# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 21:08:29 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: {5-chloro-2-[(2,6-difluoro-4-iodobenzyl)carbamoyl]phenoxy}acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cc(Cl)ccc1C(=O)NCc2c(F)cc(I)cc2F
#
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
 4O9  4O9  '{5-chloro-2-[(2,6-difluoro-4-iodobenzyl)carbamoyl]phenoxy}acetic acid'  ligand  36  25  .  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_4O9
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
 4O9  O21  O   OH1   0  -0.591  -7.8031  -2.6752  -0.2007
 4O9  C19  C   C     0   0.514  -6.4987  -2.4708  -0.1007
 4O9  O20  O   O     0  -0.418  -5.6666  -3.3352  -0.0913
 4O9  C18  C   CH2   0  -0.303  -6.2133  -0.9914  -0.0066
 4O9  O17  O   O2    0  -0.444  -4.8275  -0.8399   0.1477
 4O9  C11  C   CR6   0   0.403  -4.3125   0.3965   0.2051
 4O9  C13  C   CR16  0  -0.335  -5.0765   1.5569   0.1370
 4O9  C15  C   CR6   0  -0.025  -4.4380   2.7887   0.1816
 4O9  CL2  CL  CL    0  -0.113  -5.4055   4.2211   0.1019
 4O9  C14  C   CR16  0  -0.236  -3.0648   2.9012   0.2823
 4O9  C12  C   CR16  0  -0.251  -2.3179   1.7327   0.3398
 4O9  C10  C   CR6   0  -0.174  -2.9179   0.4834   0.3114
 4O9  C9   C   C     0   0.528  -2.0817  -0.7480   0.4704
 4O9  O16  O   O     0  -0.467  -2.2693  -1.5420   1.3746
 4O9  N8   N   NH1   0  -0.619  -1.1033  -0.8611  -0.4471
 4O9  C7   C   CH2   0  -0.350  -0.0720  -1.8715  -0.4103
 4O9  C1   C   CR6   0  -0.297   1.2946  -1.2564  -0.2559
 4O9  C2   C   CR6   0   0.561   2.2809  -1.3376  -1.2263
 4O9  F25  F   F     0  -0.299   2.0162  -2.0071  -2.3534
 4O9  C3   C   CR6   0   0.575   1.6412  -0.5432   0.8841
 4O9  F24  F   F     0  -0.297   0.7268  -0.4321   1.8525
 4O9  C5   C   CR16  0  -0.384   2.8693   0.0565   1.0771
 4O9  C6   C   CR6   0  -0.206   3.8104  -0.0680   0.0656
 4O9  I23  I   I     0   0.099   5.6938   0.8196   0.3078
 4O9  C4   C   CR16  0  -0.388   3.5341  -0.7645  -1.0989
 4O9  H1   H   HOH1  0   0.491  -7.9900  -3.6235  -0.2730
 4O9  H2   H   HCH2  0   0.282  -6.5800  -0.5013  -0.9166
 4O9  H3   H   HCH2  0   0.282  -6.7690  -0.5713   0.8400
 4O9  H4   H   HCR6  0   0.309  -6.1528   1.5223   0.0478
 4O9  H5   H   HCR6  0   0.284  -2.5822   3.8673   0.3181
 4O9  H6   H   HCR6  0   0.275  -1.2413   1.8083   0.4272
 4O9  H7   H   HNH1  0   0.412  -1.0740  -0.1994  -1.2067
 4O9  H8   H   HCH2  0   0.287  -0.2778  -2.5440   0.4210
 4O9  H9   H   HCH2  0   0.285  -0.1155  -2.4747  -1.3155
 4O9  H10  H   HCR6  0   0.305   3.0693   0.5956   1.9929
 4O9  H11  H   HCR6  0   0.306   4.2566  -0.8700  -1.8962

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
 4O9  O20  C19  double    1.200  0.020  1.200
 4O9  C18  C19  single    1.510  0.020  1.510
 4O9  C18  O17  single    1.403  0.020  1.403
 4O9  CL2  C15  single    1.730  0.020  1.730
 4O9  C19  O21  single    1.324  0.020  1.324
 4O9  C13  C15  aromatic  1.388  0.020  1.388
 4O9  C13  C11  aromatic  1.391  0.020  1.391
 4O9  O17  C11  single    1.341  0.020  1.341
 4O9  C15  C14  aromatic  1.382  0.020  1.382
 4O9  C11  C10  aromatic  1.401  0.020  1.401
 4O9  C14  C12  aromatic  1.388  0.020  1.388
