# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 19:41:51 2021
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-[(~{E})-[3,5-bis(bromanyl)-2-oxidanyl-phenyl]methylideneamino]oxypropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCO\N=C\c1cc(Br)cc(Br)c1O
#
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
 ND5  ND5  '3-[(~{E})-[3,5-bis(bromanyl)-2-oxidanyl-phenyl]methylideneamino]oxypropanoic acid'  ligand  26  17  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ND5
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
 ND5  C01   C   CR6   0   0.387   0.2057   1.1561   7.7219
 ND5  C02   C   CR6   0  -0.062  -0.2966   0.0561   7.0085
 ND5  C03   C   CR16  0  -0.256  -0.8195  -1.0354   7.6981
 ND5  C04   C   CR6   0  -0.115  -0.8459  -1.0412   9.0782
 ND5  C05   C   CR16  0  -0.211  -0.3588   0.0348   9.8045
 ND5  C06   C   CR6   0  -0.222   0.1601   1.1201   9.1192
 ND5  C09   C   C1    0  -0.043  -0.2692   0.0763   5.5441
 ND5  C13   C   CH2   0  -0.176  -0.9985  -1.9533   2.8806
 ND5  C14   C   CH2   0  -0.612  -2.4824  -2.1972   3.0526
 ND5  C15   C   C     0   0.555  -3.3364  -1.0918   2.4925
 ND5  N11   N   N     0  -0.094  -0.6193  -0.9586   4.8975
 ND5  O07   O   OH1   0  -0.600   0.7003   2.1723   7.0120
 ND5  O12   O   O2    0  -0.385  -0.5533  -0.7848   3.5525
 ND5  O16   O   O     0  -0.443  -2.9736  -0.2886   1.6700
 ND5  O17   O   OH1   0  -0.593  -4.5666  -1.1173   2.9915
 ND5  BR1   BR  BR    0  -0.029  -1.5601  -2.5253   9.9958
 ND5  BR8   BR  BR    0  -0.005   0.8208   2.5828  10.1087
 ND5  H03   H   HCR6  0   0.288  -1.2065  -1.8726   7.1333
 ND5  H05   H   HCR6  0   0.307  -0.3820   0.0345  10.8857
 ND5  H09   H   H     0   0.264   0.0467   0.9832   5.0352
 ND5  H131  H   HCH2  0   0.247  -0.4409  -2.8268   3.2283
 ND5  H132  H   HCH2  0   0.252  -0.7462  -1.7899   1.8337
 ND5  H142  H   HCH2  0   0.282  -2.7320  -2.3724   4.1005
 ND5  H141  H   HCH2  0   0.300  -2.7461  -3.1193   2.5246
 ND5  HO07  H   HOH1  0   0.484   1.0433   2.8855   7.5652
 ND5  H1    H   HOH1  0   0.479  -5.1032  -0.4204   2.5850

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
 ND5  O16  C15   double    1.205  0.020  1.205
 ND5  O17  C15   single    1.328  0.020  1.328
 ND5  C15  C14   single    1.505  0.020  1.505
 ND5  C14  C13   single    1.514  0.020  1.514
 ND5  C13  O12   single    1.419  0.020  1.419
 ND5  O12  N11   single    1.358  0.020  1.358
 ND5  N11  C09   double    1.269  0.020  1.269
 ND5  C09  C02   single    1.465  0.020  1.465
 ND5  C02  C03   aromatic  1.393  0.020  1.393
 ND5  C02  C01   aromatic  1.404  0.020  1.404
 ND5  O07  C01   single    1.335  0.020  1.335
 ND5  C03  C04   aromatic  1.380  0.020  1.380
 ND5  C01  C06   aromatic  1.399  0.020  1.399
 ND5  C04  BR1   single    1.885  0.020  1.885
 ND5  C04  C05   aromatic  1.387  0.020  1.387
 ND5  C06  C05   aromatic  1.384  0.020  1.384
 ND5  C06  BR8   single    1.886  0.020  1.886
 ND5  C03  H03   single    0.930  0.020  1.080
 ND5  C05  H05   single    0.930  0.020  1.080
 ND5  C09  H09   single    0.930  0.020  1.080
 ND5  C13  H131  single    0.970  0.020  1.090
 ND5  C13  H132  single    0.970  0.020  1.090
 ND5  C14  H142  single    0.970  0.020  1.090
 ND5  C14  H141  single    0.970  0.020  1.090
