# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:06:18 2020
#   Inital geometry file: a 86 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cc(ccc1NN2CCOCC2)C(F)(F)F
#
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
 2XY  2XY  'None                     '  ligand  32  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2XY
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
 2XY  C4   C  CH2    0  -0.300  15.8274  -40.7603  11.2065
 2XY  C1   C  CH2    0  -0.301  15.3444  -43.1168  11.3392
 2XY  C2   C  CH2    0  -0.195  16.6822  -43.3848  10.6748
 2XY  O2   O  O     -1  -0.391   9.7994  -40.8652  12.9405
 2XY  C3   C  CH2    0  -0.197  17.1502  -41.1144  10.5510
 2XY  O3   O  O      0  -0.421  11.8767  -41.0333  13.3680
 2XY  C5   C  CR6    0   0.409  12.5247  -41.4905  10.7025
 2XY  O1   O  O2     0  -0.482  17.6180  -42.3744  10.9745
 2XY  N1   N  NT     0  -0.295  14.8602  -41.8091  10.9150
 2XY  N2   N  NH1    0  -0.536  13.6283  -41.5217  11.4655
 2XY  C6   C  CR16   0  -0.337  12.6372  -41.6958   9.3040
 2XY  C7   C  CR16   0  -0.242  11.5481  -41.6748   8.4817
 2XY  C8   C  CR6    0  -0.218  10.2586  -41.4490   8.9911
 2XY  C9   C  CT     0   1.063   9.0975  -41.4374   8.0579
 2XY  F2   F  F      0  -0.301   7.9359  -41.2216   8.6815
 2XY  F3   F  F      0  -0.316   8.9792  -42.5993   7.3963
 2XY  F1   F  F      0  -0.316   9.2229  -40.4863   7.1188
 2XY  C10  C  CR16   0  -0.358  10.1070  -41.2443  10.3367
 2XY  C11  C  CR6    0   0.222  11.2114  -41.2611  11.1937
 2XY  N3   N  N      1   0.349  10.9435  -41.0397  12.5837
 2XY  H4   H  HCH2   0   0.219  15.9698  -40.6312  12.2901
 2XY  H4A  H  HCH2   0   0.259  15.4648  -39.8150  10.8002
 2XY  H1   H  HCH2   0   0.257  14.6284  -43.8801  11.0299
 2XY  H1A  H  HCH2   0   0.221  15.4502  -43.1744  12.4330
 2XY  H2   H  HCH2   0   0.247  17.0892  -44.3301  11.0353
 2XY  H2A  H  HCH2   0   0.211  16.5388  -43.4702   9.5887
 2XY  H3   H  HCH2   0   0.211  17.0313  -41.0929   9.4590
 2XY  H3A  H  HCH2   0   0.247  17.9036  -40.3738  10.8214
 2XY  HN2  H  HNH1   0   0.406  13.5466  -41.4161  12.4679
 2XY  H6   H  HCR6   0   0.295  13.6198  -41.8727   8.8944
 2XY  H7   H  HCR6   0   0.287  11.7021  -41.8366   7.4224
 2XY  H10  H  HCR6   0   0.304   9.1302  -41.0645  10.7599

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
 2XY  C4   C3   single    1.518  0.020  1.518
 2XY  C4   N1   single    1.456  0.020  1.456
 2XY  C4   H4   single    0.970  0.020  1.090
 2XY  C4   H4A  single    0.970  0.020  1.090
 2XY  C1   C2   single    1.518  0.020  1.518
 2XY  C1   N1   single    1.458  0.020  1.458
 2XY  C1   H1   single    0.970  0.020  1.090
