# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 03:29:51 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-[(2-methyl-3-nitrophenyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(Nc2ccccc2C(O)=O)cccc1[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
 BNY  BNY  '2-[(2-methyl-3-nitrophenyl)amino]benzoic acid'  ligand  31  20  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_BNY
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
 BNY  O1   O  O      0  -0.580  -0.9678  -1.9381   0.6328
 BNY  C2   C  CR6    0   0.337   0.4491   0.5739  -0.0734
 BNY  C4   C  CR16   0  -0.341  -2.7446   1.9644   0.8105
 BNY  C5   C  CR16   0  -0.263  -4.1109   1.9226   0.5858
 BNY  C6   C  CR16   0  -0.267  -4.6792   0.8002  -0.0008
 BNY  C7   C  CR16   0  -0.295  -3.8672  -0.2771  -0.3264
 BNY  C11  C  CR16   0  -0.273   1.2788   0.0909  -2.2911
 BNY  C13  C  CR6    0   0.181   2.7301  -0.0189  -0.4150
 BNY  O3   O  O      0  -0.375   4.1802  -1.1413   0.9602
 BNY  N1   N  N      0   0.322   4.0693  -0.3379   0.0640
 BNY  O2   O  O      0  -0.374   5.0023   0.1940  -0.4899
 BNY  C1   C  CR6    0   0.036   1.7234   0.3320   0.4784
 BNY  C    C  CH3    0  -0.743   1.8981   0.5009   1.9583
 BNY  C12  C  CR16   0  -0.285   2.5465  -0.1311  -1.7864
 BNY  C10  C  CR16   0  -0.270   0.2426   0.4474  -1.4475
 BNY  C3   C  CR6    0   0.310  -1.9316   0.8707   0.5025
 BNY  C8   C  CR6    0  -0.099  -2.5017  -0.2856  -0.0520
 BNY  C9   C  C      0   0.384  -1.7311  -1.5808  -0.2810
 BNY  O    O  OC    -1  -0.598  -1.9758  -2.1866  -1.3415
 BNY  H1   H  HCR6   0   0.255  -2.2939   2.8575   1.2279
 BNY  H2   H  HCR6   0   0.251  -4.7233   2.7756   0.8491
 BNY  H3   H  HCR6   0   0.245  -5.7421   0.7631  -0.2016
 BNY  H4   H  HCR6   0   0.244  -4.3082  -1.1566  -0.7783
 BNY  H5   H  HCR6   0   0.267   1.1004   0.0011  -3.3540
 BNY  H6   H  HCH3   0   0.263   1.2201  -0.1695   2.4895
 BNY  H7   H  HCH3   0   0.260   2.9037   0.3081   2.3133
 BNY  H8   H  HCH3   0   0.251   1.6497   1.5192   2.2660
 BNY  H9   H  HCR6   0   0.280   3.3636  -0.4074  -2.4378
 BNY  H10  H  HCR6   0   0.277  -0.7347   0.6479  -1.8649
 BNY  H11  H  HNH1   0   0.393  -0.3181   1.6018   1.5133
 BNY  N    N  NH1    0  -0.791  -0.5689   0.9658   0.7737

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
 BNY  C5   C6   aromatic  1.388  0.020  1.388
 BNY  C5   C4   aromatic  1.385  0.020  1.385
 BNY  C6   C7   aromatic  1.388  0.020  1.388
 BNY  C4   C3   aromatic  1.397  0.020  1.397
 BNY  C10  C11  aromatic  1.383  0.020  1.383
 BNY  C10  C2   aromatic  1.395  0.020  1.395
 BNY  C11  C12  aromatic  1.382  0.020  1.382
 BNY  C7   C8   aromatic  1.393  0.020  1.393
 BNY  C3   C8   aromatic  1.403  0.020  1.403
 BNY  C3   N    single    1.393  0.020  1.393
