# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 18:42:19 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: N,N'-dihydroxybenzene-1,4-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccc(cc1)C(=O)NO
#
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
 BYD  BYD  N,N'-dihydroxybenzene-1,4-dicarboxamide  ligand  22  14  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BYD
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
 BYD  CAA  C  CR16  0  -0.266  -0.7915  -1.1366   0.1252
 BYD  CAB  C  CR16  0  -0.252   0.5888  -1.2394   0.1461
 BYD  CAC  C  CR6   0  -0.050   1.3789  -0.0962   0.2144
 BYD  CAD  C  CR16  0  -0.270   0.7660   1.1521   0.2986
 BYD  CAE  C  CR16  0  -0.250  -0.6149   1.2536   0.3009
 BYD  CAF  C  CR6   0  -0.059  -1.4041   0.1130   0.1966
 BYD  CAG  C  C     0   0.500  -2.8888   0.2816   0.2159
 BYD  CAK  C  C     0   0.497   2.8628  -0.2723   0.2609
 BYD  NAI  N  NH1   0  -0.379  -3.5586  -0.6752  -0.4614
 BYD  NAL  N  NH1   0  -0.374   3.5552   0.7139  -0.3312
 BYD  OAH  O  O     0  -0.455  -3.4301   1.1940   0.8116
 BYD  OAJ  O  OH1   0  -0.538  -4.9028  -0.5350  -0.6337
 BYD  OAM  O  O     0  -0.465   3.3811  -1.2497   0.7725
 BYD  OAN  O  OH1   0  -0.537   4.9084   0.7593  -0.2219
 BYD  HAA  H  HCR6  0   0.274  -1.3821  -2.0424   0.0835
 BYD  HAB  H  HCR6  0   0.272   1.0511  -2.2166   0.1075
 BYD  HAD  H  HCR6  0   0.273   1.3528   2.0568   0.3948
 BYD  HAE  H  HCR6  0   0.272  -1.0774   2.2278   0.3848
 BYD  HAI  H  HNH1  0   0.420  -3.1084  -1.2247  -1.1805
 BYD  HAL  H  HNH1  0   0.425   3.1291   1.5159  -0.7711
 BYD  HAJ  H  HOH1  0   0.481  -5.3153  -1.1441  -0.0079
 BYD  HAN  H  HOH1  0   0.480   5.2628   0.3107  -1.0015

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
 BYD  OAN  NAL  single    1.358  0.020  1.358
 BYD  NAL  CAK  single    1.343  0.020  1.343
 BYD  OAM  CAK  double    1.219  0.020  1.219
 BYD  CAK  CAC  single    1.495  0.020  1.495
 BYD  CAD  CAC  aromatic  1.393  0.020  1.393
 BYD  CAD  CAE  aromatic  1.385  0.020  1.385
 BYD  CAC  CAB  aromatic  1.391  0.020  1.391
 BYD  CAE  CAF  aromatic  1.391  0.020  1.391
 BYD  CAB  CAA  aromatic  1.384  0.020  1.384
 BYD  CAF  CAA  aromatic  1.394  0.020  1.394
 BYD  CAF  CAG  single    1.494  0.020  1.494
 BYD  OAH  CAG  double    1.217  0.020  1.217
 BYD  CAG  NAI  single    1.350  0.020  1.350
 BYD  NAI  OAJ  single    1.362  0.020  1.362
 BYD  CAA  HAA  single    0.930  0.020  1.080
 BYD  CAB  HAB  single    0.930  0.020  1.080
 BYD  CAD  HAD  single    0.930  0.020  1.080
 BYD  CAE  HAE  single    0.930  0.020  1.080
 BYD  NAI  HAI  single    0.890  0.020  1.040
 BYD  NAL  HAL  single    0.860  0.020  1.020
 BYD  OAJ  HAJ  single    0.850  0.020  0.980
 BYD  OAN  HAN  single    0.850  0.020  0.980

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
 BYD  HAA  CAA  CAF  120.84  3.000
