# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 09:40:38 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1c(Cl)cc(cc1c2cc(ncn2)n3cccn3)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
 51D  51D  3-chloro-4-fluoro-5-[6-(1H-pyrazol-1-yl)pyrimidin-4-yl]benzonitrile  ligand  28  21  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_51D
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
 51D  C2   C   CR6   0   0.663   2.0346  -0.7042   0.4919
 51D  C3   C   CR6   0  -0.222   3.2894  -0.1229   0.6076
 51D  C4   C   CR16  0  -0.191   3.4923   1.1749   0.1812
 51D  C5   C   CR6   0   0.003   2.4186   1.8837  -0.3504
 51D  C6   C   CR16  0  -0.254   1.1624   1.2971  -0.4631
 51D  C7   C   CR6   0  -0.150   0.9579  -0.0122  -0.0493
 51D  C8   C   CR6   0   0.275  -0.3698  -0.6414  -0.2045
 51D  C9   C   CR16  0  -0.381  -1.5171   0.0655   0.1088
 51D  C10  C   CR6   0   0.587  -2.7169  -0.5962  -0.1298
 51D  C12  C   CR16  0   0.071  -1.6054  -2.4111  -0.8546
 51D  F1   F   F     0  -0.263   1.8730  -1.9380   0.9402
 51D  N11  N   N     0  -0.436  -2.7662  -1.8262  -0.6072
 51D  N13  N   N     0  -0.418  -0.4076  -1.8857  -0.6826
 51D  N14  N   NR5   0  -0.392  -3.9373   0.0143   0.1276
 51D  C15  C   CR15  0   0.066  -5.1780  -0.5164  -0.0558
 51D  C16  C   CR15  0  -0.513  -6.0659   0.4474   0.3225
 51D  C17  C   CR15  0  -0.009  -5.2600   1.5379   0.7240
 51D  N18  N   N     0  -0.276  -3.9840   1.2664   0.6024
 51D  C19  C   CSP   0   0.062   2.6146   3.2254  -0.7943
 51D  N20  N   NS    0  -0.237   2.7723   4.3086  -1.1514
 51D  CL   CL  CL    0  -0.060   4.5738  -1.0332   1.2893
 51D  H1   H   HCR6  0   0.319   4.4732   1.6200   0.2560
 51D  H2   H   HCR6  0   0.308   0.3450   1.8560  -0.8983
 51D  H3   H   HCR6  0   0.308  -1.4865   1.0636   0.5184
 51D  H4   H   HCR6  0   0.276  -1.6469  -3.4219  -1.2429
 51D  H5   H   HCR5  0   0.308  -5.3210  -1.5142  -0.4326
 51D  H6   H   HCR5  0   0.278  -7.1408   0.3858   0.3147
 51D  H7   H   HCR5  0   0.279  -5.5774   2.5010   1.0929

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
 51D  C17  C16  aromatic  1.414  0.020  1.414
 51D  C17  N18  aromatic  1.310  0.020  1.310
 51D  C16  C15  aromatic  1.364  0.020  1.364
 51D  N18  N14  aromatic  1.340  0.020  1.340
 51D  C15  N14  aromatic  1.362  0.020  1.362
 51D  N14  C10  single    1.389  0.020  1.389
 51D  C10  C9   aromatic  1.391  0.020  1.391
 51D  C10  N11  aromatic  1.320  0.020  1.320
 51D  C9   C8   aromatic  1.383  0.020  1.383
 51D  N11  C12  aromatic  1.323  0.020  1.323
 51D  F1   C2   single    1.323  0.020  1.323
 51D  C8   C7   single    1.477  0.020  1.477
 51D  C8   N13  aromatic  1.333  0.020  1.333
 51D  CL   C3   single    1.716  0.020  1.716
