# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 12:22:09 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 5-chloro-6'-methyl-3-[4-(methylsulfonyl)phenyl]-2,3'-bipyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(cn1)c2ncc(Cl)cc2c3ccc(cc3)[S](C)(=O)=O
#
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
 5CH  5CH  5-chloro-6'-methyl-3-[4-(methylsulfonyl)phenyl]-2,3'-bipyridine  ligand  39  24  .  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_5CH
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
 5CH  N9    N   N     0  -0.411  -3.5101   0.9642  -0.0805
 5CH  C2    C   CR16  0  -0.211   1.9409  -0.5523  -1.0545
 5CH  C4    C   CR6   0   0.009  -0.2097  -0.8146   0.0071
 5CH  C5    C   CR16  0  -0.272   0.3726  -1.6303   0.9740
 5CH  C6    C   CR16  0  -0.215   1.7316  -1.8996   0.9441
 5CH  O24   O   OS    0  -0.667   4.6995  -1.6040  -1.4945
 5CH  O23   O   OS    0  -0.667   4.5006  -2.9045   0.6479
 5CH  C22   C   CH3   0  -0.790   4.9519  -0.3127   0.7872
 5CH  C1    C   CR6   0  -0.213   2.5042  -1.3520  -0.0686
 5CH  C3    C   CR16  0  -0.263   0.5849  -0.2844  -1.0092
 5CH  C7    C   CR6   0   0.017  -1.6625  -0.5447   0.0358
 5CH  C12   C   CR16  0  -0.117  -2.5478  -1.6169   0.0511
 5CH  C11   C   CR6   0  -0.106  -3.9051  -1.3671  -0.0067
 5CH  CL20  CL  CL    0  -0.104  -5.0403  -2.6631   0.0030
 5CH  C10   C   CR16  0  -0.042  -4.3479  -0.0558  -0.0954
 5CH  C8    C   CR6   0   0.220  -2.1995   0.7507   0.0035
 5CH  C13   C   CR6   0  -0.077  -1.3618   1.9642   0.0729
 5CH  C18   C   CR16  0  -0.159  -1.6051   3.0513  -0.7588
 5CH  C17   C   CR16  0  -0.335  -0.8120   4.1794  -0.6477
 5CH  C16   C   CR6   0   0.242   0.2015   4.2103   0.3064
 5CH  C19   C   CH3   0  -0.715   1.0980   5.3988   0.4619
 5CH  N15   N   N     0  -0.420   0.4162   3.1797   1.1248
 5CH  C14   C   CR16  0  -0.086  -0.3368   2.0992   1.0065
 5CH  H2    H   HCR6  0   0.288   2.5420  -0.1427  -1.8550
 5CH  H5    H   HCR6  0   0.275  -0.2334  -2.0481   1.7676
 5CH  H6    H   HCR6  0   0.288   2.1731  -2.5272   1.7062
 5CH  H22   H   HCH3  0   0.296   4.6778   0.6195   0.2989
 5CH  H22A  H   HCH3  0   0.297   4.5878  -0.3263   1.8119
 5CH  H22B  H   HCH3  0   0.312   6.0343  -0.4383   0.7727
 5CH  H3    H   HCR6  0   0.274   0.1389   0.3298  -1.7804
 5CH  H12   H   HCR6  0   0.298  -2.1746  -2.6328   0.0765
 5CH  H10   H   HCR6  0   0.290  -5.4057   0.1681  -0.1728
 5CH  H18   H   HCR6  0   0.267  -2.3991   3.0097  -1.4931
 5CH  H17   H   HCR6  0   0.268  -0.9776   5.0303  -1.2948
 5CH  H19   H   HCH3  0   0.253   1.0974   5.7513   1.4938
 5CH  H19A  H   HCH3  0   0.254   2.1276   5.1381   0.2114