 ND5  O07  HO07  single    0.850  0.020  0.980
 ND5  O17  H1    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
 ND5  O07   C01  C06   124.27  3.000
 ND5  C06   C01  C02   118.42  3.000
 ND5  O07   C01  C02   117.31  3.000
 ND5  C09   C02  C03   120.85  3.000
 ND5  C03   C02  C01   119.78  3.000
 ND5  C09   C02  C01   119.37  3.000
 ND5  H03   C03  C04   120.80  3.000
 ND5  H03   C03  C02   118.84  3.000
 ND5  C04   C03  C02   120.36  3.000
 ND5  BR1   C04  C05   119.28  3.000
 ND5  C05   C04  C03   120.91  3.000
 ND5  BR1   C04  C03   119.81  3.000
 ND5  H05   C05  C06   120.21  3.000
 ND5  H05   C05  C04   121.05  3.000
 ND5  C06   C05  C04   118.73  3.000
 ND5  BR8   C06  C05   118.67  3.000
 ND5  BR8   C06  C01   119.54  3.000
 ND5  C05   C06  C01   121.80  3.000
 ND5  H09   C09  N11   121.46  3.000
 ND5  H09   C09  C02   119.01  3.000
 ND5  N11   C09  C02   119.52  3.000
 ND5  H132  C13  H131  107.91  3.000
 ND5  H132  C13  O12   105.00  3.000
 ND5  H131  C13  O12   110.32  3.000
 ND5  H132  C13  C14   111.13  3.000
 ND5  H131  C13  C14   109.58  3.000
 ND5  O12   C13  C14   112.73  3.000
 ND5  H141  C14  H142  105.83  3.000
 ND5  H141  C14  C15   107.60  3.000
 ND5  H142  C14  C15   110.21  3.000
 ND5  H141  C14  C13   108.49  3.000
 ND5  H142  C14  C13   111.05  3.000
 ND5  C15   C14  C13   113.30  3.000
 ND5  O17   C15  O16   123.23  3.000
 ND5  O17   C15  C14   111.82  3.000
 ND5  O16   C15  C14   124.93  3.000
 ND5  O12   N11  C09   112.76  3.000
 ND5  HO07  O07  C01   112.92  3.000
 ND5  N11   O12  C13   110.38  3.000
 ND5  H1    O17  C15   109.97  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
 ND5  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 ND5  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 ND5  CONST_03  C05  C04  C03  C02    0.00   0.0  0
 ND5  CONST_04  C05  C06  C01  C02    0.00   0.0  0
 ND5  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 ND5  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 ND5  CONST_07  BR1  C04  C03  C02  180.00   0.0  0
 ND5  CONST_08  BR8  C06  C01  C02  180.00   0.0  0
 ND5  CONST_09  O07  C01  C02  C03  180.00   0.0  0
 ND5  CONST_10  C09  C02  C03  C04  180.00   0.0  0
 ND5  CONST_11  BR8  C06  C05  C04  180.00   0.0  0
 ND5  CONST_12  O07  C01  C06  C05  180.00   0.0  0
 ND5  CONST_13  C09  C02  C01  C06  180.00   0.0  0
 ND5  CONST_14  BR1  C04  C05  C06  180.00   0.0  0
 ND5  CONST_15  H03  C03  C02  C01  180.00   0.0  0
 ND5  CONST_16  H05  C05  C06  C01  180.00   0.0  0
 ND5  CONST_17  H1   O17  C15  C14  180.00   0.0  0
 ND5  Var_01    N11  C09  C02  C01  174.22  30.0  2
 ND5  Var_02    O16  C15  C14  C13   20.24  30.0  2
 ND5  Var_03    O12  C13  C14  C15   61.57  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
 ND5  plan-1  C01  0.020
 ND5  plan-1  C02  0.020
 ND5  plan-1  C03  0.020
 ND5  plan-1  C04  0.020
 ND5  plan-1  C05  0.020
 ND5  plan-1  C06  0.020
 ND5  plan-1  C09  0.020
 ND5  plan-1  O07  0.020
 ND5  plan-1  BR1  0.020
 ND5  plan-1  BR8  0.020
 ND5  plan-1  H03  0.020
 ND5  plan-1  H05  0.020
 ND5  plan-2  C14  0.020
 ND5  plan-2  C15  0.020
 ND5  plan-2  O16  0.020
 ND5  plan-2  O17  0.020
 ND5  plan-2  H1   0.020
 ND5  plan-3  C02  0.020
 ND5  plan-3  C09  0.020
 ND5  plan-3  N11  0.020
 ND5  plan-3  O12  0.020
 ND5  plan-3  H09  0.020

