# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 23:40:15 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 2-chloro-5-nitro-N-(pyridin-4-yl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(Cl)c(c1)C(=O)Nc2ccncc2
#
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
 EEY  EEY  2-chloro-5-nitro-N-(pyridin-4-yl)benzamide  ligand  27  19  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EEY
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
 EEY  C10  C   C      0   0.519  -0.6155   0.6444   0.4592
 EEY  N12  N   NH1    0  -0.734  -1.3660  -0.2861  -0.1841
 EEY  C13  C   CR6    0   0.470  -2.7288  -0.5346  -0.0677
 EEY  C15  C   CR16   0  -0.060  -4.6054  -1.8532  -0.7528
 EEY  C17  C   CR16   0  -0.068  -4.9399  -0.2072   0.7592
 EEY  C01  C   CR16   0  -0.267   3.6036   0.3769  -0.2893
 EEY  C02  C   CR16   0  -0.190   2.9457   1.5753  -0.4946
 EEY  C03  C   CR6    0  -0.074   1.5796   1.6638  -0.2731
 EEY  C04  C   CR6    0   0.024   0.8471   0.5515   0.1410
 EEY  C05  C   CR16   0  -0.296   1.5066  -0.6536   0.3311
 EEY  C06  C   CR6    0   0.285   2.8735  -0.7257   0.1222
 EEY  C14  C   CR16   0  -0.416  -3.2565  -1.5713  -0.8395
 EEY  C18  C   CR16   0  -0.373  -3.6052   0.1692   0.7569
 EEY  N07  N   N      1   0.329   3.5554  -1.9928   0.3410
 EEY  N16  N   N      0  -0.414  -5.4511  -1.1913   0.0313
 EEY  O08  O   O     -1  -0.370   2.8918  -2.9376   0.6942
 EEY  O09  O   O      0  -0.368   4.7477  -2.0299   0.1562
 EEY  O11  O   O      0  -0.420  -1.0406   1.4707   1.2363
 EEY  H1   H   HNH1   0   0.434  -0.8847  -0.8655  -0.8568
 EEY  H2   H   HCR6   0   0.270  -5.0209  -2.6576  -1.3491
 EEY  H3   H   HCR6   0   0.268  -5.6312   0.3319   1.3975
 EEY  H4   H   HCR6   0   0.316   4.6693   0.3205  -0.4542
 EEY  H5   H   HCR6   0   0.308   3.4990   2.4422  -0.8261
 EEY  H6   H   HCR6   0   0.319   0.9536  -1.5229   0.6594
 EEY  H7   H   HCR6   0   0.288  -2.6237  -2.1513  -1.4995
 EEY  H8   H   HCR6   0   0.294  -3.2855   0.9872   1.3797
 EEY  CL1  CL  CL     0  -0.073   0.8010   3.1672  -0.5672

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
 EEY  C17  C18  aromatic  1.387  0.020  1.387
 EEY  C17  N16  aromatic  1.327  0.020  1.327
 EEY  C18  C13  aromatic  1.394  0.020  1.394
 EEY  N16  C15  aromatic  1.330  0.020  1.330
 EEY  C13  C14  aromatic  1.396  0.020  1.396
 EEY  C13  N12  single    1.390  0.020  1.390
 EEY  C15  C14  aromatic  1.381  0.020  1.381
 EEY  O11  C10  double    1.211  0.020  1.211
 EEY  C10  N12  single    1.357  0.020  1.357
 EEY  C10  C04  single    1.500  0.020  1.500
 EEY  C03  C04  aromatic  1.395  0.020  1.395
 EEY  C03  C02  aromatic  1.387  0.020  1.387
 EEY  C04  C05  aromatic  1.387  0.020  1.387
 EEY  C02  C01  aromatic  1.382  0.020  1.382
 EEY  C05  C06  aromatic  1.385  0.020  1.385
 EEY  C01  C06  aromatic  1.385  0.020  1.385
 EEY  C06  N07  single    1.455  0.020  1.455
 EEY  N07  O09  double    1.207  0.020  1.207
 EEY  N07  O08  single    1.207  0.020  1.207
 EEY  C03  CL1  single    1.718  0.020  1.718
 EEY  N12  H1   single    0.860  0.020  1.020
 EEY  C15  H2   single    0.930  0.020  1.080
 EEY  C17  H3   single    0.930  0.020  1.080
 EEY  C01  H4   single    0.930  0.020  1.080
 EEY  C02  H5   single    0.930  0.020  1.080
 EEY  C05  H6   single    0.930  0.020  1.080
 EEY  C14  H7   single    0.930  0.020  1.080
 EEY  C18  H8   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
 EEY  O11  C10  C04  121.37  3.000
 EEY  C04  C10  N12  113.34  3.000
 EEY  O11  C10  N12  125.28  3.000
 EEY  H1   N12  C13  114.86  3.000
 EEY  H1   N12  C10  116.45  3.000
 EEY  C13  N12  C10  128.67  3.000
 EEY  C18  C13  C14  117.67  3.000
 EEY  C14  C13  N12  117.19  3.000
 EEY  C18  C13  N12  125.14  3.000
 EEY  H2   C15  N16  116.74  3.000
 EEY  H2   C15  C14  119.43  3.000
 EEY  N16  C15  C14  123.83  3.000
 EEY  H3   C17  N16  116.50  3.000
