# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 08:42:15 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 2,6-dichloro-4-cyano-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)cc(cc3Cl)C#N)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
 0XP  0XP  2,6-dichloro-4-cyano-N-[2-({[(1R,2R)-2-fluorocyclopropyl]carbonyl}amino)pyridin-4-yl]benzamide  ligand  37  26  .  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_0XP
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
 0XP  C1   C   CR16  0  -0.389   0.9294   1.7683   1.6034
 0XP  C2   C   CR16  0  -0.064   2.2695   2.0523   1.7835
 0XP  N3   N   N     0  -0.432   3.2682   1.5179   1.0906
 0XP  C4   C   CR6   0   0.547   2.9475   0.6389   0.1565
 0XP  C5   C   CR16  0  -0.516   1.6326   0.2697  -0.1225
 0XP  C6   C   CR6   0   0.498   0.6023   0.8421   0.6100
 0XP  N7   N   NH1   0  -0.716  -0.6924   0.4430   0.2929
 0XP  C8   C   C     0   0.482  -1.8584   0.8237   0.8634
 0XP  O9   O   O     0  -0.401  -1.9896   1.6004   1.7809
 0XP  C10  C   CR6   0   0.099  -3.0580   0.1699   0.2305
 0XP  C11  C   CR6   0  -0.072  -3.7291   0.7884  -0.8169
 0XP  C12  C   CR16  0  -0.175  -4.8691   0.2363  -1.3703
 0XP  C13  C   CR6   0  -0.012  -5.3411  -0.9651  -0.8514
 0XP  C14  C   CR16  0  -0.175  -4.6939  -1.6100   0.1975
 0XP  C15  C   CR6   0  -0.072  -3.5575  -1.0274   0.7271
 0XP  CL1  CL  CL    0  -0.073  -2.7330  -1.8061   2.0226
 0XP  C17  C   CSP   0   0.073  -6.5171  -1.5525  -1.4107
 0XP  N18  N   NS    0  -0.229  -7.4643  -2.0264  -1.8611
 0XP  CL2  CL  CL    0  -0.073  -3.1186   2.2705  -1.4445
 0XP  N20  N   NH1   0  -0.748   3.9456   0.0507  -0.6112
 0XP  C21  C   C     0   0.586   5.3045   0.0956  -0.4517
 0XP  O22  O   O     0  -0.439   5.8757   0.6843   0.4392
 0XP  C23  C   CH1   0  -0.500   6.0202  -0.6870  -1.5025
 0XP  C25  C   CH2   0  -0.520   7.5101  -0.4777  -1.6561
 0XP  C26  C   CH1   0   0.181   7.0104  -1.7302  -1.0709
 0XP  F1   F   F     0  -0.338   7.1775  -1.9434   0.2682
 0XP  H1   H   HCR6  0   0.293   0.1930   2.2580   2.2166
 0XP  H2   H   HCR6  0   0.269   2.5536   2.7698   2.5452
 0XP  H3   H   HCR6  0   0.298   1.4199  -0.4559  -0.8983
 0XP  H4   H   HNH1  0   0.437  -0.7641  -0.2253  -0.4618
 0XP  H5   H   HCR6  0   0.316  -5.3822   0.7266  -2.1853
 0XP  H6   H   HCR6  0   0.317  -5.0672  -2.5466   0.5863
 0XP  H7   H   HNH1  0   0.425   3.6112  -0.5267  -1.3673
 0XP  H24  H   HCH1  0   0.305   5.4561  -0.9268  -2.3967
 0XP  H8   H   HCH2  0   0.281   7.9201  -0.5064  -2.6567
 0XP  H9   H   HCH2  0   0.281   7.9619   0.2482  -0.9918
 0XP  H27  H   HCH1  0   0.252   7.0500  -2.6542  -1.6342

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
 0XP  C25  C26  single    1.470  0.020  1.470
 0XP  C25  C23  single    1.512  0.020  1.512
 0XP  C26  C23  single    1.502  0.020  1.502
 0XP  C26  F1   single    1.366  0.020  1.366
 0XP  C23  C21  single    1.493  0.020  1.493
 0XP  C21  O22  double    1.211  0.020  1.211
 0XP  C21  N20  single    1.369  0.020  1.369
 0XP  N20  C4   single    1.390  0.020  1.390
 0XP  C4   C5   aromatic  1.394  0.020  1.394
 0XP  C4   N3   aromatic  1.322  0.020  1.322
 0XP  C5   C6   aromatic  1.388  0.020  1.388
 0XP  N18  C17  triple    1.151  0.020  1.151
 0XP  C17  C13  single    1.429  0.020  1.429
 0XP  N3   C2   aromatic  1.328  0.020  1.328
 0XP  C13  C14  aromatic  1.391  0.020  1.391
