1OX  C1   C3   aromatic  1.383  0.020  1.383
 1OX  C1   H1   single    0.930  0.020  1.080
 1OX  C2   H2   single    0.930  0.020  1.080
 1OX  C3   H3   single    0.930  0.020  1.080
 1OX  C4   H4   single    0.930  0.020  1.080
 1OX  C5   H5   single    0.930  0.020  1.080
 1OX  C8   H6   single    0.930  0.020  1.080
 1OX  C9   H7   single    0.930  0.020  1.080
 1OX  C10  H8   single    0.930  0.020  1.080
 1OX  C11  H9   single    0.930  0.020  1.080
 1OX  C12  H11  single    0.930  0.020  1.080
 1OX  C16  H12  single    0.970  0.020  1.090
 1OX  C16  H13  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
 1OX  H1   C1   C3   119.57  3.000
 1OX  H1   C1   C2   119.09  3.000
 1OX  C3   C1   C2   121.34  3.000
 1OX  H2   C2   C4   119.23  3.000
 1OX  H2   C2   C1   119.17  3.000
 1OX  C4   C2   C1   121.59  3.000
 1OX  H3   C3   C6   120.75  3.000
 1OX  H3   C3   C1   121.31  3.000
 1OX  C6   C3   C1   117.93  3.000
 1OX  H4   C4   C7   122.18  3.000
 1OX  H4   C4   C2   121.14  3.000
 1OX  C7   C4   C2   116.67  3.000
 1OX  H5   C5   N19  120.84  3.000
 1OX  H5   C5   N17  125.29  3.000
 1OX  N19  C5   N17  113.87  3.000
 1OX  N17  C6   C7   109.96  3.000
 1OX  N17  C6   C3   130.13  3.000
 1OX  C7   C6   C3   119.91  3.000
 1OX  N19  C7   C6   104.98  3.000
 1OX  C6   C7   C4   122.55  3.000
 1OX  N19  C7   C4   132.47  3.000
 1OX  H6   C8   C10  120.06  3.000
 1OX  H6   C8   C9   120.42  3.000
 1OX  C10  C8   C9   119.51  3.000
 1OX  H7   C9   C14  116.69  3.000
 1OX  H7   C9   C8   122.24  3.000
 1OX  C14  C9   C8   121.07  3.000
 1OX  H8   C10  C12  119.41  3.000
 1OX  H8   C10  C8   121.24  3.000
 1OX  C12  C10  C8   119.35  3.000
 1OX  H9   C11  C15  117.91  3.000
 1OX  H9   C11  C13  121.32  3.000
 1OX  C15  C11  C13  120.76  3.000
 1OX  H11  C12  N20  115.64  3.000
 1OX  H11  C12  C10  123.05  3.000
 1OX  N20  C12  C10  121.30  3.000
 1OX  N18  C13  C16  116.46  3.000
 1OX  C16  C13  C11  119.59  3.000
 1OX  N18  C13  C11  123.92  3.000
 1OX  N20  C14  N18  122.81  3.000
 1OX  N18  C14  C9   119.59  3.000
 1OX  N20  C14  C9   117.60  3.000
 1OX  O21  C15  N20  119.10  3.000
 1OX  N20  C15  C11  113.32  3.000
 1OX  O21  C15  C11  127.58  3.000
 1OX  C6   N17  C5   104.69  3.000
 1OX  C14  N18  C13  117.98  3.000
 1OX  C16  N19  C7   127.45  3.000
 1OX  C7   N19  C5   106.48  3.000
 1OX  C16  N19  C5   126.01  3.000
 1OX  C15  N20  C14  121.20  3.000
 1OX  C14  N20  C12  121.17  3.000
 1OX  C15  N20  C12  117.63  3.000
 1OX  H13  C16  H12  106.42  3.000
 1OX  H13  C16  N19  108.88  3.000
 1OX  H12  C16  N19  108.90  3.000
 1OX  H13  C16  C13  110.24  3.000
 1OX  H12  C16  C13  108.88  3.000
 1OX  N19  C16  C13  113.29  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
