# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 19:07:28 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-bromanyl-3-fluoranyl-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(Br)cnc1C(=O)NCc2ccc3OCOc3c2
#
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
 C8K  C8K  ~{N}-(1,3-benzodioxol-5-ylmethyl)-5-bromanyl-3-fluoranyl-pyridine-2-carboxamide  ligand  31  21  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C8K
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
 C8K  C3   C   CR6   0  -0.067   1.1264   0.9192   0.2168
 C8K  C4   C   CR6   0   0.524   2.0966   0.9956   1.2088
 C8K  C1   C   CR16  0  -0.042   2.4739  -0.4765  -1.0307
 C8K  N2   N   N     0  -0.415   1.3497   0.1874  -0.8697
 C8K  C5   C   CR16  0  -0.262   3.2930   0.3131   1.0753
 C8K  C6   C   CR6   0  -0.168   3.4796  -0.4376  -0.0679
 C8K  F13  F   F     0  -0.276   1.9216   1.7183   2.3076
 C8K  BR1  BR  BR    0   0.016   5.0656  -1.3957  -0.3320
 C8K  C15  C   C     0   0.568  -0.1977   1.6289   0.3069
 C8K  N16  N   NH1   0  -0.631  -0.9524   1.4928  -0.7888
 C8K  O17  O   O     0  -0.479  -0.5193   2.2642   1.2996
 C8K  C18  C   CH2   0  -0.392  -2.2817   2.0468  -0.9286
 C8K  C19  C   CR6   0   0.110  -3.3607   1.0156  -0.7139
 C8K  C20  C   CR16  0  -0.382  -3.5930   0.5192   0.5816
 C8K  C21  C   CR56  0   0.316  -4.5665  -0.4347   0.7230
 C8K  C22  C   CR56  0   0.292  -5.3031  -0.9033  -0.3557
 C8K  C23  C   CR16  0  -0.333  -5.0975  -0.4324  -1.6264
 C8K  C24  C   CR16  0  -0.323  -4.1020   0.5426  -1.7851
 C8K  O25  O   O     0  -0.486  -6.1857  -1.8370   0.0712
 C8K  O26  O   O     0  -0.488  -4.9725  -1.0625   1.8520
 C8K  C27  C   CH2   0   0.074  -6.0431  -1.9236   1.4835
 C8K  H1   H   HCR6  0   0.297   2.5854  -1.0529  -1.9408
 C8K  H2   H   HCR6  0   0.324   4.0423   0.3812   1.8531
 C8K  H3   H   HNH1  0   0.409  -0.5957   0.9071  -1.5296
 C8K  H4   H   HCH2  0   0.267  -2.3858   2.8661  -0.2183
 C8K  H5   H   HCH2  0   0.275  -2.3691   2.4743  -1.9280
 C8K  H6   H   HCR6  0   0.268  -3.0282   0.8808   1.4318
 C8K  H7   H   HCR6  0   0.273  -5.6719  -0.7916  -2.4695
 C8K  H8   H   HCR6  0   0.256  -3.9135   0.9347  -2.7767
 C8K  H9   H   HCH2  0   0.237  -6.9660  -1.5969   1.9702
 C8K  H10  H   HCH2  0   0.241  -5.8065  -2.9504   1.7693

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
 C8K  C24  C23  aromatic  1.402  0.020  1.402
 C8K  C24  C19  aromatic  1.386  0.020  1.386
 C8K  C23  C22  aromatic  1.371  0.020  1.371
 C8K  C18  C19  single    1.508  0.020  1.508
 C8K  C18  N16  single    1.447  0.020  1.447
 C8K  C19  C20  aromatic  1.407  0.020  1.407
 C8K  C22  O25  single    1.354  0.020  1.354
 C8K  C22  C21  aromatic  1.388  0.020  1.388
 C8K  O25  C27  single    1.422  0.020  1.422
 C8K  C21  C20  aromatic  1.370  0.020  1.370
