# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 01:02:23 2022
#   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  25  17  .  2022-03-23  2022-03-23
;
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   0.385   0.0742   1.1530   7.7354
 ND5  C02   C   CR6    0  -0.060  -0.1613  -0.0743   7.0958
 ND5  C03   C   CR16   0  -0.253  -0.3636  -1.2233   7.8552
 ND5  C04   C   CR6    0  -0.117  -0.3356  -1.1613   9.2348
 ND5  C05   C   CR16   0  -0.211  -0.1084   0.0387   9.8893
 ND5  C06   C   CR6    0  -0.222   0.0923   1.1821   9.1329
 ND5  C09   C   C1     0  -0.059  -0.1949  -0.1289   5.6323
 ND5  C13   C   CH2    0  -0.165  -1.3978  -2.1340   3.1201
 ND5  C14   C   CH2    0  -0.601  -2.8847  -1.8726   3.1831
 ND5  C15   C   C      0   0.409  -3.3314  -0.5889   2.4482
 ND5  N11   N   N      0  -0.086  -0.7290  -1.1305   5.0622
 ND5  O07   O   OH1    0  -0.597   0.2511   2.2210   6.9540
 ND5  O12   O   O2     0  -0.386  -0.6355  -1.0845   3.7142
 ND5  O16   O   O      0  -0.608  -2.7077  -0.2965   1.4085
 ND5  O17   O   OC    -1  -0.612  -4.2988   0.0239   2.9402
 ND5  BR1   BR  BR     0  -0.032  -0.5958  -2.7320  10.2472
 ND5  BR8   BR  BR     0  -0.009   0.3851   2.8171  10.0279
 ND5  H03   H   HCR6   0   0.285  -0.5272  -2.1630   7.3453
 ND5  H05   H   HCR6   0   0.305  -0.0843   0.0903  10.9696
 ND5  H09   H   H      0   0.259   0.2473   0.6845   5.0620
 ND5  H131  H   HCH2   0   0.217  -1.1399  -3.0851   3.5960
 ND5  H132  H   HCH2   0   0.226  -1.0581  -2.1699   2.0858
 ND5  H142  H   HCH2   0   0.216  -3.2245  -1.8609   4.2217
 ND5  H141  H   HCH2   0   0.233  -3.3865  -2.7269   2.7133
 ND5  HO07  H   HOH1   0   0.482   0.4535   3.0231   7.4522

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   deloc     1.247  0.020  1.247
 ND5  O17  C15   deloc     1.246  0.020  1.246
 ND5  C15  C14   single    1.545  0.020  1.545
 ND5  C14  C13   single    1.511  0.020  1.511
 ND5  C13  O12   single    1.427  0.020  1.427
 ND5  O12  N11   single    1.352  0.020  1.352
 ND5  N11  C09   double    1.270  0.020  1.270
 ND5  C09  C02   single    1.465  0.020  1.465
 ND5  C02  C03   aromatic  1.392  0.020  1.392
 ND5  C02  C01   aromatic  1.404  0.020  1.404
 ND5  O07  C01   single    1.335  0.020  1.335
 ND5  C03  C04   aromatic  1.381  0.020  1.381
 ND5  C01  C06   aromatic  1.398  0.020  1.398
 ND5  C04  BR1   single    1.887  0.020  1.887
 ND5  C04  C05   aromatic  1.386  0.020  1.386
 ND5  C06  C05   aromatic  1.386  0.020  1.386
 ND5  C06  BR8   single    1.887  0.020  1.887
 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

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   124.52  3.000
 ND5  C06   C01  C02   118.42  3.000
 ND5  O07   C01  C02   117.06  3.000
 ND5  C09   C02  C03   120.72  3.000
 ND5  C03   C02  C01   119.83  3.000
 ND5  C09   C02  C01   119.45  3.000
 ND5  H03   C03  C04   120.86  3.000
 ND5  H03   C03  C02   118.81  3.000
 ND5  C04   C03  C02   120.32  3.000
 ND5  BR1   C04  C05   119.35  3.000
 ND5  C05   C04  C03   120.93  3.000
 ND5  BR1   C04  C03   119.72  3.000
 ND5  H05   C05  C06   120.17  3.000
 ND5  H05   C05  C04   121.11  3.000
 ND5  C06   C05  C04   118.72  3.000
 ND5  BR8   C06  C05   118.60  3.000
 ND5  BR8   C06  C01   119.62  3.000
 ND5  C05   C06  C01   121.78  3.000
 ND5  H09   C09  N11   121.70  3.000
 ND5  H09   C09  C02   119.13  3.000
 ND5  N11   C09  C02   119.17  3.000
 ND5  H132  C13  H131  108.11  3.000
 ND5  H132  C13  O12   104.66  3.000
 ND5  H131  C13  O12   109.41  3.000
 ND5  H132  C13  C14   110.62  3.000
 ND5  H131  C13  C14   111.35  3.000
 ND5  O12   C13  C14   112.40  3.000
 ND5  H141  C14  H142  105.86  3.000
 ND5  H141  C14  C15   108.13  3.000
 ND5  H142  C14  C15   110.69  3.000
 ND5  H141  C14  C13   107.32  3.000
 ND5  H142  C14  C13   110.33  3.000
 ND5  C15   C14  C13   114.10  3.000
 ND5  O17   C15  O16   127.01  3.000
 ND5  O17   C15  C14   116.43  3.000
 ND5  O16   C15  C14   116.53  3.000
 ND5  O12   N11  C09   113.05  3.000
 ND5  HO07  O07  C01   112.97  3.000
 ND5  N11   O12  C13   110.68  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  Var_01    N11  C09  C02  C01  -162.40  30.0  2
 ND5  Var_02    O16  C15  C14  C13    35.03  30.0  2
 ND5  Var_03    O12  C13  C14  C15    60.60  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-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

