# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 07:00:33 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-{2-chloro-4-[3-(1H-imidazol-2-yl)propanoyl]phenoxy}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCOc1ccc(cc1Cl)C(=O)CCc2[nH]ccn2
#
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
 3U8  3U8  '4-{2-chloro-4-[3-(1H-imidazol-2-yl)propanoyl]phenoxy}butanoic acid'  ligand  39  23  .  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_3U8
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
 3U8  C11  C   CR6    0  -0.043  -1.2839  -0.9738  -0.0180
 3U8  C12  C   CR16   0  -0.215  -0.4324  -2.0790   0.0669
 3U8  C13  C   CR6    0  -0.150   0.9311  -1.9054   0.1069
 3U8  C8   C   CR6    0   0.476   1.5083  -0.6261   0.0580
 3U8  C5   C   CH2    0  -0.451   4.9620   0.5316   0.0775
 3U8  C6   C   CH2    0  -0.176   3.4634   0.7206   0.0045
 3U8  C4   C   CH2    0  -0.592   5.6726   1.8668  -0.0819
 3U8  O1   O   O      0  -0.606   7.7466   0.7035   0.1698
 3U8  O2   O   OC    -1  -0.630   7.7919   2.9178  -0.0663
 3U8  C3   C   C      0   0.418   7.2088   1.8171   0.0191
 3U8  O7   O   O2     0  -0.450   2.8343  -0.5585   0.1018
 3U8  C9   C   CR16   0  -0.378   0.6558   0.4735  -0.0310
 3U8  C10  C   CR16   0  -0.273  -0.7168   0.2958  -0.0646
 3U8  CL1  CL  CL     0  -0.107   1.9752  -3.2786   0.2184
 3U8  C16  C   C      0   0.386  -2.7510  -1.1965  -0.0543
 3U8  O17  O   O      0  -0.406  -3.2057  -2.3227  -0.0655
 3U8  C18  C   CH2    0  -0.588  -3.6469   0.0157  -0.0653
 3U8  C19  C   CH2    0  -0.528  -5.1290  -0.3209  -0.1075
 3U8  C20  C   CR5    0   0.478  -5.9666   0.9095  -0.0031
 3U8  N21  N   NR15   0  -0.610  -7.1675   1.0327  -0.6078
 3U8  C22  C   CR15   0  -0.111  -7.6850   2.2547  -0.2826
 3U8  C23  C   CR15   0  -0.225  -6.7473   2.8309   0.5225
 3U8  N24  N   N      0  -0.466  -5.6836   1.9866   0.6889
 3U8  H1   H   HCR6   0   0.280  -0.8422  -3.0795   0.1051
 3U8  H2   H   HCH2   0   0.226   5.2257   0.0775   1.0353
 3U8  H3   H   HCH2   0   0.226   5.2828  -0.1600  -0.7045
 3U8  H4   H   HCH2   0   0.229   3.1195   1.3650   0.8205
 3U8  H5   H   HCH2   0   0.229   3.1762   1.1957  -0.9398
 3U8  H6   H   HCH2   0   0.227   5.4128   2.3096  -1.0501
 3U8  H7   H   HCH2   0   0.225   5.3028   2.5789   0.6642
 3U8  H9   H   HCR6   0   0.298   1.0530   1.4779  -0.0737
 3U8  H10  H   HCR6   0   0.276  -1.3397   1.1771  -0.1309
 3U8  H14  H   HCH2   0   0.283  -3.4244   0.6225   0.8169
 3U8  H15  H   HCH2   0   0.281  -3.3824   0.6467  -0.9191
 3U8  H16  H   HCH2   0   0.261  -5.3745  -0.8467  -1.0321
 3U8  H17  H   HCH2   0   0.266  -5.3822  -1.0036   0.7083
 3U8  H18  H   HNR5   0   0.415  -7.6075   0.3465  -1.2000
 3U8  H19  H   HCR5   0   0.281  -8.6385   2.5945  -0.6483
 3U8  H20  H   HCR5   0   0.245  -6.7785   3.8052   0.9855

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
 3U8  C11  C12  aromatic  1.398  0.020  1.398
 3U8  C11  C10  aromatic  1.391  0.020  1.391
 3U8  C11  C16  single    1.484  0.020  1.484
 3U8  C12  C13  aromatic  1.375  0.020  1.375
 3U8  C13  C8   aromatic  1.404  0.020  1.404
 3U8  C8   O7   single    1.328  0.020  1.328
 3U8  C8   C9   aromatic  1.394  0.020  1.394
 3U8  C5   C6   single    1.512  0.020  1.512
