# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 07:53:09 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  37  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   0.268  6.0791  -2.3854  -4.4110
 393  N2    N   N      1   0.338  7.1981  -3.3117  -4.4189
 393  O3    O   O     -1  -0.389  8.3130  -2.8535  -4.3254
 393  O4    O   O      0  -0.381  6.9614  -4.4899  -4.5347
 393  C5    C   CR16   0  -0.293  4.8102  -2.8758  -4.1542
 393  C6    C   CR6    0   0.112  3.7373  -1.9969  -4.1056
 393  C7    C   CH2    0  -0.401  2.3854  -2.4978  -3.6600
 393  N8    N   NH1    0  -0.649  2.2540  -2.3948  -2.2194
 393  C9    C   C      0   0.544  1.8412  -1.2647  -1.6225
 393  C10   C   CR6    0  -0.122  1.9416  -1.1776  -0.1263
 393  C11   C   CR16   0  -0.282  1.1403  -0.2214   0.4986
 393  C12   C   CR16   0  -0.214  1.1601  -0.0268   1.8669
 393  C13   C   CR6    0  -0.035  2.0162  -0.8025   2.6342
 393  CL1   CL  CL     0  -0.115  2.0632  -0.5788   4.3482
 393  C15   C   CR16   0  -0.276  2.8340  -1.7540   2.0543
 393  C16   C   CR6    0   0.363  2.7903  -1.9485   0.6780
 393  O17   O   O2     0  -0.502  3.5655  -2.9245   0.1487
 393  C18   C   CH2    0  -0.326  4.8710  -2.5261  -0.2790
 393  C19   C   C      0   0.422  5.5010  -3.6383  -1.1338
 393  O20   O   OC    -1  -0.600  6.6959  -3.4472  -1.4177
 393  O21   O   O      0  -0.591  4.7664  -4.5838  -1.4661
 393  O22   O   O      0  -0.487  1.3659  -0.3254  -2.2494
 393  C23   C   CR16   0  -0.271  3.9542  -0.6478  -4.3766
 393  C24   C   CR16   0  -0.243  5.2292  -0.1778  -4.6588
 393  C25   C   CR16   0  -0.279  6.3120  -1.0422  -4.6608
 393  H5    H   HCR6   0   0.291  4.6594  -3.9244  -3.9438
 393  H71   H   HCH2   0   0.271  1.5833  -1.9400  -4.1387
 393  H72   H   HCH2   0   0.276  2.2620  -3.5455  -3.9317
 393  HN8   H   HNH1   0   0.414  2.7201  -3.1052  -1.6707
 393  H11   H   HCR6   0   0.273  0.4802   0.3859  -0.1047
 393  H12   H   HCR6   0   0.284  0.5203   0.7135   2.3264
 393  H15   H   HCR6   0   0.291  3.4990  -2.3590   2.6567
 393  H181  H   HCH2   0   0.231  4.8159  -1.6067  -0.8765
 393  H182  H   HCH2   0   0.247  5.4972  -2.3092   0.5928
 393  H23   H   HCR6   0   0.267  3.1214   0.0425  -4.3572
 393  H24   H   HCR6   0   0.273  5.3850   0.8712  -4.8706
 393  H25   H   HCR6   0   0.291  7.3054  -0.6710  -4.8664

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    1.453  0.020  1.453
 393  C1   C25   aromatic  1.386  0.020  1.386
 393  C1   C5    aromatic  1.384  0.020  1.384
 393  N2   O3    single    1.209  0.020  1.209
 393  N2   O4    double    1.207  0.020  1.207
 393  C5   C6    aromatic  1.388  0.020  1.388
 393  C5   H5    single    0.930  0.020  1.080
 393  C6   C23   aromatic  1.393  0.020  1.393
 393  C6   C7    single    1.509  0.020  1.509
 393  C7   N8    single    1.450  0.020  1.450
 393  C7   H71   single    0.970  0.020  1.090
 393  C7   H72   single    0.970  0.020  1.090
 393  N8   C9    single    1.343  0.020  1.343
 393  N8   HN8   single    0.860  0.020  1.020
 393  C9   O22   double    1.225  0.020  1.225
 393  C9   C10   single    1.502  0.020  1.502
 393  C10  C11   aromatic  1.395  0.020  1.395
 393  C10  C16   aromatic  1.401  0.020  1.401
 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    1.729  0.020  1.729