 5CH  H19B  H   HCH3  0   0.245   0.7923   6.2219  -0.1815
 5CH  H14   H   HCR6  0   0.261  -0.1309   1.2976   1.7084
 5CH  S21   S   S     0   1.216   4.2480  -1.6788  -0.1067

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
 5CH  N9   C10   aromatic  1.320  0.020  1.320
 5CH  N9   C8    aromatic  1.331  0.020  1.331
 5CH  C2   C1    aromatic  1.389  0.020  1.389
 5CH  C2   C3    aromatic  1.383  0.020  1.383
 5CH  C4   C5    aromatic  1.393  0.020  1.393
 5CH  C4   C3    aromatic  1.395  0.020  1.395
 5CH  C4   C7    single    1.478  0.020  1.478
 5CH  C5   C6    aromatic  1.386  0.020  1.386
 5CH  C6   C1    aromatic  1.386  0.020  1.386
 5CH  O24  S21   double    1.461  0.020  1.461
 5CH  S21  O23   double    1.461  0.020  1.461
 5CH  S21  C22   single    1.778  0.020  1.778
 5CH  S21  C1    single    1.775  0.020  1.775
 5CH  C7   C12   aromatic  1.391  0.020  1.391
 5CH  C7   C8    aromatic  1.403  0.020  1.403
 5CH  C12  C11   aromatic  1.381  0.020  1.381
 5CH  C11  CL20  single    1.723  0.020  1.723
 5CH  C11  C10   aromatic  1.387  0.020  1.387
 5CH  C8   C13   single    1.476  0.020  1.476
 5CH  C13  C18   aromatic  1.390  0.020  1.390
 5CH  C13  C14   aromatic  1.393  0.020  1.393
 5CH  C18  C17   aromatic  1.383  0.020  1.383
 5CH  C17  C16   aromatic  1.392  0.020  1.392
 5CH  C16  C19   single    1.497  0.020  1.497
 5CH  C16  N15   aromatic  1.333  0.020  1.333
 5CH  N15  C14   aromatic  1.322  0.020  1.322
 5CH  C2   H2    single    0.930  0.020  1.080
 5CH  C5   H5    single    0.930  0.020  1.080
 5CH  C6   H6    single    0.930  0.020  1.080
 5CH  C22  H22   single    0.970  0.020  1.090
 5CH  C22  H22A  single    0.970  0.020  1.090
 5CH  C22  H22B  single    0.970  0.020  1.090
 5CH  C3   H3    single    0.930  0.020  1.080
 5CH  C12  H12   single    0.930  0.020  1.080
 5CH  C10  H10   single    0.930  0.020  1.080
 5CH  C18  H18   single    0.930  0.020  1.080
 5CH  C17  H17   single    0.930  0.020  1.080
 5CH  C19  H19   single    0.970  0.020  1.090
 5CH  C19  H19A  single    0.970  0.020  1.090
 5CH  C19  H19B  single    0.970  0.020  1.090
 5CH  C14  H14   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
 5CH  C8    N9   C10   120.13  3.000
 5CH  H2    C2   C3    119.72  3.000
 5CH  H2    C2   C1    121.21  3.000
 5CH  C3    C2   C1    119.07  3.000
 5CH  C7    C4   C3    120.31  3.000
 5CH  C7    C4   C5    120.30  3.000
 5CH  C3    C4   C5    119.37  3.000
 5CH  H5    C5   C6    119.33  3.000
 5CH  H5    C5   C4    120.07  3.000
 5CH  C6    C5   C4    120.59  3.000
 5CH  H6    C6   C1    121.09  3.000
 5CH  H6    C6   C5    119.86  3.000
 5CH  C1    C6   C5    119.04  3.000
 5CH  H22B  C22  H22A  110.10  3.000
