# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 20:06:41 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 2,2'-(1,4-phenylene)bis(N-hydroxyacetamide)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)Cc1ccc(CC(=O)NO)cc1
#
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
 BYX  BYX  2,2'-(1,4-phenylene)bis(N-hydroxyacetamide)  ligand  28  16  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BYX
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
 BYX  O01   O  O     0  -0.467   2.7957  -1.1091  -1.1985
 BYX  C02   C  C     0   0.531   3.3236  -0.3217  -0.4360
 BYX  N03   N  NH1   0  -0.368   4.4050  -0.6119   0.3067
 BYX  O04   O  OH1   0  -0.543   4.9045  -1.8774   0.3277
 BYX  C05   C  CH2   0  -0.683   2.8469   1.1108  -0.2696
 BYX  C06   C  CR6   0   0.126   1.3551   1.1704  -0.1073
 BYX  C07   C  CR16  0  -0.285   0.5151   1.1700  -1.2161
 BYX  C08   C  CR16  0  -0.279  -0.8628   1.1979  -1.0592
 BYX  C09   C  CR6   0   0.124  -1.4370   1.2255   0.2083
 BYX  C10   C  CH2   0  -0.679  -2.9312   1.2156   0.3674
 BYX  C11   C  C     0   0.527  -3.4422  -0.2017   0.5495
 BYX  N12   N  NH1   0  -0.366  -4.3865  -0.5484  -0.3424
 BYX  O13   O  OH1   0  -0.544  -5.0595  -1.7234  -0.1996
 BYX  O14   O  O     0  -0.468  -3.0144  -0.9510   1.4074
 BYX  C15   C  CR16  0  -0.287  -0.5974   1.2285   1.3174
 BYX  C16   C  CR16  0  -0.280   0.7809   1.2014   1.1600
 BYX  H031  H  HNH1  0   0.418   4.7625   0.0021   1.0239
 BYX  H1    H  HOH1  0   0.478   5.6162  -1.8991  -0.3254
 BYX  H051  H  HCH2  0   0.277   3.3444   1.6029   0.5680
 BYX  H052  H  HCH2  0   0.297   3.1514   1.6489  -1.1713
 BYX  H071  H  HCR6  0   0.249   0.9376   1.1597  -2.2133
 BYX  H081  H  HCR6  0   0.251  -1.4997   1.2019  -1.9361
 BYX  H102  H  HCH2  0   0.296  -3.2245   1.7746   1.2595
 BYX  H101  H  HCH2  0   0.277  -3.4080   1.7074  -0.4823
 BYX  H121  H  HNH1  0   0.418  -4.8260   0.1199  -0.9585
 BYX  H2    H  HOH1  0   0.479  -4.6261  -2.3546  -0.7885
 BYX  H151  H  HCR6  0   0.249  -1.0199   1.2655   2.3141
 BYX  H161  H  HCR6  0   0.251   1.4179   1.2102   2.0368

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
 BYX  O13  N12   single    1.362  0.020  1.362
 BYX  N12  C11   single    1.344  0.020  1.344
 BYX  O14  C11   double    1.217  0.020  1.217
 BYX  C11  C10   single    1.518  0.020  1.518
 BYX  C10  C09   single    1.503  0.020  1.503
 BYX  C08  C09   aromatic  1.392  0.020  1.392
 BYX  C08  C07   aromatic  1.387  0.020  1.387
 BYX  C09  C15   aromatic  1.391  0.020  1.391
 BYX  C07  C06   aromatic  1.391  0.020  1.391
 BYX  C15  C16   aromatic  1.388  0.020  1.388
 BYX  C06  C16   aromatic  1.392  0.020  1.392
 BYX  C06  C05   single    1.502  0.020  1.502
 BYX  C05  C02   single    1.519  0.020  1.519
 BYX  O01  C02   double    1.217  0.020  1.217
 BYX  C02  N03   single    1.344  0.020  1.344
 BYX  N03  O04   single    1.361  0.020  1.361
 BYX  N03  H031  single    0.860  0.020  1.020
 BYX  O04  H1    single    0.850  0.020  0.980
 BYX  C05  H051  single    0.970  0.020  1.090
 BYX  C05  H052  single    0.970  0.020  1.090
 BYX  C07  H071  single    0.930  0.020  1.080
 BYX  C08  H081  single    0.930  0.020  1.080
 BYX  C10  H102  single    0.970  0.020  1.090
 BYX  C10  H101  single    0.970  0.020  1.090
 BYX  N12  H121  single    0.860  0.020  1.020
 BYX  O13  H2    single    0.850  0.020  0.980
 BYX  C15  H151  single    0.930  0.020  1.080
 BYX  C16  H161  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
 BYX  C05   C02  N03   113.32  3.000
 BYX  N03   C02  O01   123.77  3.000