 393  C15  C16   aromatic  1.391  0.020  1.391
 393  C15  H15   single    0.930  0.020  1.080
 393  C16  O17   single    1.354  0.020  1.354
 393  O17  C18   single    1.430  0.020  1.430
 393  C18  C19   single    1.538  0.020  1.538
 393  C18  H181  single    0.970  0.020  1.090
 393  C18  H182  single    0.970  0.020  1.090
 393  C19  O21   deloc     1.243  0.020  1.243
 393  C19  O20   deloc     1.243  0.020  1.243
 393  C23  C24   aromatic  1.388  0.020  1.388
 393  C23  H23   single    0.930  0.020  1.080
 393  C24  C25   aromatic  1.386  0.020  1.386
 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    122.06  3.000
 393  C5    C1   N2    118.76  3.000
 393  C25   C1   N2    119.18  3.000
 393  O4    N2   O3    123.92  3.000
 393  O4    N2   C1    118.15  3.000
 393  O3    N2   C1    117.93  3.000
 393  H5    C5   C6    120.01  3.000
 393  H5    C5   C1    120.53  3.000
 393  C6    C5   C1    119.39  3.000
 393  C23   C6   C7    121.22  3.000
 393  C7    C6   C5    119.52  3.000
 393  C23   C6   C5    119.09  3.000
 393  H72   C7   H71   107.45  3.000
 393  H72   C7   N8    107.81  3.000
 393  H71   C7   N8    109.51  3.000
 393  H72   C7   C6    110.31  3.000
 393  H71   C7   C6    111.12  3.000
 393  N8    C7   C6    110.54  3.000
 393  HN8   N8   C9    119.44  3.000
 393  HN8   N8   C7    116.57  3.000
 393  C9    N8   C7    121.94  3.000
 393  O22   C9   C10   119.41  3.000
 393  C10   C9   N8    118.10  3.000
 393  O22   C9   N8    122.48  3.000
 393  C16   C10  C11   117.91  3.000
 393  C16   C10  C9    125.49  3.000
 393  C11   C10  C9    116.58  3.000
 393  H11   C11  C12   118.83  3.000
 393  H11   C11  C10   119.06  3.000
 393  C12   C11  C10   122.11  3.000
 393  H12   C12  C13   120.88  3.000
 393  H12   C12  C11   120.58  3.000
 393  C13   C12  C11   118.54  3.000
 393  C15   C13  CL1   119.27  3.000
 393  CL1   C13  C12   119.53  3.000
 393  C15   C13  C12   121.21  3.000
 393  H15   C15  C16   119.47  3.000
 393  H15   C15  C13   120.99  3.000
 393  C16   C15  C13   119.54  3.000
 393  O17   C16  C15   118.01  3.000
 393  O17   C16  C10   121.28  3.000
 393  C15   C16  C10   120.68  3.000
 393  C18   O17  C16   116.02  3.000
 393  H182  C18  H181  107.22  3.000
 393  H182  C18  C19   110.58  3.000
 393  H181  C18  C19   108.89  3.000
 393  H182  C18  O17   109.82  3.000
 393  H181  C18  O17   110.50  3.000
 393  C19   C18  O17   109.80  3.000
 393  O21   C19  O20   128.64  3.000
 393  O20   C19  C18   114.18  3.000
 393  O21   C19  C18   117.18  3.000
 393  H23   C23  C24   119.65  3.000
 393  H23   C23  C6    119.65  3.000
 393  C24   C23  C6    120.70  3.000
 393  H24   C24  C25   119.49  3.000
 393  H24   C24  C23   120.04  3.000
 393  C25   C24  C23   120.46  3.000
 393  H25   C25  C24   120.30  3.000
 393  H25   C25  C1    121.46  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_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  Var_01    N8   C7   C6   C5     88.37  30.0  2
 393  Var_02    C11  C10  C9   N8   -160.03  30.0  2
 393  Var_03    C9   N8   C7   C6     85.79  30.0  3
 393  Var_04    C19  C18  O17  C16  -167.20  30.0  3
 393  Var_05    O21  C19  C18  O17     9.18  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