 0XP  C13  C12  aromatic  1.391  0.020  1.391
 0XP  C14  C15  aromatic  1.382  0.020  1.382
 0XP  C6   N7   single    1.391  0.020  1.391
 0XP  C6   C1   aromatic  1.397  0.020  1.397
 0XP  N7   C8   single    1.353  0.020  1.353
 0XP  C12  C11  aromatic  1.382  0.020  1.382
 0XP  C15  CL1  single    1.722  0.020  1.722
 0XP  C15  C10  aromatic  1.389  0.020  1.389
 0XP  C11  C10  aromatic  1.389  0.020  1.389
 0XP  C11  CL2  single    1.721  0.020  1.721
 0XP  C10  C8   single    1.506  0.020  1.506
 0XP  C2   C1   aromatic  1.382  0.020  1.382
 0XP  C8   O9   double    1.209  0.020  1.209
 0XP  C1   H1   single    0.930  0.020  1.080
 0XP  C2   H2   single    0.930  0.020  1.080
 0XP  C5   H3   single    0.930  0.020  1.080
 0XP  N7   H4   single    0.860  0.020  1.020
 0XP  C12  H5   single    0.930  0.020  1.080
 0XP  C14  H6   single    0.930  0.020  1.080
 0XP  N20  H7   single    0.860  0.020  1.020
 0XP  C23  H24  single    0.970  0.020  1.090
 0XP  C25  H8   single    0.970  0.020  1.090
 0XP  C25  H9   single    0.970  0.020  1.090
 0XP  C26  H27  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
 0XP  H1   C1   C6   123.14  3.000
 0XP  H1   C1   C2   119.72  3.000
 0XP  C6   C1   C2   117.14  3.000
 0XP  H2   C2   N3   115.83  3.000
 0XP  H2   C2   C1   118.80  3.000
 0XP  N3   C2   C1   125.36  3.000
 0XP  C4   N3   C2   116.99  3.000
 0XP  N20  C4   C5   117.05  3.000
 0XP  C5   C4   N3   123.11  3.000
 0XP  N20  C4   N3   119.83  3.000
 0XP  H3   C5   C6   120.57  3.000
 0XP  H3   C5   C4   120.39  3.000
 0XP  C6   C5   C4   119.04  3.000
 0XP  N7   C6   C5   116.88  3.000
 0XP  N7   C6   C1   124.76  3.000
 0XP  C5   C6   C1   118.36  3.000
 0XP  H4   N7   C8   116.09  3.000
 0XP  H4   N7   C6   115.21  3.000
 0XP  C8   N7   C6   128.70  3.000
 0XP  C10  C8   O9   120.76  3.000
 0XP  O9   C8   N7   126.46  3.000
 0XP  C10  C8   N7   112.78  3.000
 0XP  C15  C10  C11  118.65  3.000
 0XP  C11  C10  C8   120.56  3.000
 0XP  C15  C10  C8   120.70  3.000
 0XP  CL2  C11  C12  119.36  3.000
 0XP  CL2  C11  C10  119.14  3.000
 0XP  C12  C11  C10  121.50  3.000
 0XP  H5   C12  C13  120.80  3.000
 0XP  H5   C12  C11  120.82  3.000
 0XP  C13  C12  C11  118.39  3.000
 0XP  C17  C13  C14  119.18  3.000
 0XP  C14  C13  C12  121.59  3.000
 0XP  C17  C13  C12  119.23  3.000
 0XP  H6   C14  C15  120.76  3.000
 0XP  H6   C14  C13  120.83  3.000
 0XP  C15  C14  C13  118.41  3.000
 0XP  CL1  C15  C14  119.42  3.000
 0XP  CL1  C15  C10  119.11  3.000
 0XP  C14  C15  C10  121.46  3.000
 0XP  N18  C17  C13  180.00  3.000
 0XP  H7   N20  C21  115.81  3.000
 0XP  H7   N20  C4   114.73  3.000
 0XP  C21  N20  C4   129.39  3.000
 0XP  C23  C21  O22  123.13  3.000
 0XP  O22  C21  N20  124.74  3.000
 0XP  C23  C21  N20  112.12  3.000
 0XP  H24  C23  C26  115.24  3.000
 0XP  H24  C23  C25  117.35  3.000
 0XP  C26  C23  C25   58.38  3.000
 0XP  H24  C23  C21  116.56  3.000
 0XP  C26  C23  C21  118.55  3.000
 0XP  C25  C23  C21  118.11  3.000
 0XP  H9   C25  H8   115.29  3.000
 0XP  H9   C25  C26  117.95  3.000
 0XP  H8   C25  C26  118.33  3.000
 0XP  H9   C25  C23  116.21  3.000
 0XP  H8   C25  C23  117.63  3.000
 0XP  C26  C25  C23   60.45  3.000
 0XP  H27  C26  F1   111.85  3.000
 0XP  H27  C26  C25  120.50  3.000
 0XP  F1   C26  C25  118.79  3.000
 0XP  H27  C26  C23  117.86  3.000
 0XP  F1   C26  C23  118.09  3.000
 0XP  C25  C26  C23   61.17  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
