# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:47:21 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  35  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.289   3.8048   0.5973  -0.7200
 59L  C02  C  CR16   0  -0.243   3.6479   0.4342  -2.0819
 59L  C03  C  CR16   0  -0.289   2.3723   0.4564  -2.6235
 59L  C04  C  CR6    0   0.078   1.2395   0.6318  -1.8383
 59L  C05  C  CR6    0   0.266   1.3984   0.7542  -0.4457
 59L  C06  C  CR6    0  -0.113   2.6953   0.7532   0.1099
 59L  C07  C  C      0   0.546   2.8975   0.9077   1.5667
 59L  N08  N  NH1    0  -0.791   0.2810   0.9128   0.3632
 59L  C09  C  CR6    0   0.360  -0.8625   0.1376   0.3290
 59L  C10  C  CR6    0  -0.077  -0.8875  -1.1986  -0.0974
 59L  C11  C  CR16   0  -0.355  -2.0610   0.7350   0.7240
 59L  C12  C  CR6    0   0.269  -3.2377   0.0184   0.6596
 59L  C13  C  CR16   0  -0.281  -3.2916  -1.2792   0.1722
 59L  C14  C  CR16   0  -0.247  -2.1029  -1.8707  -0.2082
 59L  C15  C  C      0   0.503   0.3678  -1.9800  -0.2849
 59L  O16  O  OH1    0  -0.579   0.3447  -2.7088  -1.3888
 59L  O17  O  O      0  -0.408   1.2686  -1.9821   0.5140
 59L  O18  O  O      0  -0.456   2.0822   1.3691   2.3375
 59L  N19  N  N      1   0.328  -4.4740   0.6671   1.0875
 59L  C20  C  CH3    0  -0.737  -0.0969   0.7512  -2.5118
 59L  O21  O  O      0  -0.370  -5.5072   0.0596   0.9432
 59L  O22  O  O     -1  -0.371  -4.3998   1.7741   1.5636
 59L  O23  O  OH1    0  -0.590   4.0902   0.4943   1.9699
 59L  H1   H  HCR6   0   0.268   4.8008   0.6058  -0.3002
 59L  H2   H  HCR6   0   0.261   4.5113   0.3137  -2.7215
 59L  H3   H  HCR6   0   0.260   2.2494   0.3688  -3.6964
 59L  H4   H  HNH1   0   0.413   0.4249   1.4474   1.2083
 59L  H5   H  HCR6   0   0.309  -2.0497   1.7644   1.0539
 59L  H6   H  HCR6   0   0.300  -4.2186  -1.8270   0.0986
 59L  H7   H  HCR6   0   0.289  -2.1211  -2.8941  -0.5574
 59L  H8   H  HOH1   0   0.491   1.1424  -3.2576  -1.4459
 59L  H9   H  HCH3   0   0.252  -0.6349  -0.1976  -2.5544
 59L  H10  H  HCH3   0   0.253  -0.7457   1.4695  -2.0110
 59L  H11  H  HCH3   0   0.261   0.0356   1.0853  -3.5399
 59L  H12  H  HOH1   0   0.488   4.1896   0.6581   2.9198

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  double    1.213  0.020  1.213
 59L  O23  C07  single    1.325  0.020  1.325
 59L  C07  C06  single    1.479  0.020  1.479
 59L  O17  C15  double    1.204  0.020  1.204
 59L  C01  C06  aromatic  1.394  0.020  1.394
 59L  C01  C02  aromatic  1.381  0.020  1.381
 59L  C06  C05  aromatic  1.411  0.020  1.411
 59L  C15  O16  single    1.323  0.020  1.323
 59L  C15  C10  single    1.490  0.020  1.490
 59L  C02  C03  aromatic  1.386  0.020  1.386
 59L  N08  C05  single    1.389  0.020  1.389
 59L  N08  C09  single    1.382  0.020  1.382
 59L  C05  C04  aromatic  1.407  0.020  1.407
 59L  C10  C09  aromatic  1.403  0.020  1.403
 59L  C10  C14  aromatic  1.393  0.020  1.393
 59L  C09  C11  aromatic  1.396  0.020  1.396
 59L  C03  C04  aromatic  1.389  0.020  1.389
 59L  C04  C20  single    1.501  0.020  1.501
