# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 13:26:05 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-[[5-(3-chlorophenyl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)c1ncc(cc1O)c2cccc(Cl)c2
#
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
 A1Z  A1Z  '2-[[5-(3-chlorophenyl)-3-oxidanyl-pyridin-2-yl]carbonylamino]ethanoic acid'  ligand  31  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A1Z
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
 A1Z  O01   O   OH1    0  -0.629   1.2029  -3.2566  -0.7035
 A1Z  C02   C   CR6    0   0.368   0.6731  -2.0709  -0.4213
 A1Z  C03   C   CR6    0  -0.067   1.4498  -0.9284  -0.1816
 A1Z  C04   C   C      0   0.609   2.9341  -1.0223  -0.2433
 A1Z  N05   N   NH1    0  -0.630   3.6028   0.0882   0.0035
 A1Z  C06   C   CH2    0  -0.417   5.0382   0.2018   0.0049
 A1Z  C07   C   C      0   0.403   5.4664   1.6325   0.3946
 A1Z  O08   O   OC    -1  -0.607   6.6925   1.8294   0.4140
 A1Z  O09   O   O      0  -0.597   4.5573   2.4443   0.6507
 A1Z  O10   O   O      0  -0.547   3.4760  -2.1084  -0.5149
 A1Z  N11   N   N      0  -0.409   0.9058   0.2502   0.1038
 A1Z  C12   C   CR16   0  -0.125  -0.4014   0.3716   0.1603
 A1Z  C13   C   CR6    0   0.029  -1.2726  -0.7026  -0.0730
 A1Z  C21   C   CR16   0  -0.302  -0.7140  -1.9349  -0.3649
 A1Z  C14   C   CR6    0   0.074  -2.7332  -0.5206  -0.0004
 A1Z  C15   C   CR16   0  -0.265  -3.3158   0.6597  -0.4614
 A1Z  C16   C   CR6    0  -0.021  -4.6894   0.8183  -0.3898
 A1Z  CL    CL  CL     0  -0.124  -5.3984   2.2860  -0.9786
 A1Z  C18   C   CR16   0  -0.221  -5.5086  -0.1710   0.1309
 A1Z  C19   C   CR16   0  -0.244  -4.9240  -1.3432   0.5886
 A1Z  C20   C   CR16   0  -0.296  -3.5511  -1.5202   0.5259
 A1Z  H011  H   HOH1   0   0.477   2.1872  -3.1283  -0.6986
 A1Z  H051  H   HNH1   0   0.394   3.0929   0.9341   0.2277
 A1Z  H061  H   HCH2   0   0.249   5.4810  -0.5082   0.7096
 A1Z  H062  H   HCH2   0   0.249   5.4482  -0.0399  -0.9802
 A1Z  H121  H   HCR6   0   0.267  -0.7895   1.3502   0.4187
 A1Z  H211  H   HCR6   0   0.280  -1.3378  -2.7964  -0.5707
 A1Z  H151  H   HCR6   0   0.282  -2.7054   1.4408  -0.8952
 A1Z  H181  H   HCR6   0   0.284  -6.5798  -0.0320   0.1797
 A1Z  H191  H   HCR6   0   0.274  -5.5486  -2.1228   1.0037
 A1Z  H201  H   HCR6   0   0.267  -3.1137  -2.4333   0.9075

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
 A1Z  O09  C07   deloc     1.245  0.020  1.245
 A1Z  O08  C07   deloc     1.242  0.020  1.242
 A1Z  C07  C06   single    1.543  0.020  1.543
 A1Z  O10  C04   double    1.244  0.020  1.244
 A1Z  C06  N05   single    1.440  0.020  1.440
 A1Z  C04  N05   single    1.320  0.020  1.320
 A1Z  C04  C03   single    1.488  0.020  1.488
 A1Z  N11  C03   aromatic  1.329  0.020  1.329
 A1Z  N11  C12   aromatic  1.314  0.020  1.314
 A1Z  C03  C02   aromatic  1.402  0.020  1.402