 2XY  C1   H1A  single    0.970  0.020  1.090
 2XY  C2   O1   single    1.409  0.020  1.409
 2XY  C2   H2   single    0.970  0.020  1.090
 2XY  C2   H2A  single    0.970  0.020  1.090
 2XY  O2   N3   single    1.211  0.020  1.211
 2XY  C3   O1   single    1.409  0.020  1.409
 2XY  C3   H3   single    0.970  0.020  1.090
 2XY  C3   H3A  single    0.970  0.020  1.090
 2XY  O3   N3   double    1.219  0.020  1.219
 2XY  C5   N2   single    1.342  0.020  1.342
 2XY  C5   C6   aromatic  1.418  0.020  1.418
 2XY  C5   C11  aromatic  1.421  0.020  1.421
 2XY  N1   N2   single    1.380  0.020  1.380
 2XY  N2   HN2  single    0.860  0.020  1.020
 2XY  C6   C7   aromatic  1.365  0.020  1.365
 2XY  C6   H6   single    0.930  0.020  1.080
 2XY  C7   C8   aromatic  1.405  0.020  1.405
 2XY  C7   H7   single    0.930  0.020  1.080
 2XY  C8   C9   single    1.490  0.020  1.490
 2XY  C8   C10  aromatic  1.370  0.020  1.370
 2XY  C9   F2   single    1.336  0.020  1.336
 2XY  C9   F3   single    1.342  0.020  1.342
 2XY  C9   F1   single    1.343  0.020  1.343
 2XY  C10  C11  aromatic  1.398  0.020  1.398
 2XY  C10  H10  single    0.930  0.020  1.080
 2XY  C11  N3   single    1.433  0.020  1.433

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
 2XY  H4A  C4   H4   107.94  3.000
 2XY  H4A  C4   N1   109.19  3.000
 2XY  H4   C4   N1   111.56  3.000
 2XY  H4A  C4   C3   109.32  3.000
 2XY  H4   C4   C3   109.86  3.000
 2XY  N1   C4   C3   108.93  3.000
 2XY  H1A  C1   H1   107.96  3.000
 2XY  H1A  C1   N1   111.60  3.000
 2XY  H1   C1   N1   109.09  3.000
 2XY  H1A  C1   C2   109.95  3.000
 2XY  H1   C1   C2   109.32  3.000
 2XY  N1   C1   C2   108.90  3.000
 2XY  H2A  C2   H2   107.94  3.000
 2XY  H2A  C2   O1   110.64  3.000
 2XY  H2   C2   O1   107.65  3.000
 2XY  H2A  C2   C1   109.36  3.000
 2XY  H2   C2   C1   109.72  3.000
 2XY  O1   C2   C1   111.45  3.000
 2XY  H3A  C3   H3   107.93  3.000
 2XY  H3A  C3   O1   107.66  3.000
 2XY  H3   C3   O1   110.61  3.000
 2XY  H3A  C3   C4   109.67  3.000
 2XY  H3   C3   C4   109.29  3.000
 2XY  O1   C3   C4   111.59  3.000
 2XY  C11  C5   C6   115.96  3.000
 2XY  C11  C5   N2   124.57  3.000
 2XY  C6   C5   N2   119.48  3.000
 2XY  C3   O1   C2   110.90  3.000
 2XY  N2   N1   C1   111.55  3.000
 2XY  N2   N1   C4   111.30  3.000
 2XY  C1   N1   C4   111.55  3.000
 2XY  HN2  N2   N1   119.30  3.000
 2XY  HN2  N2   C5   119.65  3.000
 2XY  N1   N2   C5   120.82  3.000
 2XY  H6   C6   C7   120.03  3.000
 2XY  H6   C6   C5   118.06  3.000
 2XY  C7   C6   C5   121.91  3.000
 2XY  H7   C7   C8   120.63  3.000
 2XY  H7   C7   C6   118.27  3.000
 2XY  C8   C7   C6   121.10  3.000
 2XY  C10  C8   C9   121.88  3.000