 BYX  C05   C02  O01   122.88  3.000
 BYX  H031  N03  O04   115.13  3.000
 BYX  H031  N03  C02   123.12  3.000
 BYX  O04   N03  C02   120.32  3.000
 BYX  H1    O04  N03   106.31  3.000
 BYX  H052  C05  H051  106.50  3.000
 BYX  H052  C05  C06   110.27  3.000
 BYX  H051  C05  C06   110.61  3.000
 BYX  H052  C05  C02   106.65  3.000
 BYX  H051  C05  C02   111.48  3.000
 BYX  C06   C05  C02   111.17  3.000
 BYX  C16   C06  C07   118.47  3.000
 BYX  C16   C06  C05   120.61  3.000
 BYX  C07   C06  C05   120.91  3.000
 BYX  H071  C07  C08   119.46  3.000
 BYX  H071  C07  C06   119.89  3.000
 BYX  C08   C07  C06   120.64  3.000
 BYX  H081  C08  C09   119.63  3.000
 BYX  H081  C08  C07   119.49  3.000
 BYX  C09   C08  C07   120.88  3.000
 BYX  C15   C09  C10   121.05  3.000
 BYX  C15   C09  C08   118.50  3.000
 BYX  C10   C09  C08   120.44  3.000
 BYX  H101  C10  H102  106.72  3.000
 BYX  H101  C10  C11   111.54  3.000
 BYX  H102  C10  C11   106.83  3.000
 BYX  H101  C10  C09   110.42  3.000
 BYX  H102  C10  C09   110.48  3.000
 BYX  C11   C10  C09   110.71  3.000
 BYX  O14   C11  N12   123.77  3.000
 BYX  O14   C11  C10   122.78  3.000
 BYX  N12   C11  C10   113.44  3.000
 BYX  H121  N12  O13   114.84  3.000
 BYX  H121  N12  C11   122.68  3.000
 BYX  O13   N12  C11   120.01  3.000
 BYX  H2    O13  N12   106.15  3.000
 BYX  H151  C15  C16   119.51  3.000
 BYX  H151  C15  C09   119.89  3.000
 BYX  C16   C15  C09   120.60  3.000
 BYX  H161  C16  C15   119.47  3.000
 BYX  H161  C16  C06   119.62  3.000
 BYX  C15   C16  C06   120.91  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
 BYX  CONST_01  C09   C08  C07  C06     0.00   0.0  0
 BYX  CONST_02  C09   C15  C16  C06     0.00   0.0  0
 BYX  CONST_03  C15   C09  C08  C07     0.00   0.0  0
 BYX  CONST_04  C15   C16  C06  C07     0.00   0.0  0
 BYX  CONST_05  C16   C15  C09  C08     0.00   0.0  0
 BYX  CONST_06  C16   C06  C07  C08     0.00   0.0  0
 BYX  CONST_07  C08   C07  C06  C05   180.00   0.0  0
 BYX  CONST_08  C15   C16  C06  C05   180.00   0.0  0
 BYX  CONST_09  C10   C09  C08  C07   180.00   0.0  0
 BYX  CONST_10  C16   C15  C09  C10   180.00   0.0  0
 BYX  CONST_11  H081  C08  C07  C06   180.00   0.0  0
 BYX  CONST_12  H151  C15  C16  C06   180.00   0.0  0
 BYX  CONST_13  H161  C16  C06  C07   180.00   0.0  0
 BYX  CONST_14  H071  C07  C08  C09   180.00   0.0  0
 BYX  CONST_15  O04   N03  C02  O01     0.00   0.0  0
 BYX  CONST_16  C05   C02  N03  O04   180.00   0.0  0
 BYX  CONST_17  O13   N12  C11  C10   180.00   0.0  0
 BYX  CONST_18  O14   C11  N12  O13     0.00   0.0  0
 BYX  CONST_19  H031  N03  C02  O01   180.00   0.0  0
 BYX  CONST_20  H121  N12  C11  C10     0.00   0.0  0
 BYX  Var_01    C07   C06  C05  C02   -84.01  30.0  2
 BYX  Var_02    C11   C10  C09  C08    93.59  30.0  2
 BYX  Var_03    C06   C05  C02  O01    47.05  30.0  2
 BYX  Var_04    N12   C11  C10  C09  -124.76  30.0  1

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
 BYX  plan-1  C05   0.020
 BYX  plan-1  C06   0.020
 BYX  plan-1  C07   0.020
 BYX  plan-1  C08   0.020
 BYX  plan-1  C09   0.020
 BYX  plan-1  C10   0.020
 BYX  plan-1  C15   0.020
 BYX  plan-1  C16   0.020
 BYX  plan-1  H071  0.020
 BYX  plan-1  H081  0.020
 BYX  plan-1  H151  0.020
 BYX  plan-1  H161  0.020
 BYX  plan-2  O01   0.020
 BYX  plan-2  C02   0.020
 BYX  plan-2  N03   0.020
 BYX  plan-2  O04   0.020
 BYX  plan-2  C05   0.020
 BYX  plan-2  H031  0.020
 BYX  plan-3  C10   0.020
 BYX  plan-3  C11   0.020
 BYX  plan-3  N12   0.020
 BYX  plan-3  O13   0.020
 BYX  plan-3  O14   0.020
 BYX  plan-3  H121  0.020