 A1Z  C12  C13   aromatic  1.403  0.020  1.403
 A1Z  C02  O01   single    1.329  0.020  1.329
 A1Z  C02  C21   aromatic  1.395  0.020  1.395
 A1Z  C13  C21   aromatic  1.384  0.020  1.384
 A1Z  C13  C14   single    1.474  0.020  1.474
 A1Z  C20  C14   aromatic  1.395  0.020  1.395
 A1Z  C20  C19   aromatic  1.386  0.020  1.386
 A1Z  C14  C15   aromatic  1.395  0.020  1.395
 A1Z  C19  C18   aromatic  1.388  0.020  1.388
 A1Z  C15  C16   aromatic  1.385  0.020  1.385
 A1Z  C18  C16   aromatic  1.386  0.020  1.386
 A1Z  C16  CL    single    1.733  0.020  1.733
 A1Z  O01  H011  single    0.850  0.020  0.980
 A1Z  N05  H051  single    0.860  0.020  1.020
 A1Z  C06  H061  single    0.970  0.020  1.090
 A1Z  C06  H062  single    0.970  0.020  1.090
 A1Z  C12  H121  single    0.930  0.020  1.080
 A1Z  C21  H211  single    0.930  0.020  1.080
 A1Z  C15  H151  single    0.930  0.020  1.080
 A1Z  C18  H181  single    0.930  0.020  1.080
 A1Z  C19  H191  single    0.930  0.020  1.080
 A1Z  C20  H201  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
 A1Z  H011  O01  C02   106.20  3.000
 A1Z  C21   C02  C03   117.68  3.000
 A1Z  C21   C02  O01   119.47  3.000
 A1Z  C03   C02  O01   122.85  3.000
 A1Z  N11   C03  C04   118.23  3.000
 A1Z  N11   C03  C02   122.18  3.000
 A1Z  C04   C03  C02   119.60  3.000
 A1Z  O10   C04  N05   123.70  3.000
 A1Z  N05   C04  C03   116.39  3.000
 A1Z  O10   C04  C03   119.91  3.000
 A1Z  H051  N05  C06   115.83  3.000
 A1Z  H051  N05  C04   119.28  3.000
 A1Z  C06   N05  C04   124.88  3.000
 A1Z  H062  C06  H061  106.55  3.000
 A1Z  H062  C06  C07   109.16  3.000
 A1Z  H061  C06  C07   109.07  3.000
 A1Z  H062  C06  N05   110.81  3.000
 A1Z  H061  C06  N05   110.66  3.000
 A1Z  C07   C06  N05   110.49  3.000
 A1Z  O09   C07  O08   127.89  3.000
 A1Z  O08   C07  C06   115.14  3.000
 A1Z  O09   C07  C06   116.97  3.000
 A1Z  C12   N11  C03   119.89  3.000
 A1Z  H121  C12  C13   120.58  3.000
 A1Z  H121  C12  N11   116.73  3.000
 A1Z  C13   C12  N11   122.68  3.000
 A1Z  C14   C13  C21   121.36  3.000
 A1Z  C14   C13  C12   120.85  3.000
 A1Z  C21   C13  C12   117.79  3.000
 A1Z  H211  C21  C13   121.05  3.000
 A1Z  H211  C21  C02   119.17  3.000
 A1Z  C13   C21  C02   119.78  3.000
 A1Z  C20   C14  C15   119.10  3.000
 A1Z  C15   C14  C13   120.15  3.000
 A1Z  C20   C14  C13   120.75  3.000
 A1Z  H151  C15  C16   119.84  3.000
 A1Z  H151  C15  C14   120.52  3.000
 A1Z  C16   C15  C14   119.62  3.000
 A1Z  C18   C16  CL    119.36  3.000
 A1Z  CL    C16  C15   119.03  3.000
 A1Z  C18   C16  C15   121.60  3.000
 A1Z  H181  C18  C19   120.73  3.000
 A1Z  H181  C18  C16   120.71  3.000
 A1Z  C19   C18  C16   118.55  3.000
 A1Z  H191  C19  C20   119.83  3.000
 A1Z  H191  C19  C18   119.48  3.000
 A1Z  C20   C19  C18   120.69  3.000
 A1Z  H201  C20  C19   119.49  3.000
