# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 17:11:53 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: 3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1nccnc1NCc2ccccc2Cl
#
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
 0YI  0YI  3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide  ligand  29  18  .  2022-08-09  2022-08-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0YI
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
 0YI  C3   C   CR6   0   0.519  5.1081  35.7736  29.5451
 0YI  C5   C   CR16  0  -0.082  6.7748  34.2173  29.5593
 0YI  C11  C   CH2   0  -0.333  2.9333  35.1691  30.4793
 0YI  C12  C   CR6   0   0.159  2.3262  34.1682  29.5203
 0YI  C13  C   CR6   0  -0.102  1.5484  33.1122  29.9887
 0YI  C14  C   CR16  0  -0.198  0.9722  32.1827  29.1372
 0YI  C15  C   CR16  0  -0.277  1.1698  32.3004  27.7698
 0YI  C16  C   CR16  0  -0.230  1.9340  33.3459  27.2737
 0YI  N9   N   NH2   0  -0.800  6.5281  38.7680  27.8750
 0YI  C17  C   CR16  0  -0.307  2.5008  34.2661  28.1437
 0YI  C2   C   CR6   0   0.003  5.9956  36.6774  28.8955
 0YI  C6   C   CR16  0  -0.160  7.6470  35.0998  28.9374
 0YI  C7   C   C     0   0.520  5.5830  38.0545  28.4905
 0YI  N1   N   N     0  -0.370  7.2323  36.3131  28.6142
 0YI  N10  N   NH1   0  -0.683  3.8456  36.0953  29.8716
 0YI  N4   N   N     0  -0.417  5.5317  34.5438  29.8524
 0YI  O8   O   O     0  -0.489  4.4507  38.4808  28.7109
 0YI  CL1  CL  CL    0  -0.128  1.2742  32.9422  31.6977
 0YI  H1   H   HCR6  0   0.275  7.0964  33.2156  29.8219
 0YI  H2   H   HCH2  0   0.282  2.1362  35.7549  30.9408
 0YI  H3   H   HCH2  0   0.260  3.4336  34.6374  31.2902
 0YI  H4   H   HCR6  0   0.277  0.3754  31.3750  29.5393
 0YI  H5   H   HCR6  0   0.264  0.7244  31.5768  27.1002
 0YI  H6   H   HCR6  0   0.260  2.0907  33.4487  26.2081
 0YI  H7   H   HNH2  0   0.405  6.3373  39.7079  27.5704
 0YI  H8   H   HNH2  0   0.410  7.4432  38.3804  27.7172
 0YI  H9   H   HCR6  0   0.257  3.0867  35.0820  27.7411
 0YI  H10  H   HCR6  0   0.270  8.6654  34.8241  28.6980
 0YI  H11  H   HNH1  0   0.416  3.5280  37.0136  29.5965

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
 0YI  C16  C15  aromatic  1.387  0.020  1.387
 0YI  C16  C17  aromatic  1.387  0.020  1.387
 0YI  N9   C7   single    1.335  0.020  1.335
 0YI  C15  C14  aromatic  1.387  0.020  1.387
 0YI  C17  C12  aromatic  1.391  0.020  1.391
 0YI  C7   O8   double    1.230  0.020  1.230
 0YI  C7   C2   single    1.494  0.020  1.494
 0YI  C2   N1   aromatic  1.320  0.020  1.320
 0YI  C2   C3   aromatic  1.424  0.020  1.424
 0YI  N1   C6   aromatic  1.322  0.020  1.322
 0YI  C14  C13  aromatic  1.386  0.020  1.386
 0YI  C12  C13  aromatic  1.393  0.020  1.393
 0YI  C12  C11  single    1.513  0.020  1.513
 0YI  N10  C3   single    1.343  0.020  1.343
 0YI  N10  C11  single    1.435  0.020  1.435
 0YI  C3   N4   aromatic  1.337  0.020  1.337
 0YI  C6   C5   aromatic  1.388  0.020  1.388
 0YI  C13  CL1  single    1.739  0.020  1.739
 0YI  N4   C5   aromatic  1.318  0.020  1.318
 0YI  C5   H1   single    0.930  0.020  1.080
 0YI  C11  H2   single    0.970  0.020  1.090
 0YI  C11  H3   single    0.970  0.020  1.090
 0YI  C14  H4   single    0.930  0.020  1.080
 0YI  C15  H5   single    0.930  0.020  1.080
 0YI  C16  H6   single    0.930  0.020  1.080
 0YI  N9   H7   single    0.860  0.020  1.020
 0YI  N9   H8   single    0.860  0.020  1.020
 0YI  C17  H9   single    0.930  0.020  1.080
 0YI  C6   H10  single    0.930  0.020  1.080
 0YI  N10  H11  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
 0YI  N4   C3   N10  117.54  3.000
 0YI  N4   C3   C2   119.44  3.000
 0YI  N10  C3   C2   123.02  3.000
 0YI  H1   C5   N4   117.04  3.000
 0YI  H1   C5   C6   120.64  3.000
 0YI  N4   C5   C6   122.32  3.000
 0YI  H3   C11  H2   106.39  3.000
 0YI  H3   C11  N10  109.74  3.000
 0YI  H2   C11  N10  107.27  3.000
 0YI  H3   C11  C12  109.43  3.000
 0YI  H2   C11  C12  109.26  3.000
