# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:03:32 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: N-{[3,5-dibromo-2-(methoxymethoxy)phenyl]methyl}-2-nitrobenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCOc1c(Br)cc(Br)cc1CNC(=O)c2ccccc2[N+]([O-])=O
#
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
 FY1  FY1  N-{[3,5-dibromo-2-(methoxymethoxy)phenyl]methyl}-2-nitrobenzamide  ligand  39  25  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FY1
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
 FY1  N16  N   N      1   0.329  -4.1336  -1.5203   0.3606
 FY1  C15  C   CR6    0   0.230  -4.4941  -0.1497   0.6940
 FY1  C2   C   CR6    0  -0.195   2.1984  -0.7723   0.4398
 FY1  C1   C   CR6    0   0.393   1.0370  -0.4108  -0.2409
 FY1  C10  C   CR6    0  -0.046  -3.7001   0.9057   0.2549
 FY1  C9   C   C      0   0.548  -2.6213   0.7106  -0.7696
 FY1  C12  C   CR16   0  -0.220  -5.1483   2.3995   1.4831
 FY1  C14  C   CR16   0  -0.254  -5.6010   0.0421   1.4989
 FY1  C8   C   CH3    0  -0.409  -0.1380  -4.1943  -0.9148
 FY1  C7   C   CH2    0  -0.355  -0.3424   1.3688  -1.4057
 FY1  C6   C   CR6    0   0.019   0.9241   0.8927  -0.7388
 FY1  C5   C   CR16   0  -0.284   1.9744   1.7853  -0.5792
 FY1  C4   C   CR6    0  -0.107   3.1301   1.3908   0.0763
 FY1  C3   C   CR16   0  -0.225   3.2515   0.1182   0.6045
 FY1  O17  O   O      0  -0.475  -2.8480   0.0650  -1.7800
 FY1  O25  O   O2     0  -0.469   0.5275  -3.1679  -1.6255
 FY1  C21  C   CH2    0   0.052  -0.1218  -1.9559  -1.6163
 FY1  BR1  BR  BR     0  -0.003   2.3473  -2.4813   1.2056
 FY1  BR2  BR  BR     0  -0.026   4.5493   2.6148   0.2787
 FY1  N8   N   NH1    0  -0.615  -1.4719   1.3445  -0.5046
 FY1  O19  O   O      0  -0.357  -2.9723  -1.8287   0.4615
 FY1  O18  O   O     -1  -0.372  -5.0238  -2.2703   0.0383
 FY1  C11  C   CR16   0  -0.276  -4.0496   2.1873   0.6597
 FY1  C13  C   CR16   0  -0.256  -5.9235   1.3304   1.9011
 FY1  H1   H   HCR6   0   0.282  -5.4023   3.4061   1.7856
 FY1  H2   H   HCR6   0   0.301  -6.1937  -0.7984   1.8325
 FY1  H3   H   HCH3   0   0.219  -0.1361  -4.0228   0.1636
 FY1  H4   H   HCH3   0   0.215  -1.1762  -4.2992  -1.2471
 FY1  H5   H   HCH3   0   0.236   0.3876  -5.1255  -1.1178
 FY1  H6   H   HCH2   0   0.287  -0.1853   2.3878  -1.7649
 FY1  H7   H   HCH2   0   0.278  -0.5936   0.7710  -2.2799
 FY1  H8   H   HCR6   0   0.289   1.8745   2.7917  -0.9650
 FY1  H9   H   HCR6   0   0.303   4.1450  -0.1831   1.1344
 FY1  H10  H   HCH2   0   0.231   0.3114  -1.3571  -2.4214
 FY1  H11  H   HCH2   0   0.223  -1.1975  -2.0677  -1.7720
 FY1  H12  H   HNH1   0   0.415  -1.3773   1.8343   0.3719
 FY1  H13  H   HCR6   0   0.288  -3.4763   3.0353   0.3085
 FY1  H14  H   HCR6   0   0.284  -6.7805   1.4904   2.5403
 FY1  O20  O   O2     0  -0.478   0.0071  -1.2729  -0.3715

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
 FY1  O17  C9   double    1.220  0.020  1.220
 FY1  O19  N16  double    1.206  0.020  1.206
 FY1  N16  O18  single    1.208  0.020  1.208
 FY1  N16  C15  single    1.456  0.020  1.456
 FY1  C9   C10  single    1.501  0.020  1.501
 FY1  C9   N8   single    1.339  0.020  1.339
 FY1  BR2  C4   single    1.885  0.020  1.885
 FY1  C15  C10  aromatic  1.392  0.020  1.392
 FY1  C15  C14  aromatic  1.382  0.020  1.382
 FY1  C5   C4   aromatic  1.386  0.020  1.386