 5CH  H22B  C22  H22   110.07  3.000
 5CH  H22A  C22  H22   110.45  3.000
 5CH  H22B  C22  S21   107.34  3.000
 5CH  H22A  C22  S21   109.36  3.000
 5CH  H22   C22  S21   109.46  3.000
 5CH  S21   C1   C6    119.37  3.000
 5CH  S21   C1   C2    119.30  3.000
 5CH  C6    C1   C2    121.33  3.000
 5CH  H3    C3   C4    120.02  3.000
 5CH  H3    C3   C2    119.39  3.000
 5CH  C4    C3   C2    120.58  3.000
 5CH  C8    C7   C12   117.95  3.000
 5CH  C8    C7   C4    122.99  3.000
 5CH  C12   C7   C4    119.03  3.000
 5CH  H12   C12  C11   120.63  3.000
 5CH  H12   C12  C7    120.29  3.000
 5CH  C11   C12  C7    119.05  3.000
 5CH  C10   C11  CL20  120.08  3.000
 5CH  C10   C11  C12   119.18  3.000
 5CH  CL20  C11  C12   120.74  3.000
 5CH  H10   C10  C11   120.76  3.000
 5CH  H10   C10  N9    117.42  3.000
 5CH  C11   C10  N9    121.81  3.000
 5CH  C13   C8   C7    122.74  3.000
 5CH  C13   C8   N9    115.47  3.000
 5CH  C7    C8   N9    121.79  3.000
 5CH  C14   C13  C18   117.00  3.000
 5CH  C14   C13  C8    121.91  3.000
 5CH  C18   C13  C8    121.03  3.000
 5CH  H18   C18  C17   120.43  3.000
 5CH  H18   C18  C13   120.28  3.000
 5CH  C17   C18  C13   119.29  3.000
 5CH  H17   C17  C16   120.26  3.000
 5CH  H17   C17  C18   120.37  3.000
 5CH  C16   C17  C18   119.37  3.000
 5CH  N15   C16  C19   116.97  3.000
 5CH  N15   C16  C17   121.37  3.000
 5CH  C19   C16  C17   121.65  3.000
 5CH  H19B  C19  H19A  108.06  3.000
 5CH  H19B  C19  H19   108.35  3.000
 5CH  H19A  C19  H19   107.15  3.000
 5CH  H19B  C19  C16   111.77  3.000
 5CH  H19A  C19  C16   110.59  3.000
 5CH  H19   C19  C16   110.77  3.000
 5CH  C14   N15  C16   119.01  3.000
 5CH  H14   C14  N15   115.96  3.000
 5CH  H14   C14  C13   120.11  3.000
 5CH  N15   C14  C13   123.92  3.000
 5CH  C1    S21  C22   103.70  3.000
 5CH  C1    S21  O23   108.26  3.000
 5CH  C22   S21  O23   108.45  3.000
 5CH  C1    S21  O24   108.33  3.000
 5CH  C22   S21  O24   108.41  3.000
 5CH  O23   S21  O24   118.68  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
 5CH  CONST_01  C12   C11  C10  N9     0.00   0.0  0
 5CH  CONST_02  C4    C7   C8   N9   180.00   0.0  0
 5CH  CONST_03  C12   C7   C8   N9     0.00   0.0  0
 5CH  CONST_06  C5    C6   C1   C2     0.00   0.0  0
 5CH  CONST_07  C5    C4   C3   C2     0.00   0.0  0
 5CH  CONST_08  C7    C4   C3   C2   180.00   0.0  0
 5CH  CONST_09  C1    C6   C5   C4     0.00   0.0  0
 5CH  CONST_10  C1    C2   C3   C4     0.00   0.0  0
 5CH  CONST_11  C11   C12  C7   C4   180.00   0.0  0
 5CH  CONST_12  C13   C8   C7   C4     0.00   0.0  0
 5CH  CONST_15  C3    C4   C5   C6     0.00   0.0  0
 5CH  CONST_16  C7    C4   C5   C6   180.00   0.0  0