 4O9  C10  C12  aromatic  1.386  0.020  1.386
 4O9  C10  C9   single    1.497  0.020  1.497
 4O9  N8   C9   single    1.346  0.020  1.346
 4O9  N8   C7   single    1.444  0.020  1.444
 4O9  C9   O16  double    1.218  0.020  1.218
 4O9  C7   C1   single    1.507  0.020  1.507
 4O9  F24  C3   single    1.336  0.020  1.336
 4O9  C1   C3   aromatic  1.389  0.020  1.389
 4O9  C1   C2   aromatic  1.386  0.020  1.386
 4O9  C3   C5   aromatic  1.380  0.020  1.380
 4O9  F25  C2   single    1.337  0.020  1.337
 4O9  C2   C4   aromatic  1.384  0.020  1.384
 4O9  C5   C6   aromatic  1.387  0.020  1.387
 4O9  C4   C6   aromatic  1.385  0.020  1.385
 4O9  C6   I23  single    2.096  0.020  2.096
 4O9  O21  H1   single    0.850  0.020  0.980
 4O9  C18  H2   single    0.970  0.020  1.090
 4O9  C18  H3   single    0.970  0.020  1.090
 4O9  C13  H4   single    0.930  0.020  1.080
 4O9  C14  H5   single    0.930  0.020  1.080
 4O9  C12  H6   single    0.930  0.020  1.080
 4O9  N8   H7   single    0.860  0.020  1.020
 4O9  C7   H8   single    0.970  0.020  1.090
 4O9  C7   H9   single    0.970  0.020  1.090
 4O9  C5   H10  single    0.930  0.020  1.080
 4O9  C4   H11  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
 4O9  H1   O21  C19  110.29  3.000
 4O9  C18  C19  O20  125.06  3.000
 4O9  C18  C19  O21  110.02  3.000
 4O9  O20  C19  O21  124.92  3.000
 4O9  H3   C18  H2   107.46  3.000
 4O9  H3   C18  O17  111.99  3.000
 4O9  H2   C18  O17  111.93  3.000
 4O9  H3   C18  C19  109.13  3.000
 4O9  H2   C18  C19  108.84  3.000
 4O9  O17  C18  C19  107.43  3.000
 4O9  C11  O17  C18  118.94  3.000
 4O9  C10  C11  C13  119.91  3.000
 4O9  C10  C11  O17  116.28  3.000
 4O9  C13  C11  O17  123.80  3.000
 4O9  H4   C13  C15  119.29  3.000
 4O9  H4   C13  C11  121.63  3.000
 4O9  C15  C13  C11  119.08  3.000
 4O9  C14  C15  CL2  119.45  3.000
 4O9  C14  C15  C13  122.13  3.000
 4O9  CL2  C15  C13  118.42  3.000
 4O9  H5   C14  C12  120.73  3.000
 4O9  H5   C14  C15  121.28  3.000
 4O9  C12  C14  C15  117.99  3.000
 4O9  H6   C12  C10  119.66  3.000
 4O9  H6   C12  C14  118.66  3.000
 4O9  C10  C12  C14  121.67  3.000
 4O9  C9   C10  C12  119.83  3.000
 4O9  C9   C10  C11  120.86  3.000
 4O9  C12  C10  C11  119.22  3.000
 4O9  N8   C9   O16  124.28  3.000
 4O9  O16  C9   C10  121.95  3.000
 4O9  N8   C9   C10  113.75  3.000
 4O9  H7   N8   C7   117.25  3.000
 4O9  H7   N8   C9   118.67  3.000
 4O9  C7   N8   C9   124.08  3.000
 4O9  H9   C7   H8   106.56  3.000
 4O9  H9   C7   C1   110.35  3.000
 4O9  H8   C7   C1   110.20  3.000
 4O9  H9   C7   N8   109.75  3.000
 4O9  H8   C7   N8   108.46  3.000
 4O9  C1   C7   N8   111.39  3.000
 4O9  C3   C1   C2   115.29  3.000
 4O9  C2   C1   C7   123.36  3.000
 4O9  C3   C1   C7   121.35  3.000
 4O9  C4   C2   F25  117.66  3.000
 4O9  C4   C2   C1   123.76  3.000
 4O9  F25  C2   C1   118.59  3.000
 4O9  C5   C3   F24  118.12  3.000
 4O9  C5   C3   C1   124.05  3.000
 4O9  F24  C3   C1   117.83  3.000
 4O9  H10  C5   C6   122.47  3.000
 4O9  H10  C5   C3   119.97  3.000
 4O9  C6   C5   C3   117.56  3.000
 4O9  C4   C6   I23  119.30  3.000
 4O9  I23  C6   C5   119.16  3.000
 4O9  C4   C6   C5   121.53  3.000
 4O9  H11  C4   C6   122.40  3.000