 51D  C2   C7   aromatic  1.390  0.020  1.390
 51D  C2   C3   aromatic  1.388  0.020  1.388
 51D  C12  N13  aromatic  1.319  0.020  1.319
 51D  C7   C6   aromatic  1.388  0.020  1.388
 51D  C3   C4   aromatic  1.381  0.020  1.381
 51D  C6   C5   aromatic  1.391  0.020  1.391
 51D  C4   C5   aromatic  1.392  0.020  1.392
 51D  C5   C19  single    1.427  0.020  1.427
 51D  C19  N20  triple    1.151  0.020  1.151
 51D  C4   H1   single    0.930  0.020  1.080
 51D  C6   H2   single    0.930  0.020  1.080
 51D  C9   H3   single    0.930  0.020  1.080
 51D  C12  H4   single    0.930  0.020  1.080
 51D  C15  H5   single    0.930  0.020  1.080
 51D  C16  H6   single    0.930  0.020  1.080
 51D  C17  H7   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
 51D  F1   C2   C7   120.12  3.000
 51D  C7   C2   C3   121.64  3.000
 51D  F1   C2   C3   118.23  3.000
 51D  CL   C3   C4   120.75  3.000
 51D  C4   C3   C2   120.05  3.000
 51D  CL   C3   C2   119.20  3.000
 51D  H1   C4   C5   121.15  3.000
 51D  H1   C4   C3   119.97  3.000
 51D  C5   C4   C3   118.88  3.000
 51D  C19  C5   C6   119.70  3.000
 51D  C19  C5   C4   119.45  3.000
 51D  C6   C5   C4   120.85  3.000
 51D  H2   C6   C7   119.73  3.000
 51D  H2   C6   C5   119.81  3.000
 51D  C7   C6   C5   120.44  3.000
 51D  C8   C7   C6   120.18  3.000
 51D  C6   C7   C2   118.14  3.000
 51D  C8   C7   C2   121.68  3.000
 51D  N13  C8   C9   122.31  3.000
 51D  N13  C8   C7   117.42  3.000
 51D  C9   C8   C7   120.25  3.000
 51D  H3   C9   C10  121.97  3.000
 51D  H3   C9   C8   122.34  3.000
 51D  C10  C9   C8   115.69  3.000
 51D  N14  C10  N11  116.35  3.000
 51D  N11  C10  C9   122.51  3.000
 51D  N14  C10  C9   121.14  3.000
 51D  H4   C12  N13  116.94  3.000
 51D  H4   C12  N11  116.46  3.000
 51D  N13  C12  N11  126.59  3.000
 51D  C12  N11  C10  116.53  3.000
 51D  C12  N13  C8   116.37  3.000
 51D  N18  N14  C15  112.34  3.000
 51D  C15  N14  C10  127.18  3.000
 51D  N18  N14  C10  120.48  3.000
 51D  H5   C15  C16  131.75  3.000
 51D  H5   C15  N14  121.97  3.000
 51D  C16  C15  N14  106.28  3.000
 51D  H6   C16  C17  127.96  3.000
 51D  H6   C16  C15  127.41  3.000
 51D  C17  C16  C15  104.63  3.000
 51D  H7   C17  N18  120.21  3.000
 51D  H7   C17  C16  128.15  3.000
 51D  N18  C17  C16  111.65  3.000
 51D  C17  N18  N14  105.10  3.000
 51D  N20  C19  C5   180.00  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
 51D  CONST_03  C5   C6   C7   C2     0.00  0.0  0
 51D  CONST_04  C5   C4   C3   C2     0.00  0.0  0
 51D  CONST_05  C8   C7   C2   C3   180.00  0.0  0
 51D  CONST_06  C6   C7   C2   C3     0.00  0.0  0
 51D  CONST_07  C6   C5   C4   C3     0.00  0.0  0
 51D  CONST_08  C7   C2   C3   C4     0.00  0.0  0