 59L  C14  C13  aromatic  1.381  0.020  1.381
 59L  C11  C12  aromatic  1.379  0.020  1.379
 59L  C13  C12  aromatic  1.387  0.020  1.387
 59L  C12  N19  single    1.460  0.020  1.460
 59L  N19  O22  single    1.207  0.020  1.207
 59L  N19  O21  double    1.207  0.020  1.207
 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    0.860  0.020  1.020
 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  O16  H8   single    0.850  0.020  0.980
 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
 59L  O23  H12  single    0.850  0.020  0.980

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  120.08  3.000
 59L  H1   C01  C02  119.26  3.000
 59L  C06  C01  C02  120.66  3.000
 59L  H2   C02  C03  120.37  3.000
 59L  H2   C02  C01  120.39  3.000
 59L  C03  C02  C01  119.22  3.000
 59L  H3   C03  C04  118.52  3.000
 59L  H3   C03  C02  119.34  3.000
 59L  C04  C03  C02  122.11  3.000
 59L  C20  C04  C05  122.53  3.000
 59L  C20  C04  C03  118.83  3.000
 59L  C05  C04  C03  118.57  3.000
 59L  N08  C05  C06  120.69  3.000
 59L  N08  C05  C04  119.71  3.000
 59L  C06  C05  C04  119.57  3.000
 59L  C07  C06  C05  120.90  3.000
 59L  C05  C06  C01  119.81  3.000
 59L  C07  C06  C01  119.29  3.000
 59L  O23  C07  O18  122.01  3.000
 59L  O23  C07  C06  112.97  3.000
 59L  O18  C07  C06  125.02  3.000
 59L  H4   N08  C09  115.81  3.000
 59L  H4   N08  C05  115.67  3.000
 59L  C09  N08  C05  125.97  3.000
 59L  C11  C09  C10  118.57  3.000
 59L  C11  C09  N08  117.60  3.000
 59L  C10  C09  N08  123.82  3.000
 59L  C15  C10  C14  118.15  3.000
 59L  C14  C10  C09  119.94  3.000
 59L  C15  C10  C09  121.51  3.000
 59L  H5   C11  C12  121.20  3.000
 59L  H5   C11  C09  119.00  3.000
 59L  C12  C11  C09  119.79  3.000
 59L  N19  C12  C13  119.05  3.000
 59L  N19  C12  C11  118.54  3.000
 59L  C13  C12  C11  122.39  3.000
 59L  H6   C13  C14  120.21  3.000
 59L  H6   C13  C12  122.15  3.000
 59L  C14  C13  C12  117.64  3.000
 59L  H7   C14  C13  118.66  3.000
 59L  H7   C14  C10  119.79  3.000
 59L  C13  C14  C10  121.49  3.000
 59L  O17  C15  O16  124.45  3.000
 59L  O16  C15  C10  112.27  3.000
 59L  O17  C15  C10  123.20  3.000
 59L  H8   O16  C15  110.28  3.000
 59L  O22  N19  O21  124.13  3.000
 59L  O21  N19  C12  117.78  3.000
 59L  O22  N19  C12  118.09  3.000
 59L  H11  C20  H10  107.70  3.000
 59L  H11  C20  H9   106.84  3.000
 59L  H10  C20  H9   107.31  3.000
 59L  H11  C20  C04  109.85  3.000
 59L  H10  C20  C04  112.10  3.000
 59L  H9   C20  C04  112.77  3.000
 59L  H12  O23  C07  109.75  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  CONST_35  H12  O23  C07  C06  180.00   0.0  0
 59L  CONST_36  H8   O16  C15  C10  180.00   0.0  0
 59L  Var_01    C09  N08  C05  C04   49.35  30.0  2
 59L  Var_02    C10  C09  N08  C05   27.12  30.0  2
 59L  Var_03    O18  C07  C06  C01  160.85  30.0  3
 59L  Var_04    O17  C15  C10  C09   45.56  30.0  3
 59L  Var_05    H9   C20  C04  C03   95.92  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-4  H12  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
 59L  plan-5  H8   0.020