 1OX  CONST_01  C7   C4   C2   C1     0.00   0.0  0
 1OX  CONST_02  C7   C6   C3   C1     0.00   0.0  0
 1OX  CONST_03  N17  C6   C3   C1   180.00   0.0  0
 1OX  CONST_04  N19  C7   C4   C2   180.00   0.0  0
 1OX  CONST_05  C6   C7   C4   C2     0.00   0.0  0
 1OX  CONST_06  C6   C3   C1   C2     0.00   0.0  0
 1OX  CONST_07  C4   C7   C6   C3     0.00   0.0  0
 1OX  CONST_08  N19  C7   C6   C3   180.00   0.0  0
 1OX  CONST_09  C5   N17  C6   C3   180.00   0.0  0
 1OX  CONST_10  C4   C2   C1   C3     0.00   0.0  0
 1OX  CONST_11  C5   N19  C7   C4   180.00   0.0  0
 1OX  CONST_12  N17  C6   C7   C4   180.00   0.0  0
 1OX  CONST_13  C6   C7   N19  C5     0.00   0.0  0
 1OX  CONST_14  C7   C6   N17  C5     0.00   0.0  0
 1OX  CONST_15  N19  C5   N17  C6     0.00   0.0  0
 1OX  CONST_16  N17  C5   N19  C7     0.00   0.0  0
 1OX  CONST_17  N19  C7   C6   N17    0.00   0.0  0
 1OX  CONST_18  C12  N20  C14  C9     0.00   0.0  0
 1OX  CONST_19  C15  N20  C14  C9   180.00   0.0  0
 1OX  CONST_20  C13  N18  C14  C9   180.00   0.0  0
 1OX  CONST_21  C12  N20  C15  C11  180.00   0.0  0
 1OX  CONST_22  C14  N20  C15  C11    0.00   0.0  0
 1OX  CONST_23  N18  C14  N20  C12  180.00   0.0  0
 1OX  CONST_24  N20  C14  N18  C13    0.00   0.0  0
 1OX  CONST_25  N18  C14  N20  C15    0.00   0.0  0
 1OX  CONST_26  C16  N19  C7   C4     0.00   0.0  0
 1OX  CONST_27  C16  N19  C7   C6   180.00   0.0  0
 1OX  CONST_28  N17  C5   N19  C16  180.00   0.0  0
 1OX  CONST_29  O21  C15  N20  C12    0.00   0.0  0
 1OX  CONST_30  O21  C15  N20  C14  180.00   0.0  0
 1OX  CONST_31  H4   C4   C2   C1   180.00   0.0  0
 1OX  CONST_32  H3   C3   C1   C2   180.00   0.0  0
 1OX  CONST_33  H2   C2   C1   C3   180.00   0.0  0
 1OX  CONST_34  H1   C1   C2   C4   180.00   0.0  0
 1OX  CONST_35  H5   C5   N17  C6   180.00   0.0  0
 1OX  Var_01    C13  C16  N19  C5   -91.50  30.0  2
 1OX  Var_02    N19  C16  C13  C11  151.38  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
 1OX  plan-1  C1   0.020
 1OX  plan-1  C2   0.020
 1OX  plan-1  C3   0.020
 1OX  plan-1  C4   0.020
 1OX  plan-1  C5   0.020
 1OX  plan-1  C6   0.020
 1OX  plan-1  C7   0.020
 1OX  plan-1  N17  0.020
 1OX  plan-1  N19  0.020
 1OX  plan-1  H1   0.020
 1OX  plan-1  H2   0.020
 1OX  plan-1  H3   0.020
 1OX  plan-1  H4   0.020
 1OX  plan-1  H5   0.020
 1OX  plan-1  C16  0.020
 1OX  plan-2  C8   0.020
 1OX  plan-2  C9   0.020
 1OX  plan-2  C10  0.020
 1OX  plan-2  C11  0.020
 1OX  plan-2  C12  0.020
 1OX  plan-2  C13  0.020
 1OX  plan-2  C14  0.020
 1OX  plan-2  C15  0.020
 1OX  plan-2  N18  0.020
 1OX  plan-2  N20  0.020
 1OX  plan-2  O21  0.020
 1OX  plan-2  H7   0.020
 1OX  plan-2  H8   0.020
 1OX  plan-2  H9   0.020
 1OX  plan-2  H11  0.020
 1OX  plan-2  C16  0.020
 1OX  plan-2  H6   0.020