 3U8  C5   C4   single    1.521  0.020  1.521
 3U8  C6   O7   single    1.429  0.020  1.429
 3U8  C4   C3   single    1.540  0.020  1.540
 3U8  O1   C3   deloc     1.246  0.020  1.246
 3U8  O2   C3   deloc     1.249  0.020  1.249
 3U8  C9   C10  aromatic  1.384  0.020  1.384
 3U8  C16  O17  double    1.215  0.020  1.215
 3U8  C16  C18  single    1.507  0.020  1.507
 3U8  C18  C19  single    1.520  0.020  1.520
 3U8  C19  C20  single    1.492  0.020  1.492
 3U8  C20  N21  aromatic  1.350  0.020  1.350
 3U8  C20  N24  aromatic  1.311  0.020  1.311
 3U8  N21  C22  aromatic  1.366  0.020  1.366
 3U8  C22  C23  aromatic  1.364  0.020  1.364
 3U8  C23  N24  aromatic  1.368  0.020  1.368
 3U8  C13  CL1  single    1.729  0.020  1.729
 3U8  C12  H1   single    0.930  0.020  1.080
 3U8  C5   H2   single    0.970  0.020  1.090
 3U8  C5   H3   single    0.970  0.020  1.090
 3U8  C6   H4   single    0.970  0.020  1.090
 3U8  C6   H5   single    0.970  0.020  1.090
 3U8  C4   H6   single    0.970  0.020  1.090
 3U8  C4   H7   single    0.970  0.020  1.090
 3U8  C9   H9   single    0.930  0.020  1.080
 3U8  C10  H10  single    0.930  0.020  1.080
 3U8  C18  H14  single    0.970  0.020  1.090
 3U8  C18  H15  single    0.970  0.020  1.090
 3U8  C19  H16  single    0.970  0.020  1.090
 3U8  C19  H17  single    0.970  0.020  1.090
 3U8  N21  H18  single    0.860  0.020  1.020
 3U8  C22  H19  single    0.930  0.020  1.080
 3U8  C23  H20  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
 3U8  C16  C11  C10  122.61  3.000
 3U8  C16  C11  C12  119.01  3.000
 3U8  C10  C11  C12  118.37  3.000
 3U8  H1   C12  C13  119.43  3.000
 3U8  H1   C12  C11  120.17  3.000
 3U8  C13  C12  C11  120.40  3.000
 3U8  CL1  C13  C8   118.53  3.000
 3U8  CL1  C13  C12  120.03  3.000
 3U8  C8   C13  C12  121.43  3.000
 3U8  C9   C8   O7   124.92  3.000
 3U8  C9   C8   C13  117.99  3.000
 3U8  O7   C8   C13  117.09  3.000
 3U8  H3   C5   H2   107.08  3.000
 3U8  H3   C5   C4   110.10  3.000
 3U8  H2   C5   C4   110.12  3.000
 3U8  H3   C5   C6   109.61  3.000
 3U8  H2   C5   C6   109.48  3.000
 3U8  C4   C5   C6   110.38  3.000
 3U8  H5   C6   H4   107.75  3.000
 3U8  H5   C6   O7   109.36  3.000
 3U8  H4   C6   O7   109.74  3.000
 3U8  H5   C6   C5   110.83  3.000
 3U8  H4   C6   C5   110.41  3.000
 3U8  O7   C6   C5   108.73  3.000
 3U8  H7   C4   H6   105.00  3.000
 3U8  H7   C4   C3   108.24  3.000
 3U8  H6   C4   C3   107.90  3.000
 3U8  H7   C4   C5   109.97  3.000
 3U8  H6   C4   C5   109.67  3.000
 3U8  C3   C4   C5   115.52  3.000
 3U8  O2   C3   O1   126.49  3.000
 3U8  O2   C3   C4   115.65  3.000
 3U8  O1   C3   C4   117.86  3.000
 3U8  C6   O7   C8   118.86  3.000
 3U8  H9   C9   C10  118.86  3.000
 3U8  H9   C9   C8   120.71  3.000
 3U8  C10  C9   C8   120.43  3.000
 3U8  H10  C10  C9   117.91  3.000
 3U8  H10  C10  C11  120.73  3.000
 3U8  C9   C10  C11  121.36  3.000
 3U8  C18  C16  O17  121.53  3.000
 3U8  C18  C16  C11  117.84  3.000
 3U8  O17  C16  C11  120.63  3.000
 3U8  H15  C18  H14  105.09  3.000
 3U8  H15  C18  C19  109.98  3.000
 3U8  H14  C18  C19  110.09  3.000
 3U8  H15  C18  C16  109.01  3.000
 3U8  H14  C18  C16  108.63  3.000
 3U8  C19  C18  C16  113.68  3.000
 3U8  H17  C19  H16  106.20  3.000