 0YI  N10  C11  C12  114.43  3.000
 0YI  C17  C12  C13  117.15  3.000
 0YI  C13  C12  C11  120.82  3.000
 0YI  C17  C12  C11  122.02  3.000
 0YI  CL1  C13  C14  118.20  3.000
 0YI  CL1  C13  C12  119.52  3.000
 0YI  C14  C13  C12  122.28  3.000
 0YI  H4   C14  C15  120.57  3.000
 0YI  H4   C14  C13  120.11  3.000
 0YI  C15  C14  C13  119.32  3.000
 0YI  H5   C15  C16  120.65  3.000
 0YI  H5   C15  C14  119.66  3.000
 0YI  C16  C15  C14  119.69  3.000
 0YI  H6   C16  C17  119.70  3.000
 0YI  H6   C16  C15  120.25  3.000
 0YI  C17  C16  C15  120.05  3.000
 0YI  H8   N9   H7   118.99  3.000
 0YI  H8   N9   C7   120.69  3.000
 0YI  H7   N9   C7   120.31  3.000
 0YI  H9   C17  C16  119.21  3.000
 0YI  H9   C17  C12  119.28  3.000
 0YI  C16  C17  C12  121.51  3.000
 0YI  N1   C2   C7   117.11  3.000
 0YI  N1   C2   C3   120.42  3.000
 0YI  C7   C2   C3   122.47  3.000
 0YI  H10  C6   N1   118.36  3.000
 0YI  H10  C6   C5   121.91  3.000
 0YI  N1   C6   C5   119.73  3.000
 0YI  O8   C7   C2   121.70  3.000
 0YI  C2   C7   N9   114.98  3.000
 0YI  O8   C7   N9   123.32  3.000
 0YI  C6   N1   C2   119.68  3.000
 0YI  H11  N10  C11  120.16  3.000
 0YI  H11  N10  C3   116.56  3.000
 0YI  C11  N10  C3   123.08  3.000
 0YI  C5   N4   C3   118.40  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
 0YI  CONST_01  C6   N1   C2   C3      0.00   0.0  0
 0YI  CONST_02  C6   C5   N4   C3      0.00   0.0  0
 0YI  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 0YI  CONST_04  C2   C3   N4   C5      0.00   0.0  0
 0YI  CONST_05  C15  C16  C17  C12     0.00   0.0  0
 0YI  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 0YI  CONST_07  C16  C15  C14  C13     0.00   0.0  0
 0YI  CONST_08  C16  C17  C12  C13     0.00   0.0  0
 0YI  CONST_09  C17  C16  C15  C14     0.00   0.0  0
 0YI  CONST_10  C17  C12  C13  C14     0.00   0.0  0
 0YI  CONST_11  N4   C3   C2   N1      0.00   0.0  0
 0YI  CONST_12  N4   C5   C6   N1      0.00   0.0  0
 0YI  CONST_13  N10  C3   N4   C5    180.00   0.0  0
 0YI  CONST_14  C16  C17  C12  C11   180.00   0.0  0
 0YI  CONST_15  C14  C13  C12  C11   180.00   0.0  0
 0YI  CONST_16  CL1  C13  C14  C15   180.00   0.0  0
 0YI  CONST_17  CL1  C13  C12  C17   180.00   0.0  0
 0YI  CONST_18  C7   C2   N1   C6    180.00   0.0  0
 0YI  CONST_19  N4   C3   C2   C7    180.00   0.0  0
 0YI  CONST_20  N10  C3   C2   N1    180.00   0.0  0
 0YI  CONST_21  H1   C5   N4   C3    180.00   0.0  0
 0YI  CONST_22  H6   C16  C17  C12   180.00   0.0  0
 0YI  CONST_23  H4   C14  C13  C12   180.00   0.0  0
 0YI  CONST_24  H5   C15  C14  C13   180.00   0.0  0
 0YI  CONST_25  H9   C17  C12  C13   180.00   0.0  0
 0YI  CONST_26  H10  C6   N1   C2    180.00   0.0  0
 0YI  CONST_27  C2   C3   N10  C11   180.00   0.0  0
 0YI  CONST_28  N4   C3   N10  C11     0.00   0.0  0
 0YI  CONST_29  H11  N10  C3   C2      0.00   0.0  0
 0YI  CONST_30  H7   N9   C7   C2    180.00   0.0  0
 0YI  CONST_31  H8   N9   C7   C2      0.00   0.0  0
 0YI  Var_01    N9   C7   C2   C3   -179.09  30.0  2
 0YI  Var_02    C12  C11  N10  C3    -77.81  30.0  3
 0YI  Var_03    N10  C11  C12  C13   172.37  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
 0YI  plan-1  C11  0.020
 0YI  plan-1  C12  0.020
 0YI  plan-1  C13  0.020
 0YI  plan-1  C14  0.020
 0YI  plan-1  C15  0.020
 0YI  plan-1  C16  0.020
 0YI  plan-1  C17  0.020
 0YI  plan-1  CL1  0.020
 0YI  plan-1  H4   0.020
 0YI  plan-1  H5   0.020
 0YI  plan-1  H6   0.020
 0YI  plan-1  H9   0.020
 0YI  plan-2  C3   0.020
 0YI  plan-2  C5   0.020
 0YI  plan-2  C2   0.020
 0YI  plan-2  C6   0.020
 0YI  plan-2  C7   0.020
 0YI  plan-2  N1   0.020
 0YI  plan-2  N10  0.020
 0YI  plan-2  N4   0.020
 0YI  plan-2  H1   0.020
 0YI  plan-2  H10  0.020
 0YI  plan-3  N9   0.020
 0YI  plan-3  C2   0.020
 0YI  plan-3  C7   0.020
 0YI  plan-3  O8   0.020
 0YI  plan-3  H7   0.020
 0YI  plan-3  H8   0.020
 0YI  plan-4  C3   0.020
 0YI  plan-4  C11  0.020
 0YI  plan-4  N10  0.020
 0YI  plan-4  H11  0.020