 0XP  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 0XP  CONST_02  C4   N3   C2   C1      0.00   0.0  0
 0XP  CONST_03  C5   C4   N3   C2      0.00   0.0  0
 0XP  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 0XP  CONST_05  C6   C5   C4   N3      0.00   0.0  0
 0XP  CONST_06  C6   C1   C2   N3      0.00   0.0  0
 0XP  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 0XP  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 0XP  CONST_09  C14  C13  C12  C11     0.00   0.0  0
 0XP  CONST_10  C14  C15  C10  C11     0.00   0.0  0
 0XP  CONST_11  C15  C14  C13  C12     0.00   0.0  0
 0XP  CONST_12  C15  C10  C11  C12     0.00   0.0  0
 0XP  CONST_13  N20  C4   N3   C2    180.00   0.0  0
 0XP  CONST_14  N7   C6   C1   C2    180.00   0.0  0
 0XP  CONST_15  N7   C6   C5   C4    180.00   0.0  0
 0XP  CONST_16  N20  C4   C5   C6    180.00   0.0  0
 0XP  CONST_17  C14  C15  C10  C8    180.00   0.0  0
 0XP  CONST_18  C12  C11  C10  C8    180.00   0.0  0
 0XP  CONST_19  C17  C13  C12  C11   180.00   0.0  0
 0XP  CONST_20  CL1  C15  C10  C11   180.00   0.0  0
 0XP  CONST_21  CL1  C15  C14  C13   180.00   0.0  0
 0XP  CONST_22  CL2  C11  C12  C13   180.00   0.0  0
 0XP  CONST_23  C17  C13  C14  C15   180.00   0.0  0
 0XP  CONST_24  CL2  C11  C10  C15   180.00   0.0  0
 0XP  CONST_25  H3   C5   C6   C1    180.00   0.0  0
 0XP  CONST_26  H1   C1   C2   N3    180.00   0.0  0
 0XP  CONST_27  H2   C2   N3   C4    180.00   0.0  0
 0XP  CONST_28  H6   C14  C15  C10   180.00   0.0  0
 0XP  CONST_29  H5   C12  C11  C10   180.00   0.0  0
 0XP  CONST_30  C23  C21  N20  C4    180.00   0.0  0
 0XP  CONST_31  C10  C8   N7   C6    180.00   0.0  0
 0XP  CONST_32  C8   N7   C6   C1      0.00   0.0  0
 0XP  CONST_33  C21  N20  C4   N3      0.00   0.0  0
 0XP  CONST_34  C21  N20  C4   C5    180.00   0.0  0
 0XP  CONST_35  C8   N7   C6   C5    180.00   0.0  0
 0XP  CONST_36  H4   N7   C6   C1    180.00   0.0  0
 0XP  CONST_37  H7   N20  C4   N3    180.00   0.0  0
 0XP  CONST_38  O22  C21  N20  C4      0.00   0.0  0
 0XP  CONST_39  O9   C8   N7   C6      0.00   0.0  0
 0XP  Var_01    C26  C25  C23  C21   107.90  30.0  1
 0XP  Var_02    F1   C26  C25  C23  -108.11  30.0  1
 0XP  Var_03    C15  C10  C8   N7     91.48  30.0  2
 0XP  Var_04    C25  C23  C21  N20   166.10  30.0  1

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
 0XP  chir_01  C23  C25  C26  C21  both
 0XP  chir_02  C26  F1   C23  C25  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
 0XP  plan-1  C1   0.020
 0XP  plan-1  C2   0.020
 0XP  plan-1  N3   0.020
 0XP  plan-1  C4   0.020
 0XP  plan-1  C5   0.020
 0XP  plan-1  C6   0.020
 0XP  plan-1  N7   0.020
 0XP  plan-1  N20  0.020
 0XP  plan-1  H1   0.020
 0XP  plan-1  H2   0.020
 0XP  plan-1  H3   0.020
 0XP  plan-2  C8   0.020
 0XP  plan-2  C10  0.020
 0XP  plan-2  C11  0.020
 0XP  plan-2  C12  0.020
 0XP  plan-2  C13  0.020
 0XP  plan-2  C14  0.020
 0XP  plan-2  C15  0.020
 0XP  plan-2  CL1  0.020
 0XP  plan-2  C17  0.020
 0XP  plan-2  N18  0.020
 0XP  plan-2  CL2  0.020
 0XP  plan-2  H5   0.020
 0XP  plan-2  H6   0.020
 0XP  plan-3  C4   0.020
 0XP  plan-3  N20  0.020
 0XP  plan-3  C21  0.020
 0XP  plan-3  O22  0.020
 0XP  plan-3  C23  0.020
 0XP  plan-3  H7   0.020
 0XP  plan-4  C6   0.020
 0XP  plan-4  N7   0.020
 0XP  plan-4  C8   0.020
 0XP  plan-4  O9   0.020
 0XP  plan-4  C10  0.020
 0XP  plan-4  H4   0.020