 51D  CONST_09  C7   C6   C5   C4     0.00  0.0  0
 51D  CONST_10  C8   C7   C6   C5   180.00  0.0  0
 51D  CONST_13  C10  C9   C8   C7   180.00  0.0  0
 51D  CONST_14  C12  N13  C8   C7   180.00  0.0  0
 51D  CONST_15  N14  C10  C9   C8   180.00  0.0  0
 51D  CONST_16  N11  C10  C9   C8     0.00  0.0  0
 51D  CONST_17  N11  C12  N13  C8     0.00  0.0  0
 51D  CONST_18  N18  N14  C10  C9     0.00  0.0  0
 51D  CONST_19  C15  N14  C10  C9   180.00  0.0  0
 51D  CONST_20  C12  N11  C10  C9     0.00  0.0  0
 51D  CONST_21  C12  N13  C8   C9     0.00  0.0  0
 51D  CONST_22  C17  N18  N14  C10  180.00  0.0  0
 51D  CONST_23  C16  C15  N14  C10  180.00  0.0  0
 51D  CONST_24  N13  C8   C9   C10    0.00  0.0  0
 51D  CONST_25  N13  C12  N11  C10    0.00  0.0  0
 51D  CONST_26  N14  C10  N11  C12  180.00  0.0  0
 51D  CONST_27  N18  N14  C10  N11  180.00  0.0  0
 51D  CONST_28  C15  N14  C10  N11    0.00  0.0  0
 51D  CONST_29  C16  C17  N18  N14    0.00  0.0  0
 51D  CONST_30  C17  C16  C15  N14    0.00  0.0  0
 51D  CONST_31  N18  C17  C16  C15    0.00  0.0  0
 51D  CONST_32  C17  N18  N14  C15    0.00  0.0  0
 51D  CONST_33  N18  N14  C15  C16    0.00  0.0  0
 51D  CONST_34  C19  C5   C4   C3   180.00  0.0  0
 51D  CONST_35  F1   C2   C3   C4   180.00  0.0  0
 51D  CONST_36  CL   C3   C4   C5   180.00  0.0  0
 51D  CONST_37  F1   C2   C7   C6   180.00  0.0  0
 51D  CONST_38  CL   C3   C2   C7   180.00  0.0  0
 51D  CONST_39  C19  C5   C6   C7   180.00  0.0  0
 51D  CONST_40  F1   C2   C7   C8     0.00  0.0  0
 51D  CONST_41  H2   C6   C7   C2   180.00  0.0  0
 51D  CONST_42  H1   C4   C3   C2   180.00  0.0  0
 51D  CONST_43  H3   C9   C8   C7     0.00  0.0  0
 51D  CONST_44  H4   C12  N13  C8   180.00  0.0  0
 51D  CONST_45  H5   C15  N14  C10    0.00  0.0  0
 51D  CONST_46  H7   C17  N18  N14  180.00  0.0  0
 51D  CONST_47  H6   C16  C15  N14  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
 51D  plan-1  C10  0.020
 51D  plan-1  N14  0.020
 51D  plan-1  C15  0.020
 51D  plan-1  C16  0.020
 51D  plan-1  C17  0.020
 51D  plan-1  N18  0.020
 51D  plan-1  H5   0.020
 51D  plan-1  H6   0.020
 51D  plan-1  H7   0.020
 51D  plan-2  C2   0.020
 51D  plan-2  C3   0.020
 51D  plan-2  C4   0.020
 51D  plan-2  C5   0.020
 51D  plan-2  C6   0.020
 51D  plan-2  C7   0.020
 51D  plan-2  C8   0.020
 51D  plan-2  F1   0.020
 51D  plan-2  C19  0.020
 51D  plan-2  N20  0.020
 51D  plan-2  CL   0.020
 51D  plan-2  H1   0.020
 51D  plan-2  H2   0.020
 51D  plan-3  C7   0.020
 51D  plan-3  C8   0.020
 51D  plan-3  C9   0.020
 51D  plan-3  C10  0.020
 51D  plan-3  C12  0.020
 51D  plan-3  N11  0.020
 51D  plan-3  N13  0.020
 51D  plan-3  N14  0.020
 51D  plan-3  H3   0.020
 51D  plan-3  H4   0.020

