# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 00:10:00 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: N-(4-nitrophenyl)cyclopropanecarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(NC(=O)C2CC2)cc1
#
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
 1EB  1EB  N-(4-nitrophenyl)cyclopropanecarboxamide  ligand  25  15  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1EB
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
 1EB  C1   C  CR16   0  -0.314   0.3456  -0.8648   0.2127
 1EB  C2   C  CR16   0  -0.255   1.7195  -1.0096   0.2246
 1EB  C3   C  CR6    0   0.234   2.5397   0.0966   0.0570
 1EB  C4   C  CR16   0  -0.255   1.9941   1.3623  -0.1239
 1EB  C5   C  CR16   0  -0.349   0.6255   1.5065  -0.1343
 1EB  C6   C  CR6    0   0.410  -0.2221   0.4023   0.0325
 1EB  N7   N  NH1    0  -0.760  -1.5822   0.6563   0.0108
 1EB  C8   C  C      0   0.602  -2.6298  -0.2194   0.0958
 1EB  O9   O  O      0  -0.462  -2.4915  -1.4226   0.2135
 1EB  C10  C  CH1    0  -0.440  -3.9590   0.4351   0.0298
 1EB  C11  C  CH2    0  -0.462  -5.0704  -0.3064  -0.6717
 1EB  C12  C  CH2    0  -0.461  -5.0875  -0.1958   0.8059
 1EB  N13  N  N      1   0.327   3.9748  -0.0676   0.0695
 1EB  O14  O  O     -1  -0.388   4.4230  -1.1805   0.2308
 1EB  O15  O  O      0  -0.388   4.6639   0.9162  -0.0825
 1EB  H1   H  HCR6   0   0.299  -0.2712  -1.7371   0.3446
 1EB  H2   H  HCR6   0   0.298   2.1377  -1.9953   0.3680
 1EB  H3   H  HCR6   0   0.300   2.6203   2.2322  -0.2574
 1EB  H4   H  HCR6   0   0.289   0.2014   2.4926  -0.2777
 1EB  H5   H  HNH1   0   0.425  -1.8289   1.6284  -0.1019
 1EB  H6   H  HCH1   0   0.289  -3.9706   1.5154  -0.0535
 1EB  H7   H  HCH2   0   0.269  -5.7599   0.2960  -1.2474
 1EB  H8   H  HCH2   0   0.263  -4.8247  -1.2643  -1.1110
 1EB  H9   H  HCH2   0   0.263  -4.8532  -1.0781   1.3867
 1EB  H10  H  HCH2   0   0.269  -5.7915   0.4812   1.2707

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
 1EB  O15  N13  double    1.211  0.020  1.211
 1EB  N13  O14  single    1.211  0.020  1.211
 1EB  N13  C3   single    1.445  0.020  1.445
 1EB  C4   C3   aromatic  1.390  0.020  1.390
 1EB  C4   C5   aromatic  1.376  0.020  1.376
 1EB  C3   C2   aromatic  1.387  0.020  1.387
 1EB  C5   C6   aromatic  1.402  0.020  1.402
 1EB  C2   C1   aromatic  1.382  0.020  1.382
 1EB  C6   C1   aromatic  1.400  0.020  1.400
 1EB  C6   N7   single    1.384  0.020  1.384
 1EB  N7   C8   single    1.368  0.020  1.368
 1EB  C8   O9   double    1.217  0.020  1.217
 1EB  C8   C10  single    1.483  0.020  1.483
 1EB  C10  C11  single    1.509  0.020  1.509
 1EB  C10  C12  single    1.508  0.020  1.508
 1EB  C11  C12  single    1.482  0.020  1.482
 1EB  C1   H1   single    0.930  0.020  1.080
 1EB  C2   H2   single    0.930  0.020  1.080
 1EB  C4   H3   single    0.930  0.020  1.080
 1EB  C5   H4   single    0.930  0.020  1.080
 1EB  N7   H5   single    0.860  0.020  1.020
 1EB  C10  H6   single    0.970  0.020  1.090
 1EB  C11  H7   single    0.970  0.020  1.090
 1EB  C11  H8   single    0.970  0.020  1.090
 1EB  C12  H9   single    0.970  0.020  1.090
 1EB  C12  H10  single    0.970  0.020  1.090

