# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 21:35:48 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: {5-chloro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cc(Cl)ccc1C(=O)NCc2cccc(c2)[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
 393  393  '{5-chloro-2-[(3-nitrobenzyl)carbamoyl]phenoxy}acetic acid'  ligand  38  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_393
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
 393  C1    C   CR6    0   0.265  6.0713  -1.9059  -4.5006
 393  N2    N   N      1   0.332  7.3526  -2.5281  -4.1994
 393  O3    O   O     -1  -0.377  8.3432  -2.0683  -4.7162
 393  O4    O   O      0  -0.380  7.3635  -3.4715  -3.4435
 393  C5    C   CR16   0  -0.318  4.9180  -2.4636  -3.9739
 393  C6    C   CR6    0   0.127  3.6901  -1.8752  -4.2440
 393  C7    C   CH2    0  -0.389  2.4369  -2.4694  -3.6504
 393  N8    N   NH1    0  -0.652  2.4029  -2.3539  -2.2094
 393  C9    C   C      0   0.557  2.1786  -1.1723  -1.6145
 393  C10   C   CR6    0  -0.122  2.1621  -1.1219  -0.1138
 393  C11   C   CR16   0  -0.283  1.4751  -0.0533   0.4637
 393  C12   C   CR16   0  -0.207  1.3913   0.1112   1.8331
 393  C13   C   CR6    0  -0.036  2.0171  -0.8145   2.6542
 393  CL1   CL  CL     0  -0.108  1.9233  -0.6355   4.3695
 393  C15   C   CR16   0  -0.265  2.7142  -1.8839   2.1238
 393  C16   C   CR6    0   0.360  2.7801  -2.0349   0.7444
 393  O17   O   O2     0  -0.503  3.4504  -3.1087   0.2398
 393  C18   C   CH2    0  -0.276  4.8578  -3.0147   0.2956
 393  C19   C   C      0   0.515  5.4274  -4.1833  -0.4705
 393  O20   O   OH1    0  -0.582  6.7314  -4.2685  -0.2810
 393  O21   O   O      0  -0.429  4.7805  -4.9165  -1.1703
 393  O22   O   O      0  -0.475  1.9495  -0.1586  -2.2601
 393  C23   C   CR16   0  -0.267  3.6468  -0.7367  -5.0396
 393  C24   C   CR16   0  -0.238  4.8108  -0.1950  -5.5700
 393  C25   C   CR16   0  -0.278  6.0393  -0.7739  -5.3034
 393  H5    H   HCR6   0   0.288  4.9644  -3.3549  -3.3637
 393  H71   H   HCH2   0   0.272  1.5562  -1.9971  -4.0862
 393  H72   H   HCH2   0   0.286  2.3797  -3.5317  -3.8863
 393  HN8   H   HNH1   0   0.413  2.6204  -3.1673  -1.6579
 393  H11   H   HCR6   0   0.278  0.9942   0.6719  -0.1778
 393  H12   H   HCR6   0   0.288  0.8480   0.9462   2.2521
 393  H15   H   HCR6   0   0.301  3.1971  -2.6067   2.7685
 393  H181  H   HCH2   0   0.280  5.2163  -2.0853  -0.1642
 393  H182  H   HCH2   0   0.287  5.2235  -3.0311   1.3270
 393  HO20  H   HOH1   0   0.492  7.1061  -4.9960  -0.8007
 393  H23   H   HCR6   0   0.270  2.6933  -0.2676  -5.2457
 393  H24   H   HCR6   0   0.278  4.7627   0.6901  -6.1892
 393  H25   H   HCR6   0   0.298  6.9431  -0.3464  -5.7116

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
 393  C1   N2    single    1.456  0.020  1.456
 393  C1   C25   aromatic  1.388  0.020  1.388
 393  C1   C5    aromatic  1.385  0.020  1.385
 393  N2   O3    single    1.208  0.020  1.208
 393  N2   O4    double    1.209  0.020  1.209
 393  C5   C6    aromatic  1.388  0.020  1.388
 393  C5   H5    single    0.930  0.020  1.080
 393  C6   C23   aromatic  1.390  0.020  1.390
 393  C6   C7    single    1.509  0.020  1.509
 393  C7   N8    single    1.446  0.020  1.446
 393  C7   H71   single    0.970  0.020  1.090
 393  C7   H72   single    0.970  0.020  1.090
 393  N8   C9    single    1.342  0.020  1.342
 393  N8   HN8   single    0.860  0.020  1.020