 EEY  H3   C17  C18  118.65  3.000
 EEY  N16  C17  C18  124.85  3.000
 EEY  H4   C01  C06  121.60  3.000
 EEY  H4   C01  C02  119.49  3.000
 EEY  C06  C01  C02  118.91  3.000
 EEY  H5   C02  C03  120.15  3.000
 EEY  H5   C02  C01  119.82  3.000
 EEY  C03  C02  C01  120.03  3.000
 EEY  CL1  C03  C04  120.70  3.000
 EEY  CL1  C03  C02  118.35  3.000
 EEY  C04  C03  C02  120.93  3.000
 EEY  C05  C04  C03  118.94  3.000
 EEY  C05  C04  C10  119.24  3.000
 EEY  C03  C04  C10  121.72  3.000
 EEY  H6   C05  C06  120.59  3.000
 EEY  H6   C05  C04  119.80  3.000
 EEY  C06  C05  C04  119.61  3.000
 EEY  N07  C06  C05  119.02  3.000
 EEY  N07  C06  C01  119.39  3.000
 EEY  C05  C06  C01  121.58  3.000
 EEY  H7   C14  C15  119.99  3.000
 EEY  H7   C14  C13  120.92  3.000
 EEY  C15  C14  C13  119.09  3.000
 EEY  H8   C18  C17  119.41  3.000
 EEY  H8   C18  C13  122.62  3.000
 EEY  C17  C18  C13  117.97  3.000
 EEY  O09  N07  O08  124.30  3.000
 EEY  O08  N07  C06  117.89  3.000
 EEY  O09  N07  C06  117.81  3.000
 EEY  C17  N16  C15  116.60  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
 EEY  CONST_01  N16  C17  C18  C13    0.00   0.0  0
 EEY  CONST_02  N16  C15  C14  C13    0.00   0.0  0
 EEY  CONST_03  C18  C17  N16  C15    0.00   0.0  0
 EEY  CONST_04  C18  C13  C14  C15    0.00   0.0  0
 EEY  CONST_05  C14  C13  C18  C17    0.00   0.0  0
 EEY  CONST_06  C14  C15  N16  C17    0.00   0.0  0
 EEY  CONST_07  C04  C03  C02  C01    0.00   0.0  0
 EEY  CONST_08  C04  C05  C06  C01    0.00   0.0  0
 EEY  CONST_09  C05  C04  C03  C02    0.00   0.0  0
 EEY  CONST_10  C05  C06  C01  C02    0.00   0.0  0
 EEY  CONST_11  C06  C05  C04  C03    0.00   0.0  0
 EEY  CONST_12  C06  C01  C02  C03    0.00   0.0  0
 EEY  CONST_13  C02  C03  C04  C10  180.00   0.0  0
 EEY  CONST_14  C06  C05  C04  C10  180.00   0.0  0
 EEY  CONST_15  C17  C18  C13  N12  180.00   0.0  0
 EEY  CONST_16  C15  C14  C13  N12  180.00   0.0  0
 EEY  CONST_17  CL1  C03  C02  C01  180.00   0.0  0
 EEY  CONST_18  N07  C06  C01  C02  180.00   0.0  0
 EEY  CONST_19  N07  C06  C05  C04  180.00   0.0  0
 EEY  CONST_20  CL1  C03  C04  C05  180.00   0.0  0
 EEY  CONST_21  H3   C17  C18  C13  180.00   0.0  0
 EEY  CONST_22  H2   C15  C14  C13  180.00   0.0  0
 EEY  CONST_23  H6   C05  C06  C01  180.00   0.0  0
 EEY  CONST_24  H4   C01  C02  C03  180.00   0.0  0
 EEY  CONST_25  H5   C02  C03  C04  180.00   0.0  0
 EEY  CONST_26  H8   C18  C13  C14  180.00   0.0  0
 EEY  CONST_27  H7   C14  C13  C18  180.00   0.0  0
 EEY  CONST_28  C04  C10  N12  C13  180.00   0.0  0
 EEY  CONST_29  C18  C13  N12  C10    0.00   0.0  0
 EEY  CONST_30  C14  C13  N12  C10  180.00   0.0  0
 EEY  CONST_31  O09  N07  C06  C01    0.00   0.0  0
 EEY  CONST_32  O08  N07  C06  C01  180.00   0.0  0
 EEY  CONST_33  O09  N07  C06  C05  180.00   0.0  0
 EEY  CONST_34  O08  N07  C06  C05    0.00   0.0  0
 EEY  CONST_35  H1   N12  C13  C14    0.00   0.0  0
 EEY  CONST_36  O11  C10  N12  C13    0.00   0.0  0
 EEY  Var_01    C03  C04  C10  N12  128.66  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
 EEY  plan-1  N12  0.020
 EEY  plan-1  C13  0.020
 EEY  plan-1  C15  0.020
 EEY  plan-1  C17  0.020
 EEY  plan-1  C14  0.020
 EEY  plan-1  C18  0.020
 EEY  plan-1  N16  0.020
 EEY  plan-1  H2   0.020
 EEY  plan-1  H3   0.020
 EEY  plan-1  H7   0.020
 EEY  plan-1  H8   0.020
 EEY  plan-2  C10  0.020
 EEY  plan-2  C01  0.020
 EEY  plan-2  C02  0.020
 EEY  plan-2  C03  0.020
 EEY  plan-2  C04  0.020
 EEY  plan-2  C05  0.020
 EEY  plan-2  C06  0.020
 EEY  plan-2  N07  0.020
 EEY  plan-2  H4   0.020
 EEY  plan-2  H5   0.020
 EEY  plan-2  H6   0.020
 EEY  plan-2  CL1  0.020
 EEY  plan-3  C10  0.020
 EEY  plan-3  N12  0.020
 EEY  plan-3  C13  0.020
 EEY  plan-3  C04  0.020
 EEY  plan-3  O11  0.020
 EEY  plan-3  H1   0.020
 EEY  plan-4  C06  0.020
 EEY  plan-4  N07  0.020
 EEY  plan-4  O08  0.020
 EEY  plan-4  O09  0.020

