# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 23:54:55 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 2,6-dichloro-N-[2-({[(1R,2R)-2-fluorocyclopropyl]carbonyl}amino)pyridin-4-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: F[C@@H]1C[C@@H]1C(=O)Nc2cc(NC(=O)c3c(Cl)cccc3Cl)ccn2
#
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
 0XH  0XH  2,6-dichloro-N-[2-({[(1R,2R)-2-fluorocyclopropyl]carbonyl}amino)pyridin-4-yl]benzamide  ligand  36  24  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0XH
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
 0XH  C1   C   CR16  0  -0.273  -6.1578   0.7211   0.0567
 0XH  C2   C   CR16  0  -0.190  -5.3684   1.5965  -0.6733
 0XH  C3   C   CR6   0  -0.083  -3.9914   1.4632  -0.6162
 0XH  C4   C   CR6   0   0.088  -3.3889   0.4743   0.1507
 0XH  C5   C   CR6   0  -0.081  -4.2070  -0.3865   0.8711
 0XH  C6   C   CR16  0  -0.191  -5.5867  -0.2766   0.8317
 0XH  CL1  CL  CL    0  -0.097  -3.4761  -1.6265   1.8277
 0XH  C8   C   C     0   0.475  -1.8925   0.3862   0.2597
 0XH  O9   O   O     0  -0.409  -1.2863   1.0129   1.0998
 0XH  N10  N   NH1   0  -0.713  -1.3422  -0.4440  -0.6591
 0XH  C11  C   CR6   0   0.488  -0.0046  -0.7677  -0.8505
 0XH  C12  C   CR16  0  -0.425   0.2956  -1.6539  -1.8918
 0XH  C13  C   CR16  0  -0.058   1.6136  -1.9869  -2.1027
 0XH  N14  N   N     0  -0.434   2.6321  -1.5236  -1.3814
 0XH  C15  C   CR6   0   0.545   2.3401  -0.6870  -0.4035
 0XH  C16  C   CR16  0  -0.482   1.0406  -0.2724  -0.0876
 0XH  N17  N   NH1   0  -0.747   3.3590  -0.1731   0.3912
 0XH  C18  C   C     0   0.587   4.7152  -0.2889   0.2525
 0XH  O19  O   O     0  -0.440   5.2699  -0.8882  -0.6425
 0XH  C20  C   CH1   0  -0.499   5.4549   0.4305   1.3315
 0XH  C22  C   CH2   0  -0.519   6.9280   0.1341   1.5046
 0XH  C23  C   CH1   0   0.181   6.5096   1.4252   0.9401
 0XH  F1   F   F     0  -0.338   6.7125   1.6583  -0.3912
 0XH  CL2  CL  CL    0  -0.097  -2.9909   2.5391  -1.5265
 0XH  H1   H   HCR6  0   0.288  -7.2342   0.8176   0.0199
 0XH  H2   H   HCR6  0   0.294  -5.8184   2.3722  -1.2768
 0XH  H3   H   HCR6  0   0.294  -6.2055  -0.9584   1.3977
 0XH  H4   H   HNH1  0   0.434  -1.9863  -0.8927  -1.2950
 0XH  H5   H   HCR6  0   0.286  -0.4822  -2.0681  -2.5197
 0XH  H6   H   HCR6  0   0.269   1.8694  -2.6708  -2.9039
 0XH  H7   H   HCR6  0   0.304   0.8783   0.4160   0.7255
 0XH  H8   H   HNH1  0   0.425   3.0448   0.3947   1.1633
 0XH  H21  H   HCH1  0   0.305   4.8906   0.6841   2.2217
 0XH  H9   H   HCH2  0   0.281   7.3213   0.1169   2.5121
 0XH  H10  H   HCH2  0   0.281   7.3507  -0.6007   0.8308
 0XH  H24  H   HCH1  0   0.252   6.5901   2.3334   1.5246

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
 0XH  C22  C23  single    1.470  0.020  1.470
 0XH  C22  C20  single    1.512  0.020  1.512
 0XH  C23  C20  single    1.502  0.020  1.502
 0XH  C23  F1   single    1.367  0.020  1.367
 0XH  C20  C18  single    1.493  0.020  1.493
 0XH  C18  O19  double    1.212  0.020  1.212
 0XH  C18  N17  single    1.368  0.020  1.368
 0XH  N17  C15  single    1.391  0.020  1.391
 0XH  C15  C16  aromatic  1.400  0.020  1.400
 0XH  C15  N14  aromatic  1.320  0.020  1.320
 0XH  C16  C11  aromatic  1.386  0.020  1.386
 0XH  N14  C13  aromatic  1.331  0.020  1.331
 0XH  N10  C11  single    1.390  0.020  1.390
 0XH  N10  C8   single    1.355  0.020  1.355