 5CH  CONST_17  C3    C2   C1   C6     0.00   0.0  0
 5CH  CONST_20  C10   C11  C12  C7     0.00   0.0  0
 5CH  CONST_21  C10   N9   C8   C7     0.00   0.0  0
 5CH  CONST_24  C13   C8   C7   C12  180.00   0.0  0
 5CH  CONST_25  C8    C7   C12  C11    0.00   0.0  0
 5CH  CONST_26  C8    N9   C10  C11    0.00   0.0  0
 5CH  CONST_27  C13   C8   N9   C10  180.00   0.0  0
 5CH  CONST_28  C17   C18  C13  C8   180.00   0.0  0
 5CH  CONST_29  N15   C14  C13  C8   180.00   0.0  0
 5CH  CONST_30  C16   C17  C18  C13    0.00   0.0  0
 5CH  CONST_31  C16   N15  C14  C13    0.00   0.0  0
 5CH  CONST_32  N15   C14  C13  C18    0.00   0.0  0
 5CH  CONST_33  N15   C16  C17  C18    0.00   0.0  0
 5CH  CONST_34  C14   C13  C18  C17    0.00   0.0  0
 5CH  CONST_35  C14   N15  C16  C17    0.00   0.0  0
 5CH  CONST_36  CL20  C11  C10  N9   180.00   0.0  0
 5CH  CONST_37  S21   C1   C6   C5   180.00   0.0  0
 5CH  CONST_38  C3    C2   C1   S21  180.00   0.0  0
 5CH  CONST_39  CL20  C11  C12  C7   180.00   0.0  0
 5CH  CONST_40  C19   C16  C17  C18  180.00   0.0  0
 5CH  CONST_41  C14   N15  C16  C19  180.00   0.0  0
 5CH  CONST_42  H6    C6   C1   C2   180.00   0.0  0
 5CH  CONST_43  H2    C2   C3   C4   180.00   0.0  0
 5CH  CONST_44  H12   C12  C7   C4     0.00   0.0  0
 5CH  CONST_45  H3    C3   C4   C5   180.00   0.0  0
 5CH  CONST_46  H5    C5   C6   C1   180.00   0.0  0
 5CH  CONST_47  H10   C10  C11  C12  180.00   0.0  0
 5CH  CONST_48  H18   C18  C13  C8     0.00   0.0  0
 5CH  CONST_49  H14   C14  C13  C8     0.00   0.0  0
 5CH  CONST_50  H17   C17  C18  C13  180.00   0.0  0
 5CH  Var_01    O24   S21  C1   C2   -27.80  30.0  3
 5CH  Var_02    H19   C19  C16  C17  126.12  30.0  2
 5CH  Var_03    H22   C22  S21  C1   -58.78  30.0  3

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
 5CH  plan-1  N9    0.020
 5CH  plan-1  C4    0.020
 5CH  plan-1  C7    0.020
 5CH  plan-1  C12   0.020
 5CH  plan-1  C11   0.020
 5CH  plan-1  CL20  0.020
 5CH  plan-1  C10   0.020
 5CH  plan-1  C8    0.020
 5CH  plan-1  C13   0.020
 5CH  plan-1  H12   0.020
 5CH  plan-1  H10   0.020
 5CH  plan-2  C2    0.020
 5CH  plan-2  C4    0.020
 5CH  plan-2  C5    0.020
 5CH  plan-2  C6    0.020
 5CH  plan-2  C1    0.020
 5CH  plan-2  C3    0.020
 5CH  plan-2  C7    0.020
 5CH  plan-2  H2    0.020
 5CH  plan-2  H5    0.020
 5CH  plan-2  H6    0.020
 5CH  plan-2  H3    0.020
 5CH  plan-2  S21   0.020
 5CH  plan-3  C8    0.020
 5CH  plan-3  C13   0.020
 5CH  plan-3  C18   0.020
 5CH  plan-3  C17   0.020
 5CH  plan-3  C16   0.020
 5CH  plan-3  C19   0.020
 5CH  plan-3  N15   0.020
 5CH  plan-3  C14   0.020
 5CH  plan-3  H18   0.020
 5CH  plan-3  H17   0.020
 5CH  plan-3  H14   0.020

