# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 06:11:46 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: N-(pyrimidin-5-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1cncnc1)c2ccccc2
#
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
 68B  68B  N-(pyrimidin-5-yl)benzamide  ligand  24  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_68B
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
 68B  N3   N  NH1   0  -0.758   0.4304  -0.3112  -0.0323
 68B  C4   C  CR6   0   0.270   1.8116  -0.1744  -0.0002
 68B  C5   C  CR16  0  -0.062   2.5235   0.9420   0.4401
 68B  C7   C  CR16  0   0.037   4.4825  -0.1182   0.0019
 68B  C10  C  CR6   0  -0.047  -1.9230   0.1908   0.0885
 68B  C13  C  CR16  0  -0.247  -4.6047  -0.5508  -0.0400
 68B  C15  C  CR16  0  -0.261  -2.8931   1.1201  -0.2840
 68B  O1   O  O     0  -0.451  -0.2281   1.8196   0.3813
 68B  C2   C  C     0   0.537  -0.5079   0.6547   0.1667
 68B  N6   N  N     0  -0.380   3.8507   0.9572   0.4355
 68B  N8   N  N     0  -0.374   3.9052  -1.2301  -0.4308
 68B  C9   C  CR16  0  -0.102   2.5859  -1.2529  -0.4299
 68B  C11  C  CR16  0  -0.292  -2.3093  -1.1092   0.4116
 68B  C12  C  CR16  0  -0.239  -3.6460  -1.4753   0.3505
 68B  C14  C  CR16  0  -0.241  -4.2254   0.7476  -0.3581
 68B  H1   H  HNH1  0   0.427   0.1019  -1.2161  -0.3360
 68B  H2   H  HCR6  0   0.295   2.0284   1.8304   0.8000
 68B  H3   H  HCR6  0   0.266   5.5659  -0.0913   0.0009
 68B  H4   H  HCR6  0   0.267  -5.6466  -0.8388  -0.0904
 68B  H5   H  HCR6  0   0.265  -2.6038   2.1336  -0.5278
 68B  H6   H  HCR6  0   0.291   2.1060  -2.1614  -0.7823
 68B  H7   H  HCR6  0   0.266  -1.5847  -1.8433   0.7422
 68B  H8   H  HCR6  0   0.268  -3.9372  -2.4826   0.6163
 68B  H9   H  HCR6  0   0.266  -4.9700   1.4721  -0.6609

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
 68B  O1   C2   double    1.217  0.020  1.217
 68B  C11  C12  aromatic  1.387  0.020  1.387
 68B  C11  C10  aromatic  1.394  0.020  1.394
 68B  C12  C13  aromatic  1.388  0.020  1.388
 68B  C2   C10  single    1.491  0.020  1.491
 68B  C2   N3   single    1.361  0.020  1.361
 68B  C10  C15  aromatic  1.394  0.020  1.394
 68B  N6   C5   aromatic  1.327  0.020  1.327
 68B  N6   C7   aromatic  1.320  0.020  1.320
 68B  C5   C4   aromatic  1.395  0.020  1.395
 68B  C13  C14  aromatic  1.390  0.020  1.390
 68B  C7   N8   aromatic  1.325  0.020  1.325
 68B  C4   N3   single    1.388  0.020  1.388
 68B  C4   C9   aromatic  1.395  0.020  1.395
 68B  C15  C14  aromatic  1.385  0.020  1.385
 68B  N8   C9   aromatic  1.319  0.020  1.319
 68B  N3   H1   single    0.860  0.020  1.020
 68B  C5   H2   single    0.930  0.020  1.080
 68B  C7   H3   single    0.930  0.020  1.080
 68B  C13  H4   single    0.930  0.020  1.080
 68B  C15  H5   single    0.930  0.020  1.080
 68B  C9   H6   single    0.930  0.020  1.080
 68B  C11  H7   single    0.930  0.020  1.080
 68B  C12  H8   single    0.930  0.020  1.080
 68B  C14  H9   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
 68B  H1   N3   C2   117.11  3.000
 68B  H1   N3   C4   114.78  3.000
 68B  C2   N3   C4   127.76  3.000
 68B  C9   C4   C5   115.62  3.000
 68B  C9   C4   N3   117.95  3.000
 68B  C5   C4   N3   126.42  3.000
 68B  H2   C5   N6   116.78  3.000
 68B  H2   C5   C4   122.01  3.000
 68B  N6   C5   C4   121.21  3.000
 68B  H3   C7   N8   117.12  3.000
