# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 21:46:43 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 4-{[(2-carbamoyl-4-nitrophenyl)amino]methyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cc(ccc1NCc2ccc(cc2)C(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
 X9I  X9I  '4-{[(2-carbamoyl-4-nitrophenyl)amino]methyl}benzoic acid'  ligand  36  23  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X9I
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
 X9I  C1    C  CR6    0   0.241  -4.2950   0.4851  -0.0472
 X9I  N1    N  N      1   0.320  -5.7240   0.5529  -0.1052
 X9I  O1    O  O      0  -0.399  -6.2547   1.6357   0.0332
 X9I  C2    C  CR16   0  -0.303  -3.6566  -0.7388  -0.1880
 X9I  N2    N  NH2    0  -0.785  -2.3425  -3.2404   0.0489
 X9I  O2    O  O     -1  -0.403  -6.3474  -0.4725  -0.2895
 X9I  C3    C  CR6    0  -0.117  -2.2785  -0.8368  -0.1495
 X9I  N3    N  NH1    0  -0.681  -0.1592   0.3150  -0.0129
 X9I  O3    O  O      0  -0.494  -0.4644  -2.2697  -0.7049
 X9I  C4    C  CR6    0   0.423  -1.4960   0.3504  -0.0050
 X9I  C5    C  CR16   0  -0.326  -2.1795   1.5769   0.1728
 X9I  C6    C  CR16   0  -0.220  -3.5469   1.6461   0.1483
 X9I  C7    C  C      0   0.562  -1.6185  -2.1663  -0.2911
 X9I  C8    C  CH2    0  -0.333   0.6893   1.4756   0.1613
 X9I  C9    C  CR6    0   0.085   2.1290   1.0491   0.1021
 X9I  C10   C  CR16   0  -0.249   2.7474   0.8398  -1.1278
 X9I  C11   C  CR16   0  -0.220   4.0606   0.4088  -1.1896
 X9I  C12   C  CR6    0  -0.085   4.7806   0.1792  -0.0187
 X9I  C13   C  CR16   0  -0.226   4.1661   0.3883   1.2140
 X9I  C14   C  CR16   0  -0.257   2.8492   0.8168   1.2684
 X9I  C15   C  C      0   0.526   6.1872  -0.2801  -0.1352
 X9I  O16   O  OH1    0  -0.585   6.7766  -0.4491   1.0396
 X9I  O17   O  O      0  -0.397   6.7422  -0.4802  -1.1891
 X9I  H2    H  HCR6   0   0.263  -4.2531  -1.6258  -0.3484
 X9I  H1N2  H  HNH2   0   0.389  -1.9275  -4.1546  -0.0317
 X9I  H2N2  H  HNH2   0   0.391  -3.2118  -3.1816   0.5497
 X9I  HN3   H  HNH1   0   0.414   0.2648  -0.5711  -0.2549
 X9I  H5    H  HCR6   0   0.264  -1.6186   2.4893   0.3154
 X9I  H6    H  HCR6   0   0.279  -4.0286   2.6052   0.2738
 X9I  H18   H  HCH2   0   0.245   0.4901   2.2186  -0.6179
 X9I  H28   H  HCH2   0   0.243   0.4813   1.9540   1.1221
 X9I  H10   H  HCR6   0   0.235   2.2010   1.0208  -2.0453
 X9I  H11   H  HCR6   0   0.260   4.5275   0.2531  -2.1526
 X9I  H13   H  HCR6   0   0.251   4.7010   0.2198   2.1381
 X9I  H14   H  HCR6   0   0.231   2.3804   0.9766   2.2312
 X9I  H131  H  HOH1   0   0.458   7.6892  -0.7481   0.9120

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
 X9I  C1   N1    single    1.432  0.020  1.432
 X9I  C1   C6    aromatic  1.395  0.020  1.395
 X9I  N1   O1    double    1.214  0.020  1.214
 X9I  C2   C1    aromatic  1.388  0.020  1.388
 X9I  C2   H2    single    0.930  0.020  1.080
 X9I  N2   C7    single    1.339  0.020  1.339
 X9I  N2   H1N2  single    0.860  0.020  1.020
 X9I  N2   H2N2  single    0.860  0.020  1.020
 X9I  O2   N1    single    1.214  0.020  1.214
 X9I  C3   C2    aromatic  1.382  0.020  1.382
 X9I  C3   C4    aromatic  1.429  0.020  1.429
 X9I  N3   C4    single    1.337  0.020  1.337
 X9I  N3   C8    single    1.448  0.020  1.448
 X9I  N3   HN3   single    0.860  0.020  1.020
 X9I  O3   C7    double    1.230  0.020  1.230