 C8K  C21  O26  single    1.354  0.020  1.354
 C8K  C27  O26  single    1.422  0.020  1.422
 C8K  N16  C15  single    1.337  0.020  1.337
 C8K  O17  C15  double    1.222  0.020  1.222
 C8K  C15  C3   single    1.505  0.020  1.505
 C8K  C3   N2   aromatic  1.329  0.020  1.329
 C8K  C3   C4   aromatic  1.390  0.020  1.390
 C8K  N2   C1   aromatic  1.315  0.020  1.315
 C8K  F13  C4   single    1.327  0.020  1.327
 C8K  C4   C5   aromatic  1.384  0.020  1.384
 C8K  C1   C6   aromatic  1.393  0.020  1.393
 C8K  C5   C6   aromatic  1.380  0.020  1.380
 C8K  C6   BR1  single    1.872  0.020  1.872
 C8K  C1   H1   single    0.930  0.020  1.080
 C8K  C5   H2   single    0.930  0.020  1.080
 C8K  N16  H3   single    0.860  0.020  1.020
 C8K  C18  H4   single    0.970  0.020  1.090
 C8K  C18  H5   single    0.970  0.020  1.090
 C8K  C20  H6   single    0.930  0.020  1.080
 C8K  C23  H7   single    0.930  0.020  1.080
 C8K  C24  H8   single    0.930  0.020  1.080
 C8K  C27  H9   single    0.970  0.020  1.090
 C8K  C27  H10  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
 C8K  C15  C3   N2   117.16  3.000
 C8K  N2   C3   C4   119.77  3.000
 C8K  C15  C3   C4   123.07  3.000
 C8K  F13  C4   C5   117.55  3.000
 C8K  C5   C4   C3   120.51  3.000
 C8K  F13  C4   C3   121.94  3.000
 C8K  H1   C1   C6   121.43  3.000
 C8K  H1   C1   N2   117.35  3.000
 C8K  C6   C1   N2   121.23  3.000
 C8K  C1   N2   C3   121.44  3.000
 C8K  H2   C5   C6   122.41  3.000
 C8K  H2   C5   C4   119.88  3.000
 C8K  C6   C5   C4   117.71  3.000
 C8K  BR1  C6   C5   120.65  3.000
 C8K  BR1  C6   C1   120.01  3.000
 C8K  C5   C6   C1   119.35  3.000
 C8K  O17  C15  N16  124.76  3.000
 C8K  O17  C15  C3   121.70  3.000
 C8K  N16  C15  C3   113.54  3.000
 C8K  H3   N16  C18  118.42  3.000
 C8K  H3   N16  C15  117.45  3.000
 C8K  C18  N16  C15  123.96  3.000
 C8K  H5   C18  H4   107.16  3.000
 C8K  H5   C18  C19  109.95  3.000
 C8K  H4   C18  C19  110.68  3.000
 C8K  H5   C18  N16  108.20  3.000
 C8K  H4   C18  N16  108.23  3.000
 C8K  C19  C18  N16  112.44  3.000
 C8K  C24  C19  C20  120.20  3.000
 C8K  C20  C19  C18  119.38  3.000
 C8K  C24  C19  C18  120.41  3.000
 C8K  H6   C20  C21  121.47  3.000
 C8K  H6   C20  C19  121.27  3.000
 C8K  C21  C20  C19  117.26  3.000
 C8K  O26  C21  C22  109.41  3.000
 C8K  O26  C21  C20  128.45  3.000
 C8K  C22  C21  C20  122.14  3.000
 C8K  O25  C22  C23  128.83  3.000
 C8K  O25  C22  C21  109.50  3.000
 C8K  C23  C22  C21  121.67  3.000
 C8K  H7   C23  C24  121.31  3.000
 C8K  H7   C23  C22  121.93  3.000
 C8K  C24  C23  C22  116.76  3.000
 C8K  H8   C24  C23  118.61  3.000
 C8K  H8   C24  C19  119.41  3.000
 C8K  C23  C24  C19  121.97  3.000
 C8K  C27  O25  C22  106.84  3.000
 C8K  C27  O26  C21  106.88  3.000