 BYD  HAA  CAA  CAB  118.86  3.000
 BYD  CAF  CAA  CAB  120.28  3.000
 BYD  HAB  CAB  CAC  120.09  3.000
 BYD  HAB  CAB  CAA  119.52  3.000
 BYD  CAC  CAB  CAA  120.39  3.000
 BYD  CAK  CAC  CAD  122.70  3.000
 BYD  CAD  CAC  CAB  119.30  3.000
 BYD  CAK  CAC  CAB  117.93  3.000
 BYD  HAD  CAD  CAE  118.63  3.000
 BYD  HAD  CAD  CAC  121.04  3.000
 BYD  CAE  CAD  CAC  120.30  3.000
 BYD  HAE  CAE  CAF  120.12  3.000
 BYD  HAE  CAE  CAD  119.51  3.000
 BYD  CAF  CAE  CAD  120.37  3.000
 BYD  CAG  CAF  CAE  118.05  3.000
 BYD  CAG  CAF  CAA  122.59  3.000
 BYD  CAE  CAF  CAA  119.32  3.000
 BYD  OAH  CAG  NAI  123.80  3.000
 BYD  NAI  CAG  CAF  113.98  3.000
 BYD  OAH  CAG  CAF  122.20  3.000
 BYD  OAM  CAK  NAL  123.70  3.000
 BYD  OAM  CAK  CAC  121.98  3.000
 BYD  NAL  CAK  CAC  114.31  3.000
 BYD  HAI  NAI  OAJ  113.92  3.000
 BYD  HAI  NAI  CAG  121.41  3.000
 BYD  OAJ  NAI  CAG  118.68  3.000
 BYD  HAL  NAL  OAN  115.42  3.000
 BYD  HAL  NAL  CAK  123.94  3.000
 BYD  OAN  NAL  CAK  120.19  3.000
 BYD  HAJ  OAJ  NAI  105.93  3.000
 BYD  HAN  OAN  NAL  106.54  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
 BYD  CONST_01  CAD  CAC  CAB  CAA    0.00   0.0  0
 BYD  CONST_02  CAD  CAE  CAF  CAA    0.00   0.0  0
 BYD  CONST_03  CAE  CAD  CAC  CAB    0.00   0.0  0
 BYD  CONST_04  CAE  CAF  CAA  CAB    0.00   0.0  0
 BYD  CONST_05  CAF  CAE  CAD  CAC    0.00   0.0  0
 BYD  CONST_06  CAF  CAA  CAB  CAC    0.00   0.0  0
 BYD  CONST_07  CAK  CAC  CAB  CAA  180.00   0.0  0
 BYD  CONST_08  CAG  CAF  CAA  CAB  180.00   0.0  0
 BYD  CONST_09  CAG  CAF  CAE  CAD  180.00   0.0  0
 BYD  CONST_10  CAK  CAC  CAD  CAE  180.00   0.0  0
 BYD  CONST_11  HAE  CAE  CAF  CAA  180.00   0.0  0
 BYD  CONST_12  HAD  CAD  CAC  CAB  180.00   0.0  0
 BYD  CONST_13  HAA  CAA  CAB  CAC  180.00   0.0  0
 BYD  CONST_14  HAB  CAB  CAC  CAD  180.00   0.0  0
 BYD  CONST_15  OAN  NAL  CAK  CAC  180.00   0.0  0
 BYD  CONST_16  OAJ  NAI  CAG  CAF  180.00   0.0  0
 BYD  CONST_17  HAL  NAL  CAK  CAC    0.00   0.0  0
 BYD  CONST_19  OAJ  NAI  CAG  OAH    0.00   0.0  0
 BYD  CONST_20  OAN  NAL  CAK  OAM    0.00   0.0  0
 BYD  Var_01    OAH  CAG  CAF  CAA  148.22  30.0  2
 BYD  Var_02    NAL  CAK  CAC  CAB  147.88  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
 BYD  plan-1  CAA  0.020
 BYD  plan-1  CAB  0.020
 BYD  plan-1  CAC  0.020
 BYD  plan-1  CAD  0.020
 BYD  plan-1  CAE  0.020
 BYD  plan-1  CAF  0.020
 BYD  plan-1  CAG  0.020
 BYD  plan-1  CAK  0.020
 BYD  plan-1  HAA  0.020
 BYD  plan-1  HAB  0.020
 BYD  plan-1  HAD  0.020
 BYD  plan-1  HAE  0.020
 BYD  plan-2  CAF  0.020
 BYD  plan-2  CAG  0.020
 BYD  plan-2  NAI  0.020
 BYD  plan-2  OAH  0.020
 BYD  plan-2  OAJ  0.020
 BYD  plan-2  HAI  0.020
 BYD  plan-3  CAC  0.020
 BYD  plan-3  CAK  0.020
 BYD  plan-3  NAL  0.020
 BYD  plan-3  OAM  0.020
 BYD  plan-3  OAN  0.020
 BYD  plan-3  HAL  0.020

