# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:34:21 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: 2-[(2-carboxy-5-nitrophenyl)amino]-3-methylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(C(O)=O)c1Nc2cc(ccc2C(O)=O)[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
 59L  59L  '2-[(2-carboxy-5-nitrophenyl)amino]-3-methylbenzoic acid'  ligand  33  23  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_59L
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
 59L  C01  C  CR16   0  -0.315   3.7899   0.7434  -0.6631
 59L  C02  C  CR16   0  -0.263   3.6847   0.6092  -2.0366
 59L  C03  C  CR16   0  -0.316   2.4233   0.5797  -2.6122
 59L  C04  C  CR6    0   0.089   1.2659   0.6605  -1.8487
 59L  C05  C  CR6    0   0.294   1.3851   0.7462  -0.4471
 59L  C06  C  CR6    0  -0.199   2.6634   0.8195   0.1486
 59L  C07  C  C      0   0.445   2.8734   0.9873   1.6449
 59L  N08  N  NH1    0  -0.805   0.2685   0.8784   0.3611
 59L  C09  C  CR6    0   0.311  -0.8946   0.1204   0.2927
 59L  C10  C  CR6    0  -0.065  -0.9596  -1.1938  -0.1997
 59L  C11  C  CR16   0  -0.362  -2.0623   0.7312   0.7509
 59L  C12  C  CR6    0   0.242  -3.2675   0.0518   0.7065
 59L  C13  C  CR16   0  -0.286  -3.3664  -1.2207   0.1613
 59L  C14  C  CR16   0  -0.291  -2.2040  -1.8134  -0.2965
 59L  C15  C  C      0   0.395   0.2701  -2.0359  -0.5158
 59L  O16  O  OC    -1  -0.592   0.2643  -2.6441  -1.6007
 59L  O17  O  O      0  -0.568   1.1201  -2.0813   0.3871
 59L  O18  O  O      0  -0.605   1.8759   1.3033   2.3483
 59L  N19  N  N      1   0.324  -4.4611   0.7037   1.2118
 59L  C20  C  CH3    0  -0.743  -0.0607   0.7197  -2.5497
 59L  O21  O  O      0  -0.387  -5.5181   0.1243   1.1024
 59L  O22  O  O     -1  -0.388  -4.3489   1.7955   1.7219
 59L  O23  O  OC    -1  -0.577   4.0232   0.8239   2.0825
 59L  H1   H  HCR6   0   0.236   4.7665   0.7889  -0.1996
 59L  H2   H  HCR6   0   0.234   4.5704   0.5515  -2.6562
 59L  H3   H  HCR6   0   0.235   2.3288   0.5188  -3.6908
 59L  H4   H  HNH1   0   0.400   0.5643   1.1650   1.3066
 59L  H5   H  HCR6   0   0.287  -2.0081   1.7436   1.1269
 59L  H6   H  HCR6   0   0.282  -4.3090  -1.7437   0.0979
 59L  H7   H  HCR6   0   0.261  -2.2589  -2.8119  -0.7104
 59L  H9   H  HCH3   0   0.249  -0.5441  -0.2574  -2.5980
 59L  H10  H  HCH3   0   0.236  -0.7550   1.4034  -2.0602
 59L  H11  H  HCH3   0   0.242   0.0732   1.0636  -3.5756

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
 59L  O18  C07  deloc     1.261  0.020  1.261
 59L  O23  C07  deloc     1.241  0.020  1.241
 59L  C07  C06  single    1.520  0.020  1.520
 59L  O17  C15  deloc     1.241  0.020  1.241
 59L  C01  C06  aromatic  1.391  0.020  1.391
 59L  C01  C02  aromatic  1.384  0.020  1.384
 59L  C06  C05  aromatic  1.412  0.020  1.412
 59L  C15  O16  deloc     1.244  0.020  1.244
 59L  C15  C10  single    1.524  0.020  1.524
 59L  C02  C03  aromatic  1.387  0.020  1.387
 59L  N08  C05  single    1.385  0.020  1.385