 C8K  H10  C27  H9   110.33  3.000
 C8K  H10  C27  O26  109.78  3.000
 C8K  H9   C27  O26  109.82  3.000
 C8K  H10  C27  O25  109.82  3.000
 C8K  H9   C27  O25  109.83  3.000
 C8K  O26  C27  O25  107.21  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
 C8K  CONST_01  C6   C1   N2   C3      0.00   0.0  0
 C8K  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 C8K  CONST_03  C1   N2   C3   C4      0.00   0.0  0
 C8K  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 C8K  CONST_05  C5   C4   C3   N2      0.00   0.0  0
 C8K  CONST_06  C5   C6   C1   N2      0.00   0.0  0
 C8K  CONST_07  C22  C23  C24  C19     0.00   0.0  0
 C8K  CONST_08  C22  C21  C20  C19     0.00   0.0  0
 C8K  CONST_09  C23  C24  C19  C20     0.00   0.0  0
 C8K  CONST_10  C23  C22  C21  C20     0.00   0.0  0
 C8K  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 C8K  CONST_12  C24  C19  C20  C21     0.00   0.0  0
 C8K  CONST_13  BR1  C6   C5   C4    180.00   0.0  0
 C8K  CONST_14  C15  C3   N2   C1    180.00   0.0  0
 C8K  CONST_15  F13  C4   C3   N2    180.00   0.0  0
 C8K  CONST_16  BR1  C6   C1   N2    180.00   0.0  0
 C8K  CONST_17  C15  C3   C4   C5    180.00   0.0  0
 C8K  CONST_18  F13  C4   C5   C6    180.00   0.0  0
 C8K  CONST_19  C23  C24  C19  C18   180.00   0.0  0
 C8K  CONST_20  C21  C20  C19  C18   180.00   0.0  0
 C8K  CONST_21  H1   C1   N2   C3    180.00   0.0  0
 C8K  CONST_22  H2   C5   C4   C3    180.00   0.0  0
 C8K  CONST_23  H7   C23  C24  C19   180.00   0.0  0
 C8K  CONST_24  H8   C24  C19  C20   180.00   0.0  0
 C8K  CONST_25  H6   C20  C21  C22   180.00   0.0  0
 C8K  CONST_26  C18  N16  C15  C3    180.00   0.0  0
 C8K  CONST_27  H3   N16  C15  C3      0.00   0.0  0
 C8K  CONST_28  C18  N16  C15  O17     0.00   0.0  0
 C8K  Var_01    O25  C27  O26  C21     3.80  30.0  1
 C8K  Var_02    O26  C27  O25  C22    -3.87  30.0  1
 C8K  Var_03    N16  C15  C3   C4    176.04  30.0  2
 C8K  Var_04    C24  C19  C18  N16  -107.69  30.0  2
 C8K  Var_05    C19  C18  N16  C15  -100.79  30.0  2

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
 C8K  plan-1  C3   0.020
 C8K  plan-1  C4   0.020
 C8K  plan-1  C1   0.020
 C8K  plan-1  N2   0.020
 C8K  plan-1  C5   0.020
 C8K  plan-1  C6   0.020
 C8K  plan-1  F13  0.020
 C8K  plan-1  BR1  0.020
 C8K  plan-1  C15  0.020
 C8K  plan-1  H1   0.020
 C8K  plan-1  H2   0.020
 C8K  plan-2  C18  0.020
 C8K  plan-2  C19  0.020
 C8K  plan-2  C20  0.020
 C8K  plan-2  C21  0.020
 C8K  plan-2  C22  0.020
 C8K  plan-2  C23  0.020
 C8K  plan-2  C24  0.020
 C8K  plan-2  O25  0.020
 C8K  plan-2  O26  0.020
 C8K  plan-2  H6   0.020
 C8K  plan-2  H7   0.020
 C8K  plan-2  H8   0.020
 C8K  plan-3  C3   0.020
 C8K  plan-3  C15  0.020
 C8K  plan-3  N16  0.020
 C8K  plan-3  O17  0.020
 C8K  plan-3  C18  0.020
 C8K  plan-3  H3   0.020