 4O9  H11  C4   C2   119.79  3.000
 4O9  C6   C4   C2   117.80  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
 4O9  CONST_01  C14  C15  C13  C11     0.00   0.0  0
 4O9  CONST_02  C14  C12  C10  C11     0.00   0.0  0
 4O9  CONST_03  C12  C14  C15  C13     0.00   0.0  0
 4O9  CONST_04  C12  C10  C11  C13     0.00   0.0  0
 4O9  CONST_05  C10  C11  C13  C15     0.00   0.0  0
 4O9  CONST_06  C10  C12  C14  C15     0.00   0.0  0
 4O9  CONST_07  C6   C5   C3   C1      0.00   0.0  0
 4O9  CONST_08  C6   C4   C2   C1      0.00   0.0  0
 4O9  CONST_09  C5   C3   C1   C2      0.00   0.0  0
 4O9  CONST_10  C5   C6   C4   C2      0.00   0.0  0
 4O9  CONST_11  C4   C2   C1   C3      0.00   0.0  0
 4O9  CONST_12  C4   C6   C5   C3      0.00   0.0  0
 4O9  CONST_13  C15  C13  C11  O17   180.00   0.0  0
 4O9  CONST_14  C12  C10  C11  O17   180.00   0.0  0
 4O9  CONST_15  CL2  C15  C13  C11   180.00   0.0  0
 4O9  CONST_16  C9   C10  C11  C13   180.00   0.0  0
 4O9  CONST_17  C12  C14  C15  CL2   180.00   0.0  0
 4O9  CONST_18  C9   C10  C12  C14   180.00   0.0  0
 4O9  CONST_19  C5   C3   C1   C7    180.00   0.0  0
 4O9  CONST_20  C4   C2   C1   C7    180.00   0.0  0
 4O9  CONST_21  F24  C3   C1   C2    180.00   0.0  0
 4O9  CONST_22  I23  C6   C4   C2    180.00   0.0  0
 4O9  CONST_23  C3   C1   C2   F25   180.00   0.0  0
 4O9  CONST_24  C6   C4   C2   F25   180.00   0.0  0
 4O9  CONST_25  I23  C6   C5   C3    180.00   0.0  0
 4O9  CONST_26  C6   C5   C3   F24   180.00   0.0  0
 4O9  CONST_27  H6   C12  C10  C11   180.00   0.0  0
 4O9  CONST_28  H5   C14  C15  C13   180.00   0.0  0
 4O9  CONST_29  H4   C13  C15  C14   180.00   0.0  0
 4O9  CONST_30  H10  C5   C3   C1    180.00   0.0  0
 4O9  CONST_31  H11  C4   C2   C1    180.00   0.0  0
 4O9  CONST_32  C7   N8   C9   C10   180.00   0.0  0
 4O9  CONST_33  H7   N8   C9   C10     0.00   0.0  0
 4O9  CONST_34  C7   N8   C9   O16     0.00   0.0  0
 4O9  CONST_35  H1   O21  C19  O20     0.00   0.0  0
 4O9  Var_01    C13  C11  O17  C18     0.83  30.0  2
 4O9  Var_02    N8   C9   C10  C11   125.82  30.0  2
 4O9  Var_03    C3   C1   C7   N8     63.90  30.0  2
 4O9  Var_04    C1   C7   N8   C9   -117.06  30.0  3
 4O9  Var_05    H2   C18  O17  C11    58.12  30.0  1
 4O9  Var_06    O17  C18  C19  O21   177.80  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
 4O9  plan-1  O17  0.020
 4O9  plan-1  C11  0.020
 4O9  plan-1  C13  0.020
 4O9  plan-1  C15  0.020
 4O9  plan-1  CL2  0.020
 4O9  plan-1  C14  0.020
 4O9  plan-1  C12  0.020
 4O9  plan-1  C10  0.020
 4O9  plan-1  C9   0.020
 4O9  plan-1  H4   0.020
 4O9  plan-1  H5   0.020
 4O9  plan-1  H6   0.020
 4O9  plan-2  C7   0.020
 4O9  plan-2  C1   0.020
 4O9  plan-2  C2   0.020
 4O9  plan-2  F25  0.020
 4O9  plan-2  C3   0.020
 4O9  plan-2  F24  0.020
 4O9  plan-2  C5   0.020
 4O9  plan-2  C6   0.020
 4O9  plan-2  I23  0.020
 4O9  plan-2  C4   0.020
 4O9  plan-2  H10  0.020
 4O9  plan-2  H11  0.020
 4O9  plan-3  C10  0.020
 4O9  plan-3  C9   0.020
 4O9  plan-3  O16  0.020
 4O9  plan-3  N8   0.020
 4O9  plan-3  C7   0.020
 4O9  plan-3  H7   0.020
 4O9  plan-4  O21  0.020
 4O9  plan-4  C19  0.020
 4O9  plan-4  O20  0.020
 4O9  plan-4  C18  0.020
 4O9  plan-4  H1   0.020