 FY1  C5   C6   aromatic  1.388  0.020  1.388
 FY1  C10  C11  aromatic  1.389  0.020  1.389
 FY1  C7   C6   single    1.508  0.020  1.508
 FY1  C7   N8   single    1.445  0.020  1.445
 FY1  C4   C3   aromatic  1.383  0.020  1.383
 FY1  C6   C1   aromatic  1.400  0.020  1.400
 FY1  C14  C13  aromatic  1.388  0.020  1.388
 FY1  C3   C2   aromatic  1.389  0.020  1.389
 FY1  C1   C2   aromatic  1.394  0.020  1.394
 FY1  C1   O20  single    1.349  0.020  1.349
 FY1  C11  C12  aromatic  1.389  0.020  1.389
 FY1  C2   BR1  single    1.879  0.020  1.879
 FY1  O20  C21  single    1.426  0.020  1.426
 FY1  C13  C12  aromatic  1.385  0.020  1.385
 FY1  C8   O25  single    1.415  0.020  1.415
 FY1  O25  C21  single    1.375  0.020  1.375
 FY1  C12  H1   single    0.930  0.020  1.080
 FY1  C14  H2   single    0.930  0.020  1.080
 FY1  C8   H3   single    0.970  0.020  1.090
 FY1  C8   H4   single    0.970  0.020  1.090
 FY1  C8   H5   single    0.970  0.020  1.090
 FY1  C7   H6   single    0.970  0.020  1.090
 FY1  C7   H7   single    0.970  0.020  1.090
 FY1  C5   H8   single    0.930  0.020  1.080
 FY1  C3   H9   single    0.930  0.020  1.080
 FY1  C21  H10  single    0.970  0.020  1.090
 FY1  C21  H11  single    0.970  0.020  1.090
 FY1  N8   H12  single    0.860  0.020  1.020
 FY1  C11  H13  single    0.930  0.020  1.080
 FY1  C13  H14  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
 FY1  O18  N16  O19  124.99  3.000
 FY1  O18  N16  C15  117.59  3.000
 FY1  O19  N16  C15  117.39  3.000
 FY1  C14  C15  C10  122.38  3.000
 FY1  C14  C15  N16  117.54  3.000
 FY1  C10  C15  N16  120.02  3.000
 FY1  BR1  C2   C3   118.35  3.000
 FY1  BR1  C2   C1   120.07  3.000
 FY1  C3   C2   C1   121.56  3.000
 FY1  O20  C1   C6   119.92  3.000
 FY1  O20  C1   C2   121.17  3.000
 FY1  C6   C1   C2   118.84  3.000
 FY1  C11  C10  C9   120.00  3.000
 FY1  C11  C10  C15  117.66  3.000
 FY1  C9   C10  C15  121.80  3.000
 FY1  N8   C9   O17  125.02  3.000
 FY1  N8   C9   C10  114.86  3.000
 FY1  O17  C9   C10  120.03  3.000
 FY1  H1   C12  C13  120.17  3.000
 FY1  H1   C12  C11  119.59  3.000
 FY1  C13  C12  C11  120.23  3.000
 FY1  H2   C14  C13  120.33  3.000
 FY1  H2   C14  C15  120.72  3.000
 FY1  C13  C14  C15  118.93  3.000
 FY1  H5   C8   H4   108.62  3.000
 FY1  H5   C8   H3   108.52  3.000
 FY1  H4   C8   H3   108.44  3.000
 FY1  H5   C8   O25  107.44  3.000
 FY1  H4   C8   O25  111.29  3.000
 FY1  H3   C8   O25  112.42  3.000
 FY1  H7   C7   H6   106.35  3.000
 FY1  H7   C7   N8   108.13  3.000
 FY1  H6   C7   N8   109.47  3.000
 FY1  H7   C7   C6   112.06  3.000
 FY1  H6   C7   C6   108.61  3.000
 FY1  N8   C7   C6   112.04  3.000
 FY1  C5   C6   C7   118.91  3.000
 FY1  C7   C6   C1   121.25  3.000
 FY1  C5   C6   C1   119.80  3.000
 FY1  H8   C5   C4   120.68  3.000
 FY1  H8   C5   C6   119.15  3.000
 FY1  C4   C5   C6   120.17  3.000
 FY1  BR2  C4   C3   119.36  3.000
 FY1  C3   C4   C5   121.04  3.000
 FY1  BR2  C4   C5   119.59  3.000
 FY1  H9   C3   C4   121.06  3.000
 FY1  H9   C3   C2   120.39  3.000
 FY1  C4   C3   C2   118.55  3.000
 FY1  C21  O25  C8   114.46  3.000
 FY1  H11  C21  H10  109.96  3.000
 FY1  H11  C21  O20  105.22  3.000
 FY1  H10  C21  O20  110.18  3.000
 FY1  H11  C21  O25  111.95  3.000
 FY1  H10  C21  O25  106.90  3.000
 FY1  O20  C21  O25  112.67  3.000
 FY1  H12  N8   C7   117.41  3.000