 2XY  C10  C8   C7   118.81  3.000
 2XY  C9   C8   C7   119.32  3.000
 2XY  F1   C9   F3   106.06  3.000
 2XY  F1   C9   F2   107.06  3.000
 2XY  F3   C9   F2   107.06  3.000
 2XY  F1   C9   C8   111.77  3.000
 2XY  F3   C9   C8   111.76  3.000
 2XY  F2   C9   C8   112.74  3.000
 2XY  H10  C10  C11  118.46  3.000
 2XY  H10  C10  C8   120.67  3.000
 2XY  C11  C10  C8   120.87  3.000
 2XY  N3   C11  C10  116.43  3.000
 2XY  N3   C11  C5   122.22  3.000
 2XY  C10  C11  C5   121.35  3.000
 2XY  C11  N3   O3   118.80  3.000
 2XY  C11  N3   O2   118.99  3.000
 2XY  O3   N3   O2   122.20  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
 2XY  CONST_01  C8   C7   C6   C5     0.00   0.0  0
 2XY  CONST_02  C8   C10  C11  C5     0.00   0.0  0
 2XY  CONST_03  C10  C11  C5   C6     0.00   0.0  0
 2XY  CONST_04  C10  C8   C7   C6     0.00   0.0  0
 2XY  CONST_05  C11  C5   C6   C7     0.00   0.0  0
 2XY  CONST_06  C11  C10  C8   C7     0.00   0.0  0
 2XY  CONST_07  C7   C6   C5   N2   180.00   0.0  0
 2XY  CONST_08  C10  C11  C5   N2   180.00   0.0  0
 2XY  CONST_09  N3   C11  C5   C6   180.00   0.0  0
 2XY  CONST_10  C9   C8   C7   C6   180.00   0.0  0
 2XY  CONST_11  N3   C11  C10  C8   180.00   0.0  0
 2XY  CONST_12  C11  C10  C8   C9   180.00   0.0  0
 2XY  CONST_15  C6   C5   N2   N1     0.00   0.0  0
 2XY  CONST_16  C11  C5   N2   N1   180.00   0.0  0
 2XY  CONST_17  H7   C7   C6   C5   180.00   0.0  0
 2XY  CONST_18  H10  C10  C11  C5   180.00   0.0  0
 2XY  CONST_19  H6   C6   C7   C8   180.00   0.0  0
 2XY  CONST_20  C5   C11  N3   O2   180.00   0.0  0
 2XY  CONST_21  C10  C11  N3   O2     0.00   0.0  0
 2XY  CONST_22  C5   C11  N3   O3     0.00   0.0  0
 2XY  CONST_23  C10  C11  N3   O3   180.00   0.0  0
 2XY  CONST_24  HN2  N2   C5   C6   180.00   0.0  0
 2XY  Var_01    C2   C1   N1   C4   -56.19  30.0  1
 2XY  Var_02    C3   C4   N1   C1    55.98  30.0  1
 2XY  Var_03    N1   C1   C2   O1    57.03  30.0  1
 2XY  Var_04    N1   C4   C3   O1   -56.71  30.0  1
 2XY  Var_05    H3   C3   O1   C2   -63.16  30.0  1
 2XY  Var_06    H2   C2   O1   C3  -179.24  30.0  1
 2XY  Var_07    F2   C9   C8   C7   179.53  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
 2XY  plan-1  C5   0.020
 2XY  plan-1  N2   0.020
 2XY  plan-1  C6   0.020
 2XY  plan-1  C7   0.020
 2XY  plan-1  C8   0.020
 2XY  plan-1  C9   0.020
 2XY  plan-1  C10  0.020
 2XY  plan-1  C11  0.020
 2XY  plan-1  N3   0.020
 2XY  plan-1  H6   0.020
 2XY  plan-1  H7   0.020
 2XY  plan-1  H10  0.020
 2XY  plan-2  C5   0.020
 2XY  plan-2  N1   0.020
 2XY  plan-2  N2   0.020
 2XY  plan-2  HN2  0.020
 2XY  plan-3  O2   0.020
 2XY  plan-3  O3   0.020
 2XY  plan-3  C11  0.020
 2XY  plan-3  N3   0.020