 393  C9   O22   double    1.223  0.020  1.223
 393  C9   C10   single    1.502  0.020  1.502
 393  C10  C11   aromatic  1.396  0.020  1.396
 393  C10  C16   aromatic  1.397  0.020  1.397
 393  C11  C12   aromatic  1.382  0.020  1.382
 393  C11  H11   single    0.930  0.020  1.080
 393  C12  C13   aromatic  1.387  0.020  1.387
 393  C12  H12   single    0.930  0.020  1.080
 393  C13  C15   aromatic  1.382  0.020  1.382
 393  C13  CL1   single    1.727  0.020  1.727
 393  C15  C16   aromatic  1.389  0.020  1.389
 393  C15  H15   single    0.930  0.020  1.080
 393  C16  O17   single    1.363  0.020  1.363
 393  O17  C18   single    1.412  0.020  1.412
 393  C18  C19   single    1.509  0.020  1.509
 393  C18  H181  single    0.970  0.020  1.090
 393  C18  H182  single    0.970  0.020  1.090
 393  C19  O21   double    1.202  0.020  1.202
 393  C19  O20   single    1.320  0.020  1.320
 393  O20  HO20  single    0.850  0.020  0.980
 393  C23  C24   aromatic  1.389  0.020  1.389
 393  C23  H23   single    0.930  0.020  1.080
 393  C24  C25   aromatic  1.384  0.020  1.384
 393  C24  H24   single    0.930  0.020  1.080
 393  C25  H25   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
 393  C25   C1   C5    121.94  3.000
 393  C5    C1   N2    118.82  3.000
 393  C25   C1   N2    119.24  3.000
 393  O4    N2   O3    123.85  3.000
 393  O4    N2   C1    118.09  3.000
 393  O3    N2   C1    118.06  3.000
 393  H5    C5   C6    119.82  3.000
 393  H5    C5   C1    120.72  3.000
 393  C6    C5   C1    119.46  3.000
 393  C23   C6   C7    121.47  3.000
 393  C7    C6   C5    119.43  3.000
 393  C23   C6   C5    119.09  3.000
 393  H72   C7   H71   107.06  3.000
 393  H72   C7   N8    107.00  3.000
 393  H71   C7   N8    110.17  3.000
 393  H72   C7   C6    110.02  3.000
 393  H71   C7   C6    110.07  3.000
 393  N8    C7   C6    112.35  3.000
 393  HN8   N8   C9    120.32  3.000
 393  HN8   N8   C7    118.45  3.000
 393  C9    N8   C7    121.07  3.000
 393  O22   C9   C10   119.83  3.000
 393  C10   C9   N8    118.33  3.000
 393  O22   C9   N8    121.80  3.000
 393  C16   C10  C11   117.64  3.000
 393  C16   C10  C9    125.95  3.000
 393  C11   C10  C9    116.40  3.000
 393  H11   C11  C12   118.77  3.000
 393  H11   C11  C10   119.15  3.000
 393  C12   C11  C10   122.08  3.000
 393  H12   C12  C13   120.86  3.000
 393  H12   C12  C11   120.45  3.000
 393  C13   C12  C11   118.69  3.000
 393  C15   C13  CL1   119.25  3.000
 393  CL1   C13  C12   119.63  3.000
 393  C15   C13  C12   121.12  3.000
 393  H15   C15  C16   119.85  3.000
 393  H15   C15  C13   120.87  3.000
 393  C16   C15  C13   119.27  3.000
 393  O17   C16  C15   118.47  3.000
 393  O17   C16  C10   120.33  3.000
 393  C15   C16  C10   121.19  3.000
 393  C18   O17  C16   115.05  3.000
 393  H182  C18  H181  107.36  3.000
 393  H182  C18  C19   109.92  3.000
 393  H181  C18  C19   108.66  3.000
 393  H182  C18  O17   111.68  3.000
 393  H181  C18  O17   111.44  3.000
 393  C19   C18  O17   107.75  3.000
 393  O21   C19  O20   125.13  3.000
 393  O20   C19  C18   110.48  3.000
 393  O21   C19  C18   124.37  3.000
 393  HO20  O20  C19   110.68  3.000
 393  H23   C23  C24   119.76  3.000
 393  H23   C23  C6    119.44  3.000
 393  C24   C23  C6    120.80  3.000
 393  H24   C24  C25   119.49  3.000
 393  H24   C24  C23   120.04  3.000
 393  C25   C24  C23   120.47  3.000
 393  H25   C25  C24   120.29  3.000
 393  H25   C25  C1    121.48  3.000