 59L  N08  C09  single    1.390  0.020  1.390
 59L  C05  C04  aromatic  1.409  0.020  1.409
 59L  C10  C09  aromatic  1.405  0.020  1.405
 59L  C10  C14  aromatic  1.393  0.020  1.393
 59L  C09  C11  aromatic  1.395  0.020  1.395
 59L  C03  C04  aromatic  1.389  0.020  1.389
 59L  C04  C20  single    1.502  0.020  1.502
 59L  C14  C13  aromatic  1.383  0.020  1.383
 59L  C11  C12  aromatic  1.384  0.020  1.384
 59L  C13  C12  aromatic  1.388  0.020  1.388
 59L  C12  N19  single    1.451  0.020  1.451
 59L  N19  O22  single    1.210  0.020  1.210
 59L  N19  O21  double    1.210  0.020  1.210
 59L  C01  H1   single    0.930  0.020  1.080
 59L  C02  H2   single    0.930  0.020  1.080
 59L  C03  H3   single    0.930  0.020  1.080
 59L  N08  H4   single    0.890  0.020  1.040
 59L  C11  H5   single    0.930  0.020  1.080
 59L  C13  H6   single    0.930  0.020  1.080
 59L  C14  H7   single    0.930  0.020  1.080
 59L  C20  H9   single    0.970  0.020  1.090
 59L  C20  H10  single    0.970  0.020  1.090
 59L  C20  H11  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
 59L  H1   C01  C06  118.61  3.000
 59L  H1   C01  C02  119.85  3.000
 59L  C06  C01  C02  121.53  3.000
 59L  H2   C02  C03  120.36  3.000
 59L  H2   C02  C01  120.74  3.000
 59L  C03  C02  C01  118.89  3.000
 59L  H3   C03  C04  118.52  3.000
 59L  H3   C03  C02  119.55  3.000
 59L  C04  C03  C02  121.91  3.000
 59L  C20  C04  C05  122.45  3.000
 59L  C20  C04  C03  118.81  3.000
 59L  C05  C04  C03  118.67  3.000
 59L  N08  C05  C06  118.60  3.000
 59L  N08  C05  C04  121.20  3.000
 59L  C06  C05  C04  119.95  3.000
 59L  C07  C06  C05  123.09  3.000
 59L  C05  C06  C01  118.96  3.000
 59L  C07  C06  C01  117.95  3.000
 59L  O23  C07  O18  124.70  3.000
 59L  O23  C07  C06  117.42  3.000
 59L  O18  C07  C06  117.87  3.000
 59L  H4   N08  C09  115.89  3.000
 59L  H4   N08  C05  109.29  3.000
 59L  C09  N08  C05  126.44  3.000
 59L  C11  C09  C10  119.07  3.000
 59L  C11  C09  N08  116.45  3.000
 59L  C10  C09  N08  124.48  3.000
 59L  C15  C10  C14  117.43  3.000
 59L  C14  C10  C09  118.79  3.000
 59L  C15  C10  C09  123.53  3.000
 59L  H5   C11  C12  120.96  3.000
 59L  H5   C11  C09  118.82  3.000
 59L  C12  C11  C09  120.22  3.000
 59L  N19  C12  C13  119.35  3.000
 59L  N19  C12  C11  118.98  3.000
 59L  C13  C12  C11  121.65  3.000
 59L  H6   C13  C14  120.45  3.000
 59L  H6   C13  C12  121.96  3.000
 59L  C14  C13  C12  117.59  3.000
 59L  H7   C14  C13  118.65  3.000
 59L  H7   C14  C10  118.82  3.000
 59L  C13  C14  C10  122.49  3.000
 59L  O17  C15  O16  128.32  3.000
 59L  O16  C15  C10  116.58  3.000
 59L  O17  C15  C10  114.97  3.000
 59L  O22  N19  O21  123.43  3.000
 59L  O21  N19  C12  118.15  3.000
 59L  O22  N19  C12  118.41  3.000
 59L  H11  C20  H10  107.62  3.000
 59L  H11  C20  H9   107.17  3.000
 59L  H10  C20  H9   107.41  3.000
 59L  H11  C20  C04  110.07  3.000
 59L  H10  C20  C04  112.19  3.000
 59L  H9   C20  C04  112.13  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