 68B  H3   C7   N6   117.28  3.000
 68B  N8   C7   N6   125.59  3.000
 68B  C11  C10  C2   122.74  3.000
 68B  C2   C10  C15  117.84  3.000
 68B  C11  C10  C15  119.39  3.000
 68B  H4   C13  C14  120.06  3.000
 68B  H4   C13  C12  120.06  3.000
 68B  C14  C13  C12  119.89  3.000
 68B  H5   C15  C14  119.80  3.000
 68B  H5   C15  C10  119.91  3.000
 68B  C14  C15  C10  120.28  3.000
 68B  O1   C2   C10  121.67  3.000
 68B  C10  C2   N3   115.20  3.000
 68B  O1   C2   N3   123.13  3.000
 68B  C7   N6   C5   118.05  3.000
 68B  C9   N8   C7   116.73  3.000
 68B  H6   C9   N8   117.13  3.000
 68B  H6   C9   C4   120.08  3.000
 68B  N8   C9   C4   122.79  3.000
 68B  H7   C11  C12  118.63  3.000
 68B  H7   C11  C10  121.16  3.000
 68B  C12  C11  C10  120.19  3.000
 68B  H8   C12  C11  119.63  3.000
 68B  H8   C12  C13  120.23  3.000
 68B  C11  C12  C13  120.14  3.000
 68B  H9   C14  C15  119.78  3.000
 68B  H9   C14  C13  120.12  3.000
 68B  C15  C14  C13  120.10  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
 68B  CONST_01  C7   N6   C5   C4     0.00   0.0  0
 68B  CONST_02  C7   N8   C9   C4     0.00   0.0  0
 68B  CONST_03  N8   C7   N6   C5     0.00   0.0  0
 68B  CONST_04  N8   C9   C4   C5     0.00   0.0  0
 68B  CONST_05  C13  C12  C11  C10    0.00   0.0  0
 68B  CONST_06  C13  C14  C15  C10    0.00   0.0  0
 68B  CONST_07  C12  C11  C10  C15    0.00   0.0  0
 68B  CONST_08  C12  C13  C14  C15    0.00   0.0  0
 68B  CONST_09  C9   C4   C5   N6     0.00   0.0  0
 68B  CONST_10  C9   N8   C7   N6     0.00   0.0  0
 68B  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 68B  CONST_12  C14  C15  C10  C11    0.00   0.0  0
 68B  CONST_13  N6   C5   C4   N3   180.00   0.0  0
 68B  CONST_14  N8   C9   C4   N3   180.00   0.0  0
 68B  CONST_15  C12  C11  C10  C2   180.00   0.0  0
 68B  CONST_16  C14  C15  C10  C2   180.00   0.0  0
 68B  CONST_17  H3   C7   N6   C5   180.00   0.0  0
 68B  CONST_18  H6   C9   C4   C5   180.00   0.0  0
 68B  CONST_19  H2   C5   N6   C7   180.00   0.0  0
 68B  CONST_20  H8   C12  C11  C10  180.00   0.0  0
 68B  CONST_21  H9   C14  C15  C10  180.00   0.0  0
 68B  CONST_22  H7   C11  C12  C13  180.00   0.0  0
 68B  CONST_23  H5   C15  C14  C13  180.00   0.0  0
 68B  CONST_24  H4   C13  C14  C15  180.00   0.0  0
 68B  CONST_25  C10  C2   N3   C4   180.00   0.0  0
 68B  CONST_26  C2   N3   C4   C5     0.00   0.0  0
 68B  CONST_27  C9   C4   N3   C2   180.00   0.0  0
 68B  CONST_28  H1   N3   C4   C5   180.00   0.0  0
 68B  CONST_29  O1   C2   N3   C4     0.00   0.0  0
 68B  Var_01    C11  C10  C2   N3    28.79  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
 68B  plan-1  N3   0.020
 68B  plan-1  C4   0.020
 68B  plan-1  C5   0.020
 68B  plan-1  C7   0.020
 68B  plan-1  N6   0.020
 68B  plan-1  N8   0.020
 68B  plan-1  C9   0.020
 68B  plan-1  H2   0.020
 68B  plan-1  H3   0.020
 68B  plan-1  H6   0.020
 68B  plan-2  C10  0.020
 68B  plan-2  C13  0.020
 68B  plan-2  C15  0.020
 68B  plan-2  C2   0.020
 68B  plan-2  C11  0.020
 68B  plan-2  C12  0.020
 68B  plan-2  C14  0.020
 68B  plan-2  H4   0.020
 68B  plan-2  H5   0.020
 68B  plan-2  H7   0.020
 68B  plan-2  H8   0.020
 68B  plan-2  H9   0.020
 68B  plan-3  N3   0.020
 68B  plan-3  C4   0.020
 68B  plan-3  C10  0.020
 68B  plan-3  O1   0.020
 68B  plan-3  C2   0.020
 68B  plan-3  H1   0.020