 FY1  H12  N8   C9   118.85  3.000
 FY1  C7   N8   C9   123.74  3.000
 FY1  H13  C11  C12  119.45  3.000
 FY1  H13  C11  C10  119.68  3.000
 FY1  C12  C11  C10  120.85  3.000
 FY1  H14  C13  C14  119.54  3.000
 FY1  H14  C13  C12  120.52  3.000
 FY1  C14  C13  C12  119.94  3.000
 FY1  C21  O20  C1   117.36  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
 FY1  CONST_01  C12  C11  C10  C15     0.00   0.0  0
 FY1  CONST_02  C12  C13  C14  C15     0.00   0.0  0
 FY1  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 FY1  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 FY1  CONST_05  C4   C5   C6   C1      0.00   0.0  0
 FY1  CONST_06  C4   C3   C2   C1      0.00   0.0  0
 FY1  CONST_07  C13  C14  C15  C10     0.00   0.0  0
 FY1  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 FY1  CONST_09  C11  C10  C15  C14     0.00   0.0  0
 FY1  CONST_10  C11  C12  C13  C14     0.00   0.0  0
 FY1  CONST_11  C3   C4   C5   C6      0.00   0.0  0
 FY1  CONST_12  C3   C2   C1   C6      0.00   0.0  0
 FY1  CONST_13  C11  C10  C15  N16   180.00   0.0  0
 FY1  CONST_14  C13  C14  C15  N16   180.00   0.0  0
 FY1  CONST_15  BR2  C4   C3   C2    180.00   0.0  0
 FY1  CONST_16  C7   C6   C1   C2    180.00   0.0  0
 FY1  CONST_17  C14  C15  C10  C9    180.00   0.0  0
 FY1  CONST_18  C12  C11  C10  C9    180.00   0.0  0
 FY1  CONST_19  C4   C5   C6   C7    180.00   0.0  0
 FY1  CONST_20  BR2  C4   C5   C6    180.00   0.0  0
 FY1  CONST_21  BR1  C2   C1   C6    180.00   0.0  0
 FY1  CONST_22  O20  C1   C6   C5    180.00   0.0  0
 FY1  CONST_23  BR1  C2   C3   C4    180.00   0.0  0
 FY1  CONST_24  O20  C1   C2   C3    180.00   0.0  0
 FY1  CONST_25  H13  C11  C10  C15   180.00   0.0  0
 FY1  CONST_26  H14  C13  C14  C15   180.00   0.0  0
 FY1  CONST_27  H8   C5   C6   C1    180.00   0.0  0
 FY1  CONST_28  H9   C3   C2   C1    180.00   0.0  0
 FY1  CONST_29  H2   C14  C15  C10   180.00   0.0  0
 FY1  CONST_30  H1   C12  C11  C10   180.00   0.0  0
 FY1  CONST_35  C7   N8   C9   C10   180.00   0.0  0
 FY1  CONST_36  H12  N8   C9   C10     0.00   0.0  0
 FY1  CONST_37  O17  C9   N8   C7      0.00   0.0  0
 FY1  Var_01    O17  C9   C10  C15    46.14  30.0  2
 FY1  Var_02    N8   C7   C6   C1     62.24  30.0  2
 FY1  Var_03    O25  C21  O20  C1     91.83  30.0  3
 FY1  Var_04    C6   C7   N8   C9   -125.76  30.0  2
 FY1  Var_05    O20  C21  O25  C8     75.66  30.0  3
 FY1  Var_06    H3   C8   O25  C21   -68.96  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
 FY1  plan-1  N16  0.020
 FY1  plan-1  C15  0.020
 FY1  plan-1  C10  0.020
 FY1  plan-1  C9   0.020
 FY1  plan-1  C12  0.020
 FY1  plan-1  C14  0.020
 FY1  plan-1  C11  0.020
 FY1  plan-1  C13  0.020
 FY1  plan-1  H1   0.020
 FY1  plan-1  H2   0.020
 FY1  plan-1  H13  0.020
 FY1  plan-1  H14  0.020
 FY1  plan-2  C2   0.020
 FY1  plan-2  C1   0.020
 FY1  plan-2  C7   0.020
 FY1  plan-2  C6   0.020
 FY1  plan-2  C5   0.020
 FY1  plan-2  C4   0.020
 FY1  plan-2  C3   0.020
 FY1  plan-2  BR1  0.020
 FY1  plan-2  BR2  0.020
 FY1  plan-2  H8   0.020
 FY1  plan-2  H9   0.020
 FY1  plan-2  O20  0.020
 FY1  plan-3  C10  0.020
 FY1  plan-3  C9   0.020
 FY1  plan-3  C7   0.020
 FY1  plan-3  O17  0.020
 FY1  plan-3  N8   0.020
 FY1  plan-3  H12  0.020
 FY1  plan-4  N16  0.020
 FY1  plan-4  C15  0.020
 FY1  plan-4  O19  0.020
 FY1  plan-4  O18  0.020