 59L  CONST_01  C04  C05  C06  C01    0.00   0.0  0
 59L  CONST_02  C04  C03  C02  C01    0.00   0.0  0
 59L  CONST_03  C05  C06  C01  C02    0.00   0.0  0
 59L  CONST_04  C05  C04  C03  C02    0.00   0.0  0
 59L  CONST_05  C06  C01  C02  C03    0.00   0.0  0
 59L  CONST_06  C06  C05  C04  C03    0.00   0.0  0
 59L  CONST_07  C13  C14  C10  C09    0.00   0.0  0
 59L  CONST_08  C13  C12  C11  C09    0.00   0.0  0
 59L  CONST_09  C12  C11  C09  C10    0.00   0.0  0
 59L  CONST_10  C12  C13  C14  C10    0.00   0.0  0
 59L  CONST_11  C14  C10  C09  C11    0.00   0.0  0
 59L  CONST_12  C14  C13  C12  C11    0.00   0.0  0
 59L  CONST_13  N08  C05  C06  C01  180.00   0.0  0
 59L  CONST_14  C07  C06  C01  C02  180.00   0.0  0
 59L  CONST_15  C20  C04  C03  C02  180.00   0.0  0
 59L  CONST_16  N08  C05  C04  C03  180.00   0.0  0
 59L  CONST_17  C07  C06  C05  C04  180.00   0.0  0
 59L  CONST_18  C20  C04  C05  C06  180.00   0.0  0
 59L  CONST_19  C14  C10  C09  N08  180.00   0.0  0
 59L  CONST_20  C12  C11  C09  N08  180.00   0.0  0
 59L  CONST_21  N19  C12  C11  C09  180.00   0.0  0
 59L  CONST_22  C15  C10  C09  C11  180.00   0.0  0
 59L  CONST_23  C15  C10  C14  C13  180.00   0.0  0
 59L  CONST_24  N19  C12  C13  C14  180.00   0.0  0
 59L  CONST_25  H3   C03  C02  C01  180.00   0.0  0
 59L  CONST_26  H1   C01  C02  C03  180.00   0.0  0
 59L  CONST_27  H2   C02  C03  C04  180.00   0.0  0
 59L  CONST_28  H7   C14  C10  C09  180.00   0.0  0
 59L  CONST_29  H5   C11  C09  C10  180.00   0.0  0
 59L  CONST_30  H6   C13  C14  C10  180.00   0.0  0
 59L  CONST_31  O22  N19  C12  C11    0.00   0.0  0
 59L  CONST_32  O21  N19  C12  C11  180.00   0.0  0
 59L  CONST_33  O22  N19  C12  C13  180.00   0.0  0
 59L  CONST_34  O21  N19  C12  C13    0.00   0.0  0
 59L  Var_01    C09  N08  C05  C04   47.99  30.0  2
 59L  Var_02    C10  C09  N08  C05   26.63  30.0  2
 59L  Var_03    O18  C07  C06  C01  167.11  30.0  3
 59L  Var_04    O17  C15  C10  C09   50.00  30.0  3
 59L  Var_05    H9   C20  C04  C03   97.87  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
 59L  plan-1  C01  0.020
 59L  plan-1  C02  0.020
 59L  plan-1  C03  0.020
 59L  plan-1  C04  0.020
 59L  plan-1  C05  0.020
 59L  plan-1  C06  0.020
 59L  plan-1  C07  0.020
 59L  plan-1  N08  0.020
 59L  plan-1  C20  0.020
 59L  plan-1  H1   0.020
 59L  plan-1  H2   0.020
 59L  plan-1  H3   0.020
 59L  plan-2  N08  0.020
 59L  plan-2  C09  0.020
 59L  plan-2  C10  0.020
 59L  plan-2  C11  0.020
 59L  plan-2  C12  0.020
 59L  plan-2  C13  0.020
 59L  plan-2  C14  0.020
 59L  plan-2  C15  0.020
 59L  plan-2  N19  0.020
 59L  plan-2  H5   0.020
 59L  plan-2  H6   0.020
 59L  plan-2  H7   0.020
 59L  plan-3  C12  0.020
 59L  plan-3  N19  0.020
 59L  plan-3  O21  0.020
 59L  plan-3  O22  0.020
 59L  plan-4  C06  0.020
 59L  plan-4  C07  0.020
 59L  plan-4  O18  0.020
 59L  plan-4  O23  0.020
 59L  plan-5  C10  0.020
 59L  plan-5  C15  0.020
 59L  plan-5  O16  0.020
 59L  plan-5  O17  0.020

