# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 15:02:24 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  32  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  -0.624   1.1853  -3.2925   0.3850
 A1Z  C02   C   CR6   0   0.372   0.6602  -2.0826   0.2220
 A1Z  C03   C   CR6   0  -0.061   1.4347  -0.9226   0.0894
 A1Z  C04   C   C     0   0.619   2.9158  -1.0155   0.1279
 A1Z  N05   N   NH1   0  -0.651   3.5771   0.1265  -0.0180
 A1Z  C06   C   CH2   0  -0.374   5.0110   0.1921  -0.0131
 A1Z  C07   C   C     0   0.524   5.4624   1.5987  -0.3131
 A1Z  O08   O   OH1   0  -0.584   6.7805   1.6789  -0.3273
 A1Z  O09   O   O     0  -0.432   4.7193   2.5247  -0.5128
 A1Z  O10   O   O     0  -0.530   3.4765  -2.1082   0.2868
 A1Z  N11   N   N     0  -0.413   0.8910   0.2797  -0.0756
 A1Z  C12   C   CR16  0  -0.121  -0.4153   0.4076  -0.1116
 A1Z  C13   C   CR6   0   0.030  -1.2863  -0.6853   0.0211
 A1Z  C21   C   CR16  0  -0.300  -0.7273  -1.9398   0.1877
 A1Z  C14   C   CR6   0   0.074  -2.7467  -0.4947  -0.0218
 A1Z  C15   C   CR16  0  -0.265  -3.3209   0.6374   0.5559
 A1Z  C16   C   CR6   0  -0.022  -4.6945   0.8059   0.5124
 A1Z  CL    CL  CL    0  -0.123  -5.3934   2.2127   1.2446
 A1Z  C18   C   CR16  0  -0.220  -5.5215  -0.1265  -0.0937
 A1Z  C19   C   CR16  0  -0.244  -4.9452  -1.2504  -0.6680
 A1Z  C20   C   CR16  0  -0.296  -3.5725  -1.4367  -0.6346
 A1Z  H011  H   HOH1  0   0.479   2.1662  -3.1819   0.3913
 A1Z  H051  H   HNH1  0   0.413   3.0399   0.9739  -0.1458
 A1Z  H061  H   HCH2  0   0.298   5.4253  -0.1108   0.9536
 A1Z  H062  H   HCH2  0   0.298   5.4399  -0.4806  -0.7615
 A1Z  H1    H   HOH1  0   0.491   7.0617   2.5850  -0.5261
 A1Z  H121  H   HCR6  0   0.270  -0.8037   1.4074  -0.2684
 A1Z  H211  H   HCR6  0   0.283  -1.3501  -2.8174   0.3125
 A1Z  H151  H   HCR6  0   0.283  -2.7040   1.3733   1.0543
 A1Z  H181  H   HCR6  0   0.285  -6.5926   0.0200  -0.1197
 A1Z  H191  H   HCR6  0   0.274  -5.5762  -1.9841  -1.1513
 A1Z  H201  H   HCR6  0   0.267  -3.1427  -2.3102  -1.1070

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   double    1.204  0.020  1.204
 A1Z  O08  C07   single    1.321  0.020  1.321
 A1Z  C07  C06   single    1.507  0.020  1.507
 A1Z  O10  C04   double    1.238  0.020  1.238
 A1Z  C06  N05   single    1.435  0.020  1.435
 A1Z  C04  N05   single    1.328  0.020  1.328
 A1Z  C04  C03   single    1.485  0.020  1.485
 A1Z  N11  C03   aromatic  1.330  0.020  1.330
 A1Z  N11  C12   aromatic  1.313  0.020  1.313
 A1Z  C03  C02   aromatic  1.401  0.020  1.401
 A1Z  C12  C13   aromatic  1.404  0.020  1.404
 A1Z  C02  O01   single    1.329  0.020  1.329
 A1Z  C02  C21   aromatic  1.395  0.020  1.395
 A1Z  C13  C21   aromatic  1.383  0.020  1.383
 A1Z  C13  C14   single    1.473  0.020  1.473
 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  O08  H1    single    0.850  0.020  0.980
 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   106.94  3.000
 A1Z  C21   C02  C03   117.56  3.000
 A1Z  C21   C02  O01   119.28  3.000
 A1Z  C03   C02  O01   123.16  3.000
 A1Z  N11   C03  C04   117.89  3.000
 A1Z  N11   C03  C02   122.30  3.000
 A1Z  C04   C03  C02   119.81  3.000
 A1Z  O10   C04  N05   123.20  3.000
 A1Z  N05   C04  C03   116.12  3.000
 A1Z  O10   C04  C03   120.68  3.000
 A1Z  H051  N05  C06   119.52  3.000
 A1Z  H051  N05  C04   118.03  3.000
 A1Z  C06   N05  C04   122.44  3.000
 A1Z  H062  C06  H061  106.60  3.000
 A1Z  H062  C06  C07   108.67  3.000
 A1Z  H061  C06  C07   108.70  3.000
 A1Z  H062  C06  N05   111.18  3.000
 A1Z  H061  C06  N05   111.62  3.000
 A1Z  C07   C06  N05   109.94  3.000
 A1Z  O09   C07  O08   124.58  3.000
 A1Z  O08   C07  C06   110.96  3.000
 A1Z  O09   C07  C06   124.46  3.000
 A1Z  H1    O08  C07   110.39  3.000
 A1Z  C12   N11  C03   119.88  3.000
 A1Z  H121  C12  C13   120.63  3.000
 A1Z  H121  C12  N11   116.76  3.000
 A1Z  C13   C12  N11   122.60  3.000
 A1Z  C14   C13  C21   121.42  3.000
 A1Z  C14   C13  C12   120.76  3.000
 A1Z  C21   C13  C12   117.82  3.000
 A1Z  H211  C21  C13   121.07  3.000
 A1Z  H211  C21  C02   119.08  3.000
 A1Z  C13   C21  C02   119.84  3.000
 A1Z  C20   C14  C15   119.11  3.000
 A1Z  C15   C14  C13   120.07  3.000
 A1Z  C20   C14  C13   120.82  3.000
 A1Z  H151  C15  C16   119.82  3.000
 A1Z  H151  C15  C14   120.55  3.000
 A1Z  C16   C15  C14   119.62  3.000
 A1Z  C18   C16  CL    119.36  3.000
 A1Z  CL    C16  C15   119.05  3.000
 A1Z  C18   C16  C15   121.59  3.000
 A1Z  H181  C18  C19   120.74  3.000
 A1Z  H181  C18  C16   120.70  3.000
 A1Z  C19   C18  C16   118.56  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   119.44  3.000
 A1Z  H201  C20  C14   120.13  3.000
 A1Z  C19   C20  C14   120.42  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  CONST_36  H1    O08  C07  C06  180.00   0.0  0
 A1Z  Var_01    O10   C04  C03  C02   -0.57  30.0  2
 A1Z  Var_02    C07   C06  N05  C04  175.31  30.0  2
 A1Z  Var_03    O09   C07  C06  N05    0.66  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
 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
 A1Z  plan-4  H1    0.020