 393  C24   C25  C1    118.23  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
 393  CONST_01  C23   C24  C25  C1      0.00   0.0  0
 393  CONST_02  C23   C6   C5   C1      0.00   0.0  0
 393  CONST_03  C24   C25  C1   C5      0.00   0.0  0
 393  CONST_04  C24   C23  C6   C5      0.00   0.0  0
 393  CONST_05  C25   C1   C5   C6      0.00   0.0  0
 393  CONST_06  C25   C24  C23  C6      0.00   0.0  0
 393  CONST_07  C13   C12  C11  C10     0.00   0.0  0
 393  CONST_08  C13   C15  C16  C10     0.00   0.0  0
 393  CONST_09  C15   C16  C10  C11     0.00   0.0  0
 393  CONST_10  C15   C13  C12  C11     0.00   0.0  0
 393  CONST_11  C16   C10  C11  C12     0.00   0.0  0
 393  CONST_12  C16   C15  C13  C12     0.00   0.0  0
 393  CONST_13  C7    C6   C5   C1    180.00   0.0  0
 393  CONST_14  C24   C25  C1   N2    180.00   0.0  0
 393  CONST_15  C6    C5   C1   N2    180.00   0.0  0
 393  CONST_16  C24   C23  C6   C7    180.00   0.0  0
 393  CONST_17  C12   C11  C10  C9    180.00   0.0  0
 393  CONST_18  C15   C16  C10  C9    180.00   0.0  0
 393  CONST_19  O17   C16  C10  C11   180.00   0.0  0
 393  CONST_20  CL1   C13  C12  C11   180.00   0.0  0
 393  CONST_21  O17   C16  C15  C13   180.00   0.0  0
 393  CONST_22  C16   C15  C13  CL1   180.00   0.0  0
 393  CONST_23  H24   C24  C25  C1    180.00   0.0  0
 393  CONST_24  H25   C25  C1   C5    180.00   0.0  0
 393  CONST_25  H23   C23  C6   C5    180.00   0.0  0
 393  CONST_26  H12   C12  C11  C10   180.00   0.0  0
 393  CONST_27  H15   C15  C16  C10   180.00   0.0  0
 393  CONST_28  H11   C11  C12  C13   180.00   0.0  0
 393  CONST_29  H5    C5   C6   C23   180.00   0.0  0
 393  CONST_30  C25   C1   N2   O3      0.00   0.0  0
 393  CONST_31  C5    C1   N2   O3    180.00   0.0  0
 393  CONST_32  C25   C1   N2   O4    180.00   0.0  0
 393  CONST_33  C5    C1   N2   O4      0.00   0.0  0
 393  CONST_34  C10   C9   N8   C7    180.00   0.0  0
 393  CONST_35  HN8   N8   C9   C10     0.00   0.0  0
 393  CONST_36  O22   C9   N8   C7      0.00   0.0  0
 393  CONST_37  HO20  O20  C19  C18   180.00   0.0  0
 393  Var_01    N8    C7   C6   C5     66.13  30.0  2
 393  Var_02    C11   C10  C9   N8   -157.63  30.0  2
 393  Var_03    C9    N8   C7   C6     73.14  30.0  3
 393  Var_04    C19   C18  O17  C16  -172.21  30.0  3
 393  Var_05    O21   C19  C18  O17    10.85  30.0  3

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
 393  plan-1  C1    0.020
 393  plan-1  N2    0.020
 393  plan-1  C5    0.020
 393  plan-1  C6    0.020
 393  plan-1  C7    0.020
 393  plan-1  C23   0.020
 393  plan-1  C24   0.020
 393  plan-1  C25   0.020
 393  plan-1  H5    0.020
 393  plan-1  H23   0.020
 393  plan-1  H24   0.020
 393  plan-1  H25   0.020
 393  plan-2  C9    0.020
 393  plan-2  C10   0.020
 393  plan-2  C11   0.020
 393  plan-2  C12   0.020
 393  plan-2  C13   0.020
 393  plan-2  CL1   0.020
 393  plan-2  C15   0.020
 393  plan-2  C16   0.020
 393  plan-2  O17   0.020
 393  plan-2  H11   0.020
 393  plan-2  H12   0.020
 393  plan-2  H15   0.020
 393  plan-3  C7    0.020
 393  plan-3  N8    0.020
 393  plan-3  C9    0.020
 393  plan-3  C10   0.020
 393  plan-3  O22   0.020
 393  plan-3  HN8   0.020
 393  plan-4  C1    0.020
 393  plan-4  N2    0.020
 393  plan-4  O3    0.020
 393  plan-4  O4    0.020
 393  plan-5  C18   0.020
 393  plan-5  C19   0.020
 393  plan-5  O20   0.020
 393  plan-5  O21   0.020
 393  plan-5  HO20  0.020

