# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 09:47:07 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(nc1)c2cc(ncn2)c3cc(Cl)cc(c3)C#N
#
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
 51E  51E  3-chloro-5-[6-(5-fluoropyridin-2-yl)pyrimidin-4-yl]benzonitrile  ligand  30  22  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_51E
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
 51E  C01  C   CR16  0  -0.263   1.9980   0.9994  -0.0769
 51E  C02  C   CR6   0  -0.007   3.2448   1.6031  -0.0695
 51E  C03  C   CR16  0  -0.209   4.4064   0.8583   0.0146
 51E  C04  C   CR6   0   0.029   4.2905  -0.5275   0.0918
 51E  C6   C   CR16  0  -0.264   3.0496  -1.1527   0.0840
 51E  C7   C   CR6   0   0.067   1.8905  -0.3874   0.0010
 51E  C8   C   CR6   0   0.314   0.5714  -1.0607  -0.0069
 51E  C9   C   CR16  0  -0.340  -0.6274  -0.3615   0.0089
 51E  C10  C   CR6   0   0.256  -1.8008  -1.1060  -0.0021
 51E  N11  N   N     0  -0.430  -1.7756  -2.4354  -0.0241
 51E  C12  C   CR16  0   0.060  -0.5847  -3.0081  -0.0341
 51E  N13  N   N     0  -0.432   0.5831  -2.3928  -0.0275
 51E  C19  C   CSP   0   0.064   5.4747  -1.3221   0.1805
 51E  N20  N   NS    0  -0.238   6.4272  -1.9650   0.2514
 51E  CL   CL  CL    0  -0.093   3.3507   3.3224  -0.1709
 51E  C1   C   CR6   0   0.452  -5.4912   0.8408   0.0346
 51E  C2   C   CR16  0  -0.305  -5.5166  -0.5372   0.0087
 51E  C3   C   CR16  0  -0.267  -4.2998  -1.1976  -0.0031
 51E  C4   C   CR6   0   0.188  -3.1261  -0.4493   0.0109
 51E  N1   N   N     0  -0.416  -3.1322   0.8804   0.0357
 51E  C5   C   CR16  0  -0.204  -4.2847   1.5230   0.0475
 51E  H1   H   HCR6  0   0.293   1.1193   1.6243  -0.1487
 51E  H2   H   HCR6  0   0.310   5.3769   1.3343   0.0197
 51E  H3   H   HCR6  0   0.290   2.9836  -2.2294   0.1431
 51E  H4   H   HCR6  0   0.286  -0.6785   0.7159   0.0330
 51E  H5   H   HCR6  0   0.268  -0.5642  -4.0919  -0.0502
 51E  H6   H   HCR6  0   0.305  -6.4519  -1.0809  -0.0025
 51E  H7   H   HCR6  0   0.289  -4.2629  -2.2768  -0.0229
 51E  H8   H   HCR6  0   0.290  -4.2618   2.6070   0.0677
 51E  F1   F   F     0  -0.293  -6.6310   1.5337   0.0473

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
 51E  F1   C1   single    1.334  0.020  1.334
 51E  C1   C5   aromatic  1.386  0.020  1.386
 51E  C1   C2   aromatic  1.378  0.020  1.378
 51E  C5   N1   aromatic  1.320  0.020  1.320
 51E  C2   C3   aromatic  1.384  0.020  1.384
 51E  N1   C4   aromatic  1.330  0.020  1.330
 51E  C3   C4   aromatic  1.392  0.020  1.392
 51E  C4   C10  single    1.479  0.020  1.479
 51E  C10  C9   aromatic  1.390  0.020  1.390
 51E  C10  N11  aromatic  1.330  0.020  1.330
 51E  C9   C8   aromatic  1.388  0.020  1.388
 51E  N11  C12  aromatic  1.321  0.020  1.321
 51E  C8   C7   single    1.481  0.020  1.481
 51E  C8   N13  aromatic  1.332  0.020  1.332
 51E  C01  C7   aromatic  1.393  0.020  1.393
 51E  C01  C02  aromatic  1.385  0.020  1.385