 A1Z  H201  C20  C14   120.06  3.000
 A1Z  C19   C20  C14   120.44  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
 A1Z  CONST_01  C12   N11  C03  C02     0.00   0.0  0
 A1Z  CONST_02  C12   C13  C21  C02     0.00   0.0  0
 A1Z  CONST_03  C14   C13  C21  C02   180.00   0.0  0
 A1Z  CONST_04  C13   C12  N11  C03     0.00   0.0  0
 A1Z  CONST_05  C13   C21  C02  C03     0.00   0.0  0
 A1Z  CONST_06  C21   C02  C03  N11     0.00   0.0  0
 A1Z  CONST_07  C21   C13  C12  N11     0.00   0.0  0
 A1Z  CONST_08  C14   C13  C12  N11   180.00   0.0  0
 A1Z  CONST_11  C19   C20  C14  C13   180.00   0.0  0
 A1Z  CONST_12  C16   C15  C14  C13   180.00   0.0  0
 A1Z  CONST_15  C18   C19  C20  C14     0.00   0.0  0
 A1Z  CONST_16  C18   C16  C15  C14     0.00   0.0  0
 A1Z  CONST_17  C19   C20  C14  C15     0.00   0.0  0
 A1Z  CONST_18  C19   C18  C16  C15     0.00   0.0  0
 A1Z  CONST_19  C20   C14  C15  C16     0.00   0.0  0
 A1Z  CONST_20  C20   C19  C18  C16     0.00   0.0  0
 A1Z  CONST_21  N11   C03  C02  O01   180.00   0.0  0
 A1Z  CONST_22  C13   C21  C02  O01   180.00   0.0  0
 A1Z  CONST_23  C12   N11  C03  C04   180.00   0.0  0
 A1Z  CONST_24  C21   C02  C03  C04   180.00   0.0  0
 A1Z  CONST_25  CL    C16  C15  C14   180.00   0.0  0
 A1Z  CONST_26  C19   C18  C16  CL    180.00   0.0  0
 A1Z  CONST_27  H121  C12  N11  C03   180.00   0.0  0
 A1Z  CONST_28  H211  C21  C02  C03   180.00   0.0  0
 A1Z  CONST_29  H201  C20  C14  C13     0.00   0.0  0
 A1Z  CONST_30  H151  C15  C14  C13     0.00   0.0  0
 A1Z  CONST_31  H191  C19  C20  C14   180.00   0.0  0
 A1Z  CONST_32  H181  C18  C16  C15   180.00   0.0  0
 A1Z  CONST_33  C06   N05  C04  C03   180.00   0.0  0
 A1Z  CONST_34  H051  N05  C04  C03     0.00   0.0  0
 A1Z  CONST_35  O10   C04  N05  C06     0.00   0.0  0
 A1Z  Var_01    O10   C04  C03  C02     0.46  30.0  2
 A1Z  Var_02    C07   C06  N05  C04  -177.53  30.0  1
 A1Z  Var_03    O09   C07  C06  N05     0.53  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
 A1Z  plan-1  O01   0.020
 A1Z  plan-1  C02   0.020
 A1Z  plan-1  C03   0.020
 A1Z  plan-1  C04   0.020
 A1Z  plan-1  N11   0.020
 A1Z  plan-1  C12   0.020
 A1Z  plan-1  C13   0.020
 A1Z  plan-1  C21   0.020
 A1Z  plan-1  C14   0.020
 A1Z  plan-1  H121  0.020
 A1Z  plan-1  H211  0.020
 A1Z  plan-2  C13   0.020
 A1Z  plan-2  C14   0.020
 A1Z  plan-2  C15   0.020
 A1Z  plan-2  C16   0.020
 A1Z  plan-2  CL    0.020
 A1Z  plan-2  C18   0.020
 A1Z  plan-2  C19   0.020
 A1Z  plan-2  C20   0.020
 A1Z  plan-2  H151  0.020
 A1Z  plan-2  H181  0.020
 A1Z  plan-2  H191  0.020
 A1Z  plan-2  H201  0.020
 A1Z  plan-3  C03   0.020
 A1Z  plan-3  C04   0.020
 A1Z  plan-3  N05   0.020
 A1Z  plan-3  C06   0.020
 A1Z  plan-3  O10   0.020
 A1Z  plan-3  H051  0.020
 A1Z  plan-4  C06   0.020
 A1Z  plan-4  C07   0.020
 A1Z  plan-4  O08   0.020
 A1Z  plan-4  O09   0.020