 BNY  C8   C9   single    1.524  0.020  1.524
 BNY  C2   N    single    1.381  0.020  1.381
 BNY  C2   C1   aromatic  1.410  0.020  1.410
 BNY  C12  C13  aromatic  1.388  0.020  1.388
 BNY  C9   O1   deloc     1.243  0.020  1.243
 BNY  C9   O    deloc     1.246  0.020  1.246
 BNY  C1   C13  aromatic  1.391  0.020  1.391
 BNY  C1   C    single    1.500  0.020  1.500
 BNY  C13  N1   single    1.458  0.020  1.458
 BNY  N1   O2   double    1.208  0.020  1.208
 BNY  N1   O3   double    1.209  0.020  1.209
 BNY  C4   H1   single    0.930  0.020  1.080
 BNY  C5   H2   single    0.930  0.020  1.080
 BNY  C6   H3   single    0.930  0.020  1.080
 BNY  C7   H4   single    0.930  0.020  1.080
 BNY  C11  H5   single    0.930  0.020  1.080
 BNY  C    H6   single    0.970  0.020  1.090
 BNY  C    H7   single    0.970  0.020  1.090
 BNY  C    H8   single    0.970  0.020  1.090
 BNY  C12  H9   single    0.930  0.020  1.080
 BNY  C10  H10  single    0.930  0.020  1.080
 BNY  N    H11  single    0.860  0.020  1.020

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
 BNY  N    C2   C10  121.38  3.000
 BNY  N    C2   C1   118.36  3.000
 BNY  C10  C2   C1   120.25  3.000
 BNY  H1   C4   C3   119.20  3.000
 BNY  H1   C4   C5   119.83  3.000
 BNY  C3   C4   C5   120.97  3.000
 BNY  H2   C5   C6   120.55  3.000
 BNY  H2   C5   C4   119.65  3.000
 BNY  C6   C5   C4   119.78  3.000
 BNY  H3   C6   C7   120.30  3.000
 BNY  H3   C6   C5   120.54  3.000
 BNY  C7   C6   C5   119.16  3.000
 BNY  H4   C7   C8   118.46  3.000
 BNY  H4   C7   C6   119.35  3.000
 BNY  C8   C7   C6   122.16  3.000
 BNY  H5   C11  C10  119.82  3.000
 BNY  H5   C11  C12  119.78  3.000
 BNY  C10  C11  C12  120.39  3.000
 BNY  C12  C13  C1   124.00  3.000
 BNY  C1   C13  N1   120.60  3.000
 BNY  C12  C13  N1   115.37  3.000
 BNY  O2   N1   O3   124.17  3.000
 BNY  O3   N1   C13  118.26  3.000
 BNY  O2   N1   C13  117.54  3.000
 BNY  C    C1   C13  125.30  3.000
 BNY  C    C1   C2   118.18  3.000
 BNY  C13  C1   C2   116.50  3.000
 BNY  H8   C    H7   106.53  3.000
 BNY  H8   C    H6   107.11  3.000
 BNY  H7   C    H6   107.92  3.000
 BNY  H8   C    C1   110.88  3.000
 BNY  H7   C    C1   114.29  3.000
 BNY  H6   C    C1   109.80  3.000
 BNY  H9   C12  C13  121.07  3.000
 BNY  H9   C12  C11  120.95  3.000
 BNY  C13  C12  C11  117.97  3.000
 BNY  H10  C10  C11  119.31  3.000
 BNY  H10  C10  C2   119.80  3.000
 BNY  C11  C10  C2   120.88  3.000
 BNY  C8   C3   N    122.05  3.000
 BNY  N    C3   C4   118.23  3.000
 BNY  C8   C3   C4   119.72  3.000
 BNY  C9   C8   C3   123.65  3.000
 BNY  C9   C8   C7   118.12  3.000
 BNY  C3   C8   C7   118.10  3.000
 BNY  O    C9   C8   116.22  3.000
 BNY  O    C9   O1   127.35  3.000
 BNY  C8   C9   O1   116.38  3.000