 51E  CL   C02  single    1.726  0.020  1.726
 51E  C12  N13  aromatic  1.320  0.020  1.320
 51E  C7   C6   aromatic  1.391  0.020  1.391
 51E  C02  C03  aromatic  1.382  0.020  1.382
 51E  C6   C04  aromatic  1.390  0.020  1.390
 51E  C03  C04  aromatic  1.393  0.020  1.393
 51E  C04  C19  single    1.429  0.020  1.429
 51E  C19  N20  triple    1.151  0.020  1.151
 51E  C01  H1   single    0.930  0.020  1.080
 51E  C03  H2   single    0.930  0.020  1.080
 51E  C6   H3   single    0.930  0.020  1.080
 51E  C9   H4   single    0.930  0.020  1.080
 51E  C12  H5   single    0.930  0.020  1.080
 51E  C2   H6   single    0.930  0.020  1.080
 51E  C3   H7   single    0.930  0.020  1.080
 51E  C5   H8   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
 51E  H1   C01  C7   121.10  3.000
 51E  H1   C01  C02  118.70  3.000
 51E  C7   C01  C02  120.19  3.000
 51E  CL   C02  C03  119.26  3.000
 51E  C03  C02  C01  121.46  3.000
 51E  CL   C02  C01  119.28  3.000
 51E  H2   C03  C04  120.83  3.000
 51E  H2   C03  C02  121.16  3.000
 51E  C04  C03  C02  118.00  3.000
 51E  C19  C04  C6   119.36  3.000
 51E  C19  C04  C03  119.20  3.000
 51E  C6   C04  C03  121.44  3.000
 51E  H3   C6   C7   120.04  3.000
 51E  H3   C6   C04  120.18  3.000
 51E  C7   C6   C04  119.79  3.000
 51E  C8   C7   C6   119.49  3.000
 51E  C6   C7   C01  119.12  3.000
 51E  C8   C7   C01  121.40  3.000
 51E  N13  C8   C9   120.76  3.000
 51E  N13  C8   C7   116.54  3.000
 51E  C9   C8   C7   122.70  3.000
 51E  H4   C9   C10  119.68  3.000
 51E  H4   C9   C8   122.97  3.000
 51E  C10  C9   C8   117.34  3.000
 51E  C4   C10  N11  117.45  3.000
 51E  N11  C10  C9   121.31  3.000
 51E  C4   C10  C9   121.24  3.000
 51E  C12  N11  C10  116.77  3.000
 51E  H5   C12  N13  116.70  3.000
 51E  H5   C12  N11  116.77  3.000
 51E  N13  C12  N11  126.53  3.000
 51E  C12  N13  C8   117.28  3.000
 51E  N20  C19  C04  180.00  3.000
 51E  F1   C1   C5   119.21  3.000
 51E  C5   C1   C2   120.55  3.000
 51E  F1   C1   C2   120.25  3.000
 51E  H6   C2   C3   121.33  3.000
 51E  H6   C2   C1   121.23  3.000
 51E  C3   C2   C1   117.44  3.000
 51E  H7   C3   C4   120.56  3.000
 51E  H7   C3   C2   120.46  3.000
 51E  C4   C3   C2   118.98  3.000
 51E  N1   C4   C3   122.26  3.000
 51E  C3   C4   C10  121.11  3.000
 51E  N1   C4   C10  116.62  3.000
 51E  C5   N1   C4   119.41  3.000
 51E  H8   C5   N1   117.94  3.000
 51E  H8   C5   C1   120.70  3.000
 51E  N1   C5   C1   121.36  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
 51E  CONST_01  C9   C8   C7   C01    0.00  0.0  0
 51E  CONST_02  N13  C8   C7   C01  180.00  0.0  0
 51E  CONST_03  C04  C6   C7   C01    0.00  0.0  0
 51E  CONST_04  C04  C03  C02  C01    0.00  0.0  0
 51E  CONST_05  C8   C7   C01  C02  180.00  0.0  0
 51E  CONST_06  C6   C7   C01  C02    0.00  0.0  0
 51E  CONST_07  C6   C04  C03  C02    0.00  0.0  0
 51E  CONST_08  C7   C01  C02  C03    0.00  0.0  0