 0XH  C1   C2   aromatic  1.387  0.020  1.387
 0XH  C1   C6   aromatic  1.386  0.020  1.386
 0XH  C11  C12  aromatic  1.400  0.020  1.400
 0XH  C2   C3   aromatic  1.385  0.020  1.385
 0XH  C6   C5   aromatic  1.385  0.020  1.385
 0XH  C3   CL2  single    1.728  0.020  1.728
 0XH  C3   C4   aromatic  1.389  0.020  1.389
 0XH  C5   C4   aromatic  1.389  0.020  1.389
 0XH  C5   CL1  single    1.728  0.020  1.728
 0XH  C4   C8   single    1.503  0.020  1.503
 0XH  C8   O9   double    1.211  0.020  1.211
 0XH  C13  C12  aromatic  1.376  0.020  1.376
 0XH  C1   H1   single    0.930  0.020  1.080
 0XH  C2   H2   single    0.930  0.020  1.080
 0XH  C6   H3   single    0.930  0.020  1.080
 0XH  N10  H4   single    0.860  0.020  1.020
 0XH  C12  H5   single    0.930  0.020  1.080
 0XH  C13  H6   single    0.930  0.020  1.080
 0XH  C16  H7   single    0.930  0.020  1.080
 0XH  N17  H8   single    0.860  0.020  1.020
 0XH  C20  H21  single    0.970  0.020  1.090
 0XH  C22  H9   single    0.970  0.020  1.090
 0XH  C22  H10  single    0.970  0.020  1.090
 0XH  C23  H24  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
 0XH  H1   C1   C6   119.56  3.000
 0XH  H1   C1   C2   119.50  3.000
 0XH  C6   C1   C2   120.94  3.000
 0XH  H2   C2   C3   120.41  3.000
 0XH  H2   C2   C1   120.67  3.000
 0XH  C3   C2   C1   118.93  3.000
 0XH  CL2  C3   C4   118.88  3.000
 0XH  C4   C3   C2   121.52  3.000
 0XH  CL2  C3   C2   119.60  3.000
 0XH  C8   C4   C5   120.83  3.000
 0XH  C8   C4   C3   120.91  3.000
 0XH  C5   C4   C3   118.17  3.000
 0XH  CL1  C5   C6   119.61  3.000
 0XH  CL1  C5   C4   118.86  3.000
 0XH  C6   C5   C4   121.53  3.000
 0XH  H3   C6   C5   120.37  3.000
 0XH  H3   C6   C1   120.72  3.000
 0XH  C5   C6   C1   118.91  3.000
 0XH  N10  C8   O9   125.75  3.000
 0XH  O9   C8   C4   121.23  3.000
 0XH  N10  C8   C4   113.02  3.000
 0XH  H4   N10  C11  115.05  3.000
 0XH  H4   N10  C8   116.11  3.000
 0XH  C11  N10  C8   128.84  3.000
 0XH  C16  C11  C12  118.30  3.000
 0XH  C12  C11  N10  117.15  3.000
 0XH  C16  C11  N10  124.54  3.000
 0XH  H5   C12  C13  120.46  3.000
 0XH  H5   C12  C11  121.33  3.000
 0XH  C13  C12  C11  118.21  3.000
 0XH  H6   C13  N14  116.07  3.000
 0XH  H6   C13  C12  119.48  3.000
 0XH  N14  C13  C12  124.45  3.000
 0XH  C15  N14  C13  116.92  3.000
 0XH  N17  C15  C16  116.21  3.000
 0XH  C16  C15  N14  124.08  3.000
 0XH  N17  C15  N14  119.71  3.000
 0XH  H7   C16  C15  119.94  3.000
 0XH  H7   C16  C11  122.02  3.000
 0XH  C15  C16  C11  118.03  3.000
 0XH  H8   N17  C18  115.73  3.000
 0XH  H8   N17  C15  114.66  3.000
 0XH  C18  N17  C15  129.57  3.000
 0XH  C20  C18  O19  123.05  3.000
 0XH  O19  C18  N17  124.79  3.000
 0XH  C20  C18  N17  112.15  3.000
 0XH  H21  C20  C23  115.13  3.000
 0XH  H21  C20  C22  117.31  3.000
 0XH  C23  C20  C22   58.37  3.000
 0XH  H21  C20  C18  116.63  3.000
 0XH  C23  C20  C18  118.61  3.000
 0XH  C22  C20  C18  118.09  3.000
 0XH  H10  C22  H9   115.27  3.000
 0XH  H10  C22  C23  117.92  3.000
 0XH  H9   C22  C23  118.37  3.000
 0XH  H10  C22  C20  116.23  3.000
 0XH  H9   C22  C20  117.64  3.000
 0XH  C23  C22  C20   60.44  3.000
 0XH  H24  C23  F1   111.82  3.000
 0XH  H24  C23  C22  120.54  3.000
 0XH  F1   C23  C22  118.79  3.000
 0XH  H24  C23  C20  117.85  3.000
 0XH  F1   C23  C20  118.10  3.000