 BNY  H11  N    C3   115.45  3.000
 BNY  H11  N    C2   116.49  3.000
 BNY  C3   N    C2   125.62  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
 BNY  CONST_01  C12  C11  C10  C2      0.00   0.0  0
 BNY  CONST_02  C12  C13  C1   C2      0.00   0.0  0
 BNY  CONST_03  C7   C6   C5   C4      0.00   0.0  0
 BNY  CONST_04  C7   C8   C3   C4      0.00   0.0  0
 BNY  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 BNY  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 BNY  CONST_07  C3   C4   C5   C6      0.00   0.0  0
 BNY  CONST_08  C3   C8   C7   C6      0.00   0.0  0
 BNY  CONST_09  C1   C2   C10  C11     0.00   0.0  0
 BNY  CONST_10  C1   C13  C12  C11     0.00   0.0  0
 BNY  CONST_11  C10  C11  C12  C13     0.00   0.0  0
 BNY  CONST_12  C10  C2   C1   C13     0.00   0.0  0
 BNY  CONST_13  N1   C13  C1   C2    180.00   0.0  0
 BNY  CONST_14  C9   C8   C3   C4    180.00   0.0  0
 BNY  CONST_15  N    C3   C4   C5    180.00   0.0  0
 BNY  CONST_16  C9   C8   C7   C6    180.00   0.0  0
 BNY  CONST_17  N    C3   C8   C7    180.00   0.0  0
 BNY  CONST_18  N    C2   C10  C11   180.00   0.0  0
 BNY  CONST_19  N1   C13  C12  C11   180.00   0.0  0
 BNY  CONST_20  N    C2   C1   C13   180.00   0.0  0
 BNY  CONST_21  C10  C2   C1   C     180.00   0.0  0
 BNY  CONST_22  C12  C13  C1   C     180.00   0.0  0
 BNY  CONST_23  H5   C11  C10  C2    180.00   0.0  0
 BNY  CONST_24  H3   C6   C5   C4    180.00   0.0  0
 BNY  CONST_25  H4   C7   C6   C5    180.00   0.0  0
 BNY  CONST_26  H1   C4   C5   C6    180.00   0.0  0
 BNY  CONST_27  H2   C5   C6   C7    180.00   0.0  0
 BNY  CONST_28  H10  C10  C2   C1    180.00   0.0  0
 BNY  CONST_29  H9   C12  C13  C1    180.00   0.0  0
 BNY  Var_01    C4   C3   N    C2   -135.49  30.0  2
 BNY  Var_02    C3   N    C2   C1   -160.07  30.0  2
 BNY  Var_03    C7   C8   C9   O1   -133.03  30.0  2
 BNY  Var_04    H6   C    C1   C2     59.12  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
 BNY  plan-1  C4   0.020
 BNY  plan-1  C5   0.020
 BNY  plan-1  C6   0.020
 BNY  plan-1  C7   0.020
 BNY  plan-1  C3   0.020
 BNY  plan-1  C8   0.020
 BNY  plan-1  C9   0.020
 BNY  plan-1  H1   0.020
 BNY  plan-1  H2   0.020
 BNY  plan-1  H3   0.020
 BNY  plan-1  H4   0.020
 BNY  plan-1  N    0.020
 BNY  plan-2  C2   0.020
 BNY  plan-2  C11  0.020
 BNY  plan-2  C13  0.020
 BNY  plan-2  N1   0.020
 BNY  plan-2  C1   0.020
 BNY  plan-2  C    0.020
 BNY  plan-2  C12  0.020
 BNY  plan-2  C10  0.020
 BNY  plan-2  H5   0.020
 BNY  plan-2  H9   0.020
 BNY  plan-2  H10  0.020
 BNY  plan-2  N    0.020
 BNY  plan-3  C13  0.020
 BNY  plan-3  O3   0.020
 BNY  plan-3  N1   0.020
 BNY  plan-3  O2   0.020
 BNY  plan-4  O1   0.020
 BNY  plan-4  C8   0.020
 BNY  plan-4  C9   0.020
 BNY  plan-4  O    0.020

