# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 04:01:12 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: ~{N}-(6-chloranylpyridin-3-yl)-4-fluoranyl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)C(=O)Nc2ccc(Cl)nc2
#
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
 GB9  GB9  ~{N}-(6-chloranylpyridin-3-yl)-4-fluoranyl-benzamide  ligand  25  17  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GB9
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
 GB9  C1   C   CR6   0  -0.058  86.7096  130.1716  103.6378
 GB9  C10  C   CR6   0   0.537  84.9731  129.1751  101.7383
 GB9  C11  C   CR16  0  -0.249  91.1821  133.9394  105.2191
 GB9  C12  C   CR6   0   0.141  91.4476  133.4857  106.5023
 GB9  C2   C   CR6   0   0.311  89.5036  132.2217  105.0959
 GB9  C3   C   C     0   0.539  87.6085  130.6722  104.7171
 GB9  C4   C   CR16  0  -0.242  85.4667  129.6629  104.0127
 GB9  C5   C   CR16  0  -0.272  87.0697  130.1534  102.2910
 GB9  C6   C   CR16  0  -0.243  90.1918  133.2891  104.5151
 GB9  C7   C   CR16  0  -0.398  84.5864  129.1698  103.0658
 GB9  C8   C   CR16  0  -0.396  86.2040  129.6526  101.3319
 GB9  C9   C   CR16  0  -0.108  89.8644  131.8565  106.3941
 GB9  F1   F   F     0  -0.305  84.1279  128.6980  100.8176
 GB9  N1   N   NH1   0  -0.766  88.5261  131.5969  104.3265
 GB9  N2   N   N     0  -0.378  90.8203  132.4890  107.0678
 GB9  O1   O   O     0  -0.452  87.5025  130.2783  105.8642
 GB9  H8   H   HCR6  0   0.298  91.7247  134.7664  104.7845
 GB9  H2   H   HCR6  0   0.276  85.1760  129.6586  105.0543
 GB9  H3   H   HCR6  0   0.274  88.0397  130.5029  101.9624
 GB9  H4   H   HCR6  0   0.300  89.9520  133.6116  103.5092
 GB9  H5   H   HCR6  0   0.290  83.6170  128.7868  103.3551
 GB9  H6   H   HCR6  0   0.292  86.4865  129.6295  100.2880
 GB9  H7   H   HCR6  0   0.293  89.3820  131.0422  106.9100
 GB9  H1   H   HNH1  0   0.428  88.4484  131.9505  103.3853
 GB9  CL1  CL  CL    0  -0.109  92.6852  134.2661  107.4371

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
 GB9  F1   C10  single    1.338  0.020  1.338
 GB9  C8   C10  aromatic  1.381  0.020  1.381
 GB9  C8   C5   aromatic  1.386  0.020  1.386
 GB9  C10  C7   aromatic  1.383  0.020  1.383
 GB9  C5   C1   aromatic  1.394  0.020  1.394
 GB9  C7   C4   aromatic  1.384  0.020  1.384
 GB9  C1   C4   aromatic  1.394  0.020  1.394
 GB9  C1   C3   single    1.491  0.020  1.491
 GB9  N1   C3   single    1.360  0.020  1.360
 GB9  N1   C2   single    1.392  0.020  1.392
 GB9  C6   C2   aromatic  1.397  0.020  1.397
 GB9  C6   C11  aromatic  1.378  0.020  1.378
 GB9  C3   O1   double    1.217  0.020  1.217
 GB9  C2   C9   aromatic  1.396  0.020  1.396
 GB9  C11  C12  aromatic  1.387  0.020  1.387
 GB9  C9   N2   aromatic  1.330  0.020  1.330
 GB9  C12  N2   aromatic  1.306  0.020  1.306
 GB9  C12  CL1  single    1.736  0.020  1.736
 GB9  C11  H8   single    0.930  0.020  1.080
 GB9  C4   H2   single    0.930  0.020  1.080
 GB9  C5   H3   single    0.930  0.020  1.080
 GB9  C6   H4   single    0.930  0.020  1.080
 GB9  C7   H5   single    0.930  0.020  1.080
 GB9  C8   H6   single    0.930  0.020  1.080
 GB9  C9   H7   single    0.930  0.020  1.080
 GB9  N1   H1   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
 GB9  C5   C1   C4   119.03  3.000
 GB9  C4   C1   C3   117.72  3.000
 GB9  C5   C1   C3   123.22  3.000
 GB9  F1   C10  C8   118.94  3.000
 GB9  C8   C10  C7   122.20  3.000
 GB9  F1   C10  C7   118.86  3.000
 GB9  H8   C11  C6   121.10  3.000
 GB9  H8   C11  C12  121.77  3.000
 GB9  C6   C11  C12  117.12  3.000
 GB9  CL1  C12  N2   116.88  3.000