 0XH  C22  C23  C20   61.18  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
 0XH  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 0XH  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 0XH  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 0XH  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 0XH  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 0XH  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 0XH  CONST_07  N14  C15  C16  C11     0.00   0.0  0
 0XH  CONST_08  N14  C13  C12  C11     0.00   0.0  0
 0XH  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 0XH  CONST_10  C15  N14  C13  C12     0.00   0.0  0
 0XH  CONST_11  C16  C15  N14  C13     0.00   0.0  0
 0XH  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 0XH  CONST_13  CL2  C3   C2   C1    180.00   0.0  0
 0XH  CONST_14  CL1  C5   C6   C1    180.00   0.0  0
 0XH  CONST_15  C8   C4   C3   C2    180.00   0.0  0
 0XH  CONST_16  CL1  C5   C4   C3    180.00   0.0  0
 0XH  CONST_17  CL2  C3   C4   C5    180.00   0.0  0
 0XH  CONST_18  C8   C4   C5   C6    180.00   0.0  0
 0XH  CONST_19  C15  C16  C11  N10   180.00   0.0  0
 0XH  CONST_20  C13  C12  C11  N10   180.00   0.0  0
 0XH  CONST_21  N17  C15  C16  C11   180.00   0.0  0
 0XH  CONST_22  N17  C15  N14  C13   180.00   0.0  0
 0XH  CONST_23  H3   C6   C1   C2    180.00   0.0  0
 0XH  CONST_24  H1   C1   C2   C3    180.00   0.0  0
 0XH  CONST_25  H2   C2   C3   C4    180.00   0.0  0
 0XH  CONST_26  H6   C13  C12  C11   180.00   0.0  0
 0XH  CONST_27  H7   C16  C11  C12   180.00   0.0  0
 0XH  CONST_28  H5   C12  C13  N14   180.00   0.0  0
 0XH  CONST_29  C11  N10  C8   C4    180.00   0.0  0
 0XH  CONST_30  C20  C18  N17  C15   180.00   0.0  0
 0XH  CONST_31  C16  C11  N10  C8      0.00   0.0  0
 0XH  CONST_32  C12  C11  N10  C8    180.00   0.0  0
 0XH  CONST_33  C18  N17  C15  N14     0.00   0.0  0
 0XH  CONST_34  C18  N17  C15  C16   180.00   0.0  0
 0XH  CONST_35  H4   N10  C11  C12     0.00   0.0  0
 0XH  CONST_36  H8   N17  C15  N14   180.00   0.0  0
 0XH  CONST_37  C11  N10  C8   O9      0.00   0.0  0
 0XH  CONST_38  O19  C18  N17  C15     0.00   0.0  0
 0XH  Var_01    C23  C22  C20  C18   107.99  30.0  1
 0XH  Var_02    F1   C23  C22  C20  -108.13  30.0  1
 0XH  Var_03    N10  C8   C4   C3    -92.69  30.0  2
 0XH  Var_04    C22  C20  C18  N17   166.00  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 0XH  chir_01  C20  C22  C23  C18  both
 0XH  chir_02  C23  F1   C20  C22  both

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
 0XH  plan-1  C1   0.020
 0XH  plan-1  C2   0.020
 0XH  plan-1  C3   0.020
 0XH  plan-1  C4   0.020
 0XH  plan-1  C5   0.020
 0XH  plan-1  C6   0.020
 0XH  plan-1  CL1  0.020
 0XH  plan-1  C8   0.020
 0XH  plan-1  CL2  0.020
 0XH  plan-1  H1   0.020
 0XH  plan-1  H2   0.020
 0XH  plan-1  H3   0.020
 0XH  plan-2  N10  0.020
 0XH  plan-2  C11  0.020
 0XH  plan-2  C12  0.020
 0XH  plan-2  C13  0.020
 0XH  plan-2  N14  0.020
 0XH  plan-2  C15  0.020
 0XH  plan-2  C16  0.020
 0XH  plan-2  N17  0.020
 0XH  plan-2  H5   0.020
 0XH  plan-2  H6   0.020
 0XH  plan-2  H7   0.020
 0XH  plan-3  C15  0.020
 0XH  plan-3  N17  0.020
 0XH  plan-3  C18  0.020
 0XH  plan-3  O19  0.020
 0XH  plan-3  C20  0.020
 0XH  plan-3  H8   0.020
 0XH  plan-4  C4   0.020
 0XH  plan-4  C8   0.020
 0XH  plan-4  O9   0.020
 0XH  plan-4  N10  0.020
 0XH  plan-4  C11  0.020
 0XH  plan-4  H4   0.020