 X9I  C4   C5    aromatic  1.415  0.020  1.415
 X9I  C5   C6    aromatic  1.369  0.020  1.369
 X9I  C5   H5    single    0.930  0.020  1.080
 X9I  C6   H6    single    0.930  0.020  1.080
 X9I  C7   C3    single    1.491  0.020  1.491
 X9I  C8   C9    single    1.503  0.020  1.503
 X9I  C8   H18   single    0.970  0.020  1.090
 X9I  C8   H28   single    0.970  0.020  1.090
 X9I  C9   C10   aromatic  1.392  0.020  1.392
 X9I  C10  C11   aromatic  1.384  0.020  1.384
 X9I  C10  H10   single    0.930  0.020  1.080
 X9I  C11  H11   single    0.930  0.020  1.080
 X9I  C12  C11   aromatic  1.394  0.020  1.394
 X9I  C12  C15   single    1.484  0.020  1.484
 X9I  C13  C12   aromatic  1.393  0.020  1.393
 X9I  C13  H13   single    0.930  0.020  1.080
 X9I  C14  C9    aromatic  1.390  0.020  1.390
 X9I  C14  C13   aromatic  1.386  0.020  1.386
 X9I  C14  H14   single    0.930  0.020  1.080
 X9I  C15  O16   single    1.325  0.020  1.325
 X9I  O17  C15   double    1.208  0.020  1.208
 X9I  O16  H131  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
 X9I  C6    C1   C2    120.11  3.000
 X9I  C2    C1   N1    119.79  3.000
 X9I  C6    C1   N1    120.10  3.000
 X9I  O2    N1   O1    123.12  3.000
 X9I  O2    N1   C1    118.59  3.000
 X9I  O1    N1   C1    118.29  3.000
 X9I  H2    C2   C3    119.75  3.000
 X9I  C3    C2   C1    121.23  3.000
 X9I  H2    C2   C1    119.02  3.000
 X9I  H2N2  N2   H1N2  116.71  3.000
 X9I  H2N2  N2   C7    123.17  3.000
 X9I  H1N2  N2   C7    119.00  3.000
 X9I  C7    C3   C4    120.52  3.000
 X9I  C7    C3   C2    120.13  3.000
 X9I  C4    C3   C2    119.33  3.000
 X9I  HN3   N3   C8    119.03  3.000
 X9I  HN3   N3   C4    116.33  3.000
 X9I  C8    N3   C4    124.32  3.000
 X9I  C5    C4   N3    120.42  3.000
 X9I  C5    C4   C3    117.91  3.000
 X9I  N3    C4   C3    121.65  3.000
 X9I  H5    C5   C6    118.56  3.000
 X9I  H5    C5   C4    119.85  3.000
 X9I  C6    C5   C4    121.59  3.000
 X9I  H6    C6   C5    119.21  3.000
 X9I  H6    C6   C1    121.06  3.000
 X9I  C5    C6   C1    119.73  3.000
 X9I  O3    C7   C3    121.47  3.000
 X9I  C3    C7   N2    116.85  3.000
 X9I  O3    C7   N2    121.67  3.000
 X9I  H28   C8   H18   107.09  3.000
 X9I  H28   C8   C9    109.94  3.000
 X9I  H18   C8   C9    109.81  3.000
 X9I  H28   C8   N3    110.18  3.000
 X9I  H18   C8   N3    110.59  3.000
 X9I  C9    C8   N3    109.22  3.000
 X9I  C14   C9   C10   119.07  3.000
 X9I  C14   C9   C8    120.71  3.000
 X9I  C10   C9   C8    120.19  3.000
 X9I  H10   C10  C11   119.54  3.000
 X9I  H10   C10  C9    119.94  3.000
 X9I  C11   C10  C9    120.51  3.000
 X9I  H11   C11  C12   120.09  3.000
 X9I  C12   C11  C10   120.28  3.000
 X9I  H11   C11  C10   119.63  3.000
 X9I  C15   C12  C13   122.27  3.000
 X9I  C13   C12  C11   119.39  3.000
 X9I  C15   C12  C11   118.33  3.000
 X9I  H13   C13  C14   119.00  3.000
 X9I  C14   C13  C12   120.02  3.000
 X9I  H13   C13  C12   120.98  3.000
 X9I  H14   C14  C13   119.46  3.000
 X9I  H14   C14  C9    119.81  3.000
 X9I  C13   C14  C9    120.73  3.000
 X9I  O17   C15  O16   123.23  3.000
 X9I  O17   C15  C12   123.73  3.000
 X9I  O16   C15  C12   113.04  3.000
 X9I  H131  O16  C15   109.98  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
 X9I  CONST_01  C4    C5   C6   C1     0.00   0.0  0
 X9I  CONST_02  C4    C3   C2   C1     0.00   0.0  0