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
 1EB  H1   C1   C6   121.12  3.000
 1EB  H1   C1   C2   118.93  3.000
 1EB  C6   C1   C2   119.95  3.000
 1EB  H2   C2   C3   120.98  3.000
 1EB  H2   C2   C1   118.80  3.000
 1EB  C3   C2   C1   120.22  3.000
 1EB  N13  C3   C4   119.64  3.000
 1EB  C4   C3   C2   120.65  3.000
 1EB  N13  C3   C2   119.71  3.000
 1EB  H3   C4   C5   119.42  3.000
 1EB  H3   C4   C3   121.46  3.000
 1EB  C5   C4   C3   119.12  3.000
 1EB  H4   C5   C6   119.74  3.000
 1EB  H4   C5   C4   119.07  3.000
 1EB  C6   C5   C4   121.19  3.000
 1EB  N7   C6   C5   116.60  3.000
 1EB  N7   C6   C1   124.52  3.000
 1EB  C5   C6   C1   118.88  3.000
 1EB  H5   N7   C8   115.87  3.000
 1EB  H5   N7   C6   114.76  3.000
 1EB  C8   N7   C6   129.36  3.000
 1EB  C10  C8   O9   122.86  3.000
 1EB  C10  C8   N7   113.64  3.000
 1EB  O9   C8   N7   123.50  3.000
 1EB  H6   C10  C12  116.66  3.000
 1EB  H6   C10  C11  116.50  3.000
 1EB  C12  C10  C11   58.84  3.000
 1EB  H6   C10  C8   116.94  3.000
 1EB  C12  C10  C8   117.60  3.000
 1EB  C11  C10  C8   117.64  3.000
 1EB  H8   C11  H7   114.94  3.000
 1EB  H8   C11  C12  118.26  3.000
 1EB  H7   C11  C12  118.81  3.000
 1EB  H8   C11  C10  117.16  3.000
 1EB  H7   C11  C10  116.32  3.000
 1EB  C12  C11  C10   60.55  3.000
 1EB  H10  C12  H9   114.88  3.000
 1EB  H10  C12  C11  118.86  3.000
 1EB  H9   C12  C11  118.15  3.000
 1EB  H10  C12  C10  116.51  3.000
 1EB  H9   C12  C10  117.08  3.000
 1EB  C11  C12  C10   60.62  3.000
 1EB  O15  N13  O14  123.58  3.000
 1EB  O14  N13  C3   118.26  3.000
 1EB  O15  N13  C3   118.16  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
 1EB  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 1EB  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 1EB  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 1EB  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 1EB  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 1EB  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 1EB  CONST_07  N13  C3   C2   C1    180.00   0.0  0
 1EB  CONST_08  N7   C6   C1   C2    180.00   0.0  0
 1EB  CONST_09  N7   C6   C5   C4    180.00   0.0  0
 1EB  CONST_10  N13  C3   C4   C5    180.00   0.0  0
 1EB  CONST_11  H4   C5   C6   C1    180.00   0.0  0
 1EB  CONST_12  H3   C4   C3   C2    180.00   0.0  0
 1EB  CONST_13  H1   C1   C2   C3    180.00   0.0  0
 1EB  CONST_14  H2   C2   C3   C4    180.00   0.0  0
 1EB  CONST_15  C10  C8   N7   C6    180.00   0.0  0
 1EB  CONST_16  C8   N7   C6   C1      0.00   0.0  0
 1EB  CONST_17  O15  N13  C3   C2    180.00   0.0  0
 1EB  CONST_18  O14  N13  C3   C2      0.00   0.0  0
 1EB  CONST_19  O15  N13  C3   C4      0.00   0.0  0
 1EB  CONST_20  O14  N13  C3   C4    180.00   0.0  0
 1EB  CONST_21  C8   N7   C6   C5    180.00   0.0  0
 1EB  CONST_22  H5   N7   C6   C1    180.00   0.0  0
 1EB  CONST_23  O9   C8   N7   C6      0.00   0.0  0
 1EB  Var_01    C12  C11  C10  C8    107.12  30.0  1
 1EB  Var_02    H9   C12  C11  C10  -106.94  30.0  1
 1EB  Var_03    C11  C10  C8   N7    144.85  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 1EB  chir_01  C10  C8  C11  C12  both

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
 1EB  plan-1  C1   0.020
 1EB  plan-1  C2   0.020
 1EB  plan-1  C3   0.020
 1EB  plan-1  C4   0.020
 1EB  plan-1  C5   0.020
 1EB  plan-1  C6   0.020
 1EB  plan-1  N7   0.020
 1EB  plan-1  N13  0.020
 1EB  plan-1  H1   0.020
 1EB  plan-1  H2   0.020
 1EB  plan-1  H3   0.020
 1EB  plan-1  H4   0.020
 1EB  plan-2  C3   0.020
 1EB  plan-2  N13  0.020
 1EB  plan-2  O14  0.020
 1EB  plan-2  O15  0.020
 1EB  plan-3  C6   0.020
 1EB  plan-3  N7   0.020
 1EB  plan-3  C8   0.020
 1EB  plan-3  O9   0.020
 1EB  plan-3  C10  0.020
 1EB  plan-3  H5   0.020