 3U8  H17  C19  C20  109.43  3.000
 3U8  H16  C19  C20  109.28  3.000
 3U8  H17  C19  C18  110.08  3.000
 3U8  H16  C19  C18  110.45  3.000
 3U8  C20  C19  C18  111.27  3.000
 3U8  N24  C20  N21  110.69  3.000
 3U8  N24  C20  C19  126.38  3.000
 3U8  N21  C20  C19  122.91  3.000
 3U8  H18  N21  C22  125.71  3.000
 3U8  H18  N21  C20  126.12  3.000
 3U8  C22  N21  C20  108.18  3.000
 3U8  H19  C22  C23  132.56  3.000
 3U8  H19  C22  N21  122.49  3.000
 3U8  C23  C22  N21  104.95  3.000
 3U8  H20  C23  N24  121.84  3.000
 3U8  H20  C23  C22  127.94  3.000
 3U8  N24  C23  C22  110.22  3.000
 3U8  C23  N24  C20  105.96  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
 3U8  CONST_01  C8   C13  C12  C11     0.00   0.0  0
 3U8  CONST_02  C8   C9   C10  C11     0.00   0.0  0
 3U8  CONST_03  C9   C10  C11  C12     0.00   0.0  0
 3U8  CONST_04  C9   C8   C13  C12     0.00   0.0  0
 3U8  CONST_05  C10  C11  C12  C13     0.00   0.0  0
 3U8  CONST_06  C10  C9   C8   C13     0.00   0.0  0
 3U8  CONST_07  C23  C22  N21  C20     0.00   0.0  0
 3U8  CONST_08  C22  C23  N24  C20     0.00   0.0  0
 3U8  CONST_09  C23  N24  C20  N21     0.00   0.0  0
 3U8  CONST_10  N24  C23  C22  N21     0.00   0.0  0
 3U8  CONST_11  N24  C20  N21  C22     0.00   0.0  0
 3U8  CONST_12  CL1  C13  C12  C11   180.00   0.0  0
 3U8  CONST_13  O7   C8   C13  C12   180.00   0.0  0
 3U8  CONST_14  C16  C11  C12  C13   180.00   0.0  0
 3U8  CONST_15  C10  C9   C8   O7    180.00   0.0  0
 3U8  CONST_16  CL1  C13  C8   C9    180.00   0.0  0
 3U8  CONST_17  C16  C11  C10  C9    180.00   0.0  0
 3U8  CONST_18  C22  N21  C20  C19   180.00   0.0  0
 3U8  CONST_19  C23  N24  C20  C19   180.00   0.0  0
 3U8  CONST_20  H9   C9   C10  C11   180.00   0.0  0
 3U8  CONST_21  H10  C10  C11  C12   180.00   0.0  0
 3U8  CONST_22  H1   C12  C13  C8    180.00   0.0  0
 3U8  CONST_23  H19  C22  N21  C20   180.00   0.0  0
 3U8  CONST_24  H20  C23  N24  C20   180.00   0.0  0
 3U8  CONST_25  H18  N21  C22  C23   180.00   0.0  0
 3U8  Var_01    O17  C16  C11  C12    -2.99  30.0  2
 3U8  Var_02    C9   C8   O7   C6     -2.36  30.0  1
 3U8  Var_03    N21  C20  C19  C18   147.82  30.0  2
 3U8  Var_04    C19  C18  C16  C11   179.81  30.0  3
 3U8  Var_05    C5   C6   O7   C8   -179.94  30.0  1
 3U8  Var_06    C20  C19  C18  C16   175.31  30.0  3
 3U8  Var_07    O1   C3   C4   C5      2.62  30.0  3
 3U8  Var_08    C3   C4   C5   C6    178.13  30.0  3
 3U8  Var_09    O7   C6   C5   C4    177.61  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
 3U8  plan-1  C19  0.020
 3U8  plan-1  C20  0.020
 3U8  plan-1  N21  0.020
 3U8  plan-1  C22  0.020
 3U8  plan-1  C23  0.020
 3U8  plan-1  N24  0.020
 3U8  plan-1  H18  0.020
 3U8  plan-1  H19  0.020
 3U8  plan-1  H20  0.020
 3U8  plan-2  C11  0.020
 3U8  plan-2  C12  0.020
 3U8  plan-2  C13  0.020
 3U8  plan-2  C8   0.020
 3U8  plan-2  O7   0.020
 3U8  plan-2  C9   0.020
 3U8  plan-2  C10  0.020
 3U8  plan-2  CL1  0.020
 3U8  plan-2  C16  0.020
 3U8  plan-2  H1   0.020
 3U8  plan-2  H9   0.020
 3U8  plan-2  H10  0.020
 3U8  plan-3  C11  0.020
 3U8  plan-3  C16  0.020
 3U8  plan-3  O17  0.020
 3U8  plan-3  C18  0.020
 3U8  plan-4  C4   0.020
 3U8  plan-4  O1   0.020
 3U8  plan-4  O2   0.020
 3U8  plan-4  C3   0.020