 X9I  CONST_03  C5    C6   C1   C2     0.00   0.0  0
 X9I  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 X9I  CONST_05  C6    C1   C2   C3     0.00   0.0  0
 X9I  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 X9I  CONST_07  C12   C11  C10  C9     0.00   0.0  0
 X9I  CONST_08  C12   C13  C14  C9     0.00   0.0  0
 X9I  CONST_09  C13   C14  C9   C10    0.00   0.0  0
 X9I  CONST_10  C13   C12  C11  C10    0.00   0.0  0
 X9I  CONST_11  C14   C9   C10  C11    0.00   0.0  0
 X9I  CONST_12  C14   C13  C12  C11    0.00   0.0  0
 X9I  CONST_13  C7    C3   C2   C1   180.00   0.0  0
 X9I  CONST_14  C5    C6   C1   N1   180.00   0.0  0
 X9I  CONST_15  C3    C2   C1   N1   180.00   0.0  0
 X9I  CONST_16  N3    C4   C3   C2   180.00   0.0  0
 X9I  CONST_17  C6    C5   C4   N3   180.00   0.0  0
 X9I  CONST_18  C7    C3   C4   C5   180.00   0.0  0
 X9I  CONST_19  C11   C10  C9   C8   180.00   0.0  0
 X9I  CONST_20  C13   C14  C9   C8   180.00   0.0  0
 X9I  CONST_21  C15   C12  C11  C10  180.00   0.0  0
 X9I  CONST_22  C15   C12  C13  C14  180.00   0.0  0
 X9I  CONST_23  H5    C5   C6   C1   180.00   0.0  0
 X9I  CONST_24  H6    C6   C1   C2   180.00   0.0  0
 X9I  CONST_25  H2    C2   C3   C4   180.00   0.0  0
 X9I  CONST_26  H11   C11  C10  C9   180.00   0.0  0
 X9I  CONST_27  H13   C13  C14  C9   180.00   0.0  0
 X9I  CONST_28  H14   C14  C9   C10  180.00   0.0  0
 X9I  CONST_29  H10   C10  C11  C12  180.00   0.0  0
 X9I  CONST_30  C6    C1   N1   O1     0.00   0.0  0
 X9I  CONST_31  C2    C1   N1   O1   180.00   0.0  0
 X9I  CONST_32  O2    N1   C1   C2     0.00   0.0  0
 X9I  CONST_33  C6    C1   N1   O2   180.00   0.0  0
 X9I  CONST_34  C8    N3   C4   C3   180.00   0.0  0
 X9I  CONST_35  C8    N3   C4   C5     0.00   0.0  0
 X9I  CONST_36  HN3   N3   C4   C3     0.00   0.0  0
 X9I  CONST_37  H1N2  N2   C7   C3   180.00   0.0  0
 X9I  CONST_38  H2N2  N2   C7   C3     0.00   0.0  0
 X9I  CONST_39  H131  O16  C15  C12  180.00   0.0  0
 X9I  Var_01    N2    C7   C3   C2   -24.56  30.0  2
 X9I  Var_02    C10   C9   C8   N3    80.69  30.0  2
 X9I  Var_03    C9    C8   N3   C4   179.67  30.0  3
 X9I  Var_04    O16   C15  C12  C11  179.20  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
 X9I  plan-1  C1    0.020
 X9I  plan-1  N1    0.020
 X9I  plan-1  C2    0.020
 X9I  plan-1  C3    0.020
 X9I  plan-1  N3    0.020
 X9I  plan-1  C4    0.020
 X9I  plan-1  C5    0.020
 X9I  plan-1  C6    0.020
 X9I  plan-1  C7    0.020
 X9I  plan-1  H2    0.020
 X9I  plan-1  H5    0.020
 X9I  plan-1  H6    0.020
 X9I  plan-2  C8    0.020
 X9I  plan-2  C9    0.020
 X9I  plan-2  C10   0.020
 X9I  plan-2  C11   0.020
 X9I  plan-2  C12   0.020
 X9I  plan-2  C13   0.020
 X9I  plan-2  C14   0.020
 X9I  plan-2  C15   0.020
 X9I  plan-2  H10   0.020
 X9I  plan-2  H11   0.020
 X9I  plan-2  H13   0.020
 X9I  plan-2  H14   0.020
 X9I  plan-3  N2    0.020
 X9I  plan-3  C3    0.020
 X9I  plan-3  O3    0.020
 X9I  plan-3  C7    0.020
 X9I  plan-3  H1N2  0.020
 X9I  plan-3  H2N2  0.020
 X9I  plan-4  C1    0.020
 X9I  plan-4  N1    0.020
 X9I  plan-4  O1    0.020
 X9I  plan-4  O2    0.020
 X9I  plan-5  N3    0.020
 X9I  plan-5  C4    0.020
 X9I  plan-5  C8    0.020
 X9I  plan-5  HN3   0.020
 X9I  plan-6  C12   0.020
 X9I  plan-6  C15   0.020
 X9I  plan-6  O16   0.020
 X9I  plan-6  O17   0.020
 X9I  plan-6  H131  0.020