 51E  CONST_09  C7   C6   C04  C03    0.00  0.0  0
 51E  CONST_10  C8   C7   C6   C04  180.00  0.0  0
 51E  CONST_11  C9   C8   C7   C6   180.00  0.0  0
 51E  CONST_12  N13  C8   C7   C6     0.00  0.0  0
 51E  CONST_13  C10  C9   C8   C7   180.00  0.0  0
 51E  CONST_14  C12  N13  C8   C7   180.00  0.0  0
 51E  CONST_15  C4   C10  C9   C8   180.00  0.0  0
 51E  CONST_16  N11  C10  C9   C8     0.00  0.0  0
 51E  CONST_17  N11  C12  N13  C8     0.00  0.0  0
 51E  CONST_18  N1   C4   C10  C9     0.00  0.0  0
 51E  CONST_19  C3   C4   C10  C9   180.00  0.0  0
 51E  CONST_20  C12  N11  C10  C9     0.00  0.0  0
 51E  CONST_21  C12  N13  C8   C9     0.00  0.0  0
 51E  CONST_22  C5   N1   C4   C10  180.00  0.0  0
 51E  CONST_23  C2   C3   C4   C10  180.00  0.0  0
 51E  CONST_24  N13  C8   C9   C10    0.00  0.0  0
 51E  CONST_25  N13  C12  N11  C10    0.00  0.0  0
 51E  CONST_26  N1   C4   C10  N11  180.00  0.0  0
 51E  CONST_27  C3   C4   C10  N11    0.00  0.0  0
 51E  CONST_28  C4   C10  N11  C12  180.00  0.0  0
 51E  CONST_29  C4   N1   C5   C1     0.00  0.0  0
 51E  CONST_30  C4   C3   C2   C1     0.00  0.0  0
 51E  CONST_31  N1   C5   C1   C2     0.00  0.0  0
 51E  CONST_32  N1   C4   C3   C2     0.00  0.0  0
 51E  CONST_33  C5   C1   C2   C3     0.00  0.0  0
 51E  CONST_34  C5   N1   C4   C3     0.00  0.0  0
 51E  CONST_35  C19  C04  C03  C02  180.00  0.0  0
 51E  CONST_36  CL   C02  C03  C04  180.00  0.0  0
 51E  CONST_37  CL   C02  C01  C7   180.00  0.0  0
 51E  CONST_38  C19  C04  C6   C7   180.00  0.0  0
 51E  CONST_39  F1   C1   C2   C3   180.00  0.0  0
 51E  CONST_40  F1   C1   C5   N1   180.00  0.0  0
 51E  CONST_41  H3   C6   C7   C01  180.00  0.0  0
 51E  CONST_42  H2   C03  C02  C01  180.00  0.0  0
 51E  CONST_43  H1   C01  C02  C03  180.00  0.0  0
 51E  CONST_44  H4   C9   C8   C7     0.00  0.0  0
 51E  CONST_45  H5   C12  N13  C8   180.00  0.0  0
 51E  CONST_46  H7   C3   C4   C10    0.00  0.0  0
 51E  CONST_47  H8   C5   C1   C2   180.00  0.0  0
 51E  CONST_48  H6   C2   C3   C4   180.00  0.0  0

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
 51E  plan-1  C01  0.020
 51E  plan-1  C02  0.020
 51E  plan-1  C03  0.020
 51E  plan-1  C04  0.020
 51E  plan-1  C6   0.020
 51E  plan-1  C7   0.020
 51E  plan-1  C8   0.020
 51E  plan-1  C19  0.020
 51E  plan-1  N20  0.020
 51E  plan-1  CL   0.020
 51E  plan-1  H1   0.020
 51E  plan-1  H2   0.020
 51E  plan-1  H3   0.020
 51E  plan-2  C7   0.020
 51E  plan-2  C8   0.020
 51E  plan-2  C9   0.020
 51E  plan-2  C10  0.020
 51E  plan-2  N11  0.020
 51E  plan-2  C12  0.020
 51E  plan-2  N13  0.020
 51E  plan-2  C4   0.020
 51E  plan-2  H4   0.020
 51E  plan-2  H5   0.020
 51E  plan-3  C10  0.020
 51E  plan-3  C1   0.020
 51E  plan-3  C2   0.020
 51E  plan-3  C3   0.020
 51E  plan-3  C4   0.020
 51E  plan-3  N1   0.020
 51E  plan-3  C5   0.020
 51E  plan-3  H6   0.020
 51E  plan-3  H7   0.020
 51E  plan-3  H8   0.020
 51E  plan-3  F1   0.020