 GB9  CL1  C12  C11  119.18  3.000
 GB9  N2   C12  C11  123.94  3.000
 GB9  N1   C2   C9   125.31  3.000
 GB9  C9   C2   C6   117.35  3.000
 GB9  N1   C2   C6   117.34  3.000
 GB9  O1   C3   N1   123.32  3.000
 GB9  O1   C3   C1   121.39  3.000
 GB9  N1   C3   C1   115.29  3.000
 GB9  H2   C4   C7   119.12  3.000
 GB9  H2   C4   C1   120.01  3.000
 GB9  C7   C4   C1   120.87  3.000
 GB9  H3   C5   C8   117.81  3.000
 GB9  H3   C5   C1   121.38  3.000
 GB9  C8   C5   C1   120.80  3.000
 GB9  H4   C6   C2   120.31  3.000
 GB9  H4   C6   C11  119.54  3.000
 GB9  C2   C6   C11  120.15  3.000
 GB9  H5   C7   C4   120.88  3.000
 GB9  H5   C7   C10  120.58  3.000
 GB9  C4   C7   C10  118.54  3.000
 GB9  H6   C8   C5   120.84  3.000
 GB9  H6   C8   C10  120.61  3.000
 GB9  C5   C8   C10  118.55  3.000
 GB9  H7   C9   N2   116.01  3.000
 GB9  H7   C9   C2   121.81  3.000
 GB9  N2   C9   C2   122.18  3.000
 GB9  H1   N1   C3   117.03  3.000
 GB9  H1   N1   C2   114.36  3.000
 GB9  C3   N1   C2   128.33  3.000
 GB9  C9   N2   C12  119.26  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
 GB9  CONST_01  C10  C8   C5   C1      0.00   0.0  0
 GB9  CONST_02  C10  C7   C4   C1      0.00   0.0  0
 GB9  CONST_03  C9   C2   C6   C11     0.00   0.0  0
 GB9  CONST_04  C9   N2   C12  C11     0.00   0.0  0
 GB9  CONST_05  C2   C6   C11  C12     0.00   0.0  0
 GB9  CONST_06  C2   C9   N2   C12     0.00   0.0  0
 GB9  CONST_07  C8   C10  C7   C4      0.00   0.0  0
 GB9  CONST_08  C8   C5   C1   C4      0.00   0.0  0
 GB9  CONST_09  C7   C10  C8   C5      0.00   0.0  0
 GB9  CONST_10  C7   C4   C1   C5      0.00   0.0  0
 GB9  CONST_11  N2   C9   C2   C6      0.00   0.0  0
 GB9  CONST_12  N2   C12  C11  C6      0.00   0.0  0
 GB9  CONST_13  N1   C2   C6   C11   180.00   0.0  0
 GB9  CONST_14  C8   C5   C1   C3    180.00   0.0  0
 GB9  CONST_15  C7   C4   C1   C3    180.00   0.0  0
 GB9  CONST_16  F1   C10  C7   C4    180.00   0.0  0
 GB9  CONST_17  F1   C10  C8   C5    180.00   0.0  0
 GB9  CONST_18  CL1  C12  C11  C6    180.00   0.0  0
 GB9  CONST_19  CL1  C12  N2   C9    180.00   0.0  0
 GB9  CONST_20  N2   C9   C2   N1    180.00   0.0  0
 GB9  CONST_21  H6   C8   C5   C1    180.00   0.0  0
 GB9  CONST_22  H5   C7   C4   C1    180.00   0.0  0
 GB9  CONST_23  H3   C5   C8   C10   180.00   0.0  0
 GB9  CONST_24  H2   C4   C7   C10   180.00   0.0  0
 GB9  CONST_25  H4   C6   C11  C12   180.00   0.0  0
 GB9  CONST_26  H7   C9   N2   C12   180.00   0.0  0
 GB9  CONST_27  H8   C11  C6   C2    180.00   0.0  0
 GB9  CONST_28  C2   N1   C3   C1    180.00   0.0  0
 GB9  CONST_29  C6   C2   N1   C3    180.00   0.0  0
 GB9  CONST_30  C9   C2   N1   C3      0.00   0.0  0
 GB9  CONST_31  H1   N1   C2   C6      0.00   0.0  0
 GB9  CONST_32  O1   C3   N1   C2      0.00   0.0  0
 GB9  Var_01    N1   C3   C1   C4   -155.45  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
 GB9  plan-1  C11  0.020
 GB9  plan-1  C12  0.020
 GB9  plan-1  C2   0.020
 GB9  plan-1  C6   0.020
 GB9  plan-1  C9   0.020
 GB9  plan-1  N1   0.020
 GB9  plan-1  N2   0.020
 GB9  plan-1  H8   0.020
 GB9  plan-1  H4   0.020
 GB9  plan-1  H7   0.020
 GB9  plan-1  CL1  0.020
 GB9  plan-2  C1   0.020
 GB9  plan-2  C10  0.020
 GB9  plan-2  C3   0.020
 GB9  plan-2  C4   0.020
 GB9  plan-2  C5   0.020
 GB9  plan-2  C7   0.020
 GB9  plan-2  C8   0.020
 GB9  plan-2  F1   0.020
 GB9  plan-2  H2   0.020
 GB9  plan-2  H3   0.020
 GB9  plan-2  H5   0.020
 GB9  plan-2  H6   0.020
 GB9  plan-3  C1   0.020
 GB9  plan-3  C2   0.020
 GB9  plan-3  C3   0.020
 GB9  plan-3  N1   0.020
 GB9  plan-3  O1   0.020
 GB9  plan-3  H1   0.020

