# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:45:25 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 4-{2,3-dichloro-4-[3-(1H-imidazol-2-yl)propanoyl]phenoxy}butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCOc1ccc(C(=O)CCc2[nH]ccn2)c(Cl)c1Cl
#
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
 3U7  3U7  '4-{2,3-dichloro-4-[3-(1H-imidazol-2-yl)propanoyl]phenoxy}butanoic acid'  ligand  40  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3U7
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
 3U7  C3   C   C     0   0.555   7.3128  -1.9256  -0.1346
 3U7  C4   C   CH2   0  -0.590   5.8385  -2.0534   0.1302
 3U7  C5   C   CH2   0  -0.462   5.0602  -0.7877  -0.1892
 3U7  C6   C   CH2   0  -0.178   3.5892  -1.0023   0.0942
 3U7  C8   C   CR6   0   0.478   1.5895   0.2699  -0.0483
 3U7  C9   C   CR16  0  -0.375   0.7950  -0.7748   0.4085
 3U7  C10  C   CR16  0  -0.289  -0.5709  -0.5979   0.5311
 3U7  C11  C   CR6   0   0.029  -1.1973   0.6080   0.2362
 3U7  C12  C   CR6   0  -0.036  -0.3927   1.6586  -0.2246
 3U7  O1   O   O     0  -0.442   7.8635  -0.9296  -0.5315
 3U7  O2   O   OH1   0  -0.596   7.9575  -3.0583   0.1251
 3U7  O7   O   O2    0  -0.449   2.9071   0.2107  -0.2105
 3U7  C13  C   CR6   0  -0.111   0.9749   1.4879  -0.3770
 3U7  CL1  CL  CL    0  -0.068   1.9691   2.7580  -0.9682
 3U7  CL2  CL  CL    0  -0.080  -1.0730   3.1680  -0.6904
 3U7  C16  C   C     0   0.380  -2.6648   0.7591   0.4700
 3U7  O17  O   O     0  -0.384  -3.1270   1.7970   0.8843
 3U7  C18  C   CH2   0  -0.576  -3.5312  -0.4323   0.1522
 3U7  C19  C   CH2   0  -0.528  -5.0089  -0.1797   0.3962
 3U7  C20  C   CR5   0   0.475  -5.8383  -1.3623   0.0231
 3U7  N21  N   NR15  0  -0.611  -7.1092  -1.5244   0.4515
 3U7  C22  C   CR15  0  -0.107  -7.5976  -2.6785  -0.0924
 3U7  C23  C   CR15  0  -0.227  -6.5731  -3.1763  -0.8417
 3U7  N24  N   N     0  -0.466  -5.4849  -2.3503  -0.7623
 3U7  H1   H   HCH2  0   0.285   5.4590  -2.9012  -0.4488
 3U7  H2   H   HCH2  0   0.286   5.7076  -2.3352   1.1799
 3U7  H3   H   HCH2  0   0.251   5.4308   0.0447   0.4123
 3U7  H4   H   HCH2  0   0.251   5.1933  -0.5183  -1.2387
 3U7  H5   H   HCH2  0   0.239   3.1942  -1.8191  -0.5190
 3U7  H6   H   HCH2  0   0.238   3.4335  -1.2657   1.1457
 3U7  H7   H   HCR6  0   0.304   1.2254  -1.7286   0.6776
 3U7  H8   H   HCR6  0   0.281  -1.1533  -1.4319   0.8960
 3U7  H9   H   HOH1  0   0.480   8.9041  -2.9472  -0.0478
 3U7  H16  H   HCH2  0   0.288  -3.3495  -0.7124  -0.8891
 3U7  H17  H   HCH2  0   0.284  -3.1991  -1.2944   0.7373
 3U7  H18  H   HCH2  0   0.263  -5.1815   0.0689   1.4457
 3U7  H19  H   HCH2  0   0.269  -5.3411   0.6897  -0.1786
 3U7  H20  H   HNR5  0   0.415  -7.6114  -0.9075   1.0701
 3U7  H21  H   HCR5  0   0.281  -8.5959  -3.0317   0.1008
 3U7  H22  H   HCR5  0   0.245  -6.5588  -4.0823  -1.4276

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
 3U7  C3   C4   single    1.503  0.020  1.503
 3U7  C3   O1   double    1.205  0.020  1.205
 3U7  C3   O2   single    1.329  0.020  1.329
 3U7  C4   C5   single    1.520  0.020  1.520
 3U7  C5   C6   single    1.513  0.020  1.513
 3U7  C6   O7   single    1.425  0.020  1.425
 3U7  C8   C9   aromatic  1.390  0.020  1.390
 3U7  C8   O7   single    1.329  0.020  1.329
 3U7  C8   C13  aromatic  1.403  0.020  1.403
 3U7  C9   C10  aromatic  1.383  0.020  1.383
 3U7  C10  C11  aromatic  1.391  0.020  1.391
 3U7  C11  C12  aromatic  1.401  0.020  1.401
 3U7  C11  C16  single    1.494  0.020  1.494
 3U7  C12  C13  aromatic  1.387  0.020  1.387
 3U7  C16  O17  double    1.209  0.020  1.209
 3U7  C16  C18  single    1.507  0.020  1.507
 3U7  C18  C19  single    1.519  0.020  1.519
 3U7  C19  C20  single    1.492  0.020  1.492
 3U7  C20  N21  aromatic  1.351  0.020  1.351
 3U7  C20  N24  aromatic  1.311  0.020  1.311
 3U7  N21  C22  aromatic  1.366  0.020  1.366
 3U7  C22  C23  aromatic  1.363  0.020  1.363
 3U7  C23  N24  aromatic  1.369  0.020  1.369
 3U7  C12  CL2  single    1.720  0.020  1.720
 3U7  C13  CL1  single    1.718  0.020  1.718
 3U7  C4   H1   single    0.970  0.020  1.090
 3U7  C4   H2   single    0.970  0.020  1.090
 3U7  C5   H3   single    0.970  0.020  1.090
 3U7  C5   H4   single    0.970  0.020  1.090
 3U7  C6   H5   single    0.970  0.020  1.090
 3U7  C6   H6   single    0.970  0.020  1.090
 3U7  C9   H7   single    0.930  0.020  1.080
 3U7  C10  H8   single    0.930  0.020  1.080
 3U7  O2   H9   single    0.850  0.020  0.980
 3U7  C18  H16  single    0.970  0.020  1.090
 3U7  C18  H17  single    0.970  0.020  1.090
 3U7  C19  H18  single    0.970  0.020  1.090
 3U7  C19  H19  single    0.970  0.020  1.090
 3U7  N21  H20  single    0.860  0.020  1.020
 3U7  C22  H21  single    0.930  0.020  1.080
 3U7  C23  H22  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
 3U7  O2   C3   O1   123.16  3.000
 3U7  O2   C3   C4   111.64  3.000
 3U7  O1   C3   C4   125.19  3.000
 3U7  H2   C4   H1   105.45  3.000
 3U7  H2   C4   C5   110.77  3.000
 3U7  H1   C4   C5   110.88  3.000
 3U7  H2   C4   C3   107.94  3.000
 3U7  H1   C4   C3   108.22  3.000
 3U7  C5   C4   C3   113.23  3.000
 3U7  H4   C5   H3   107.46  3.000
 3U7  H4   C5   C6   109.48  3.000
 3U7  H3   C5   C6   109.57  3.000
 3U7  H4   C5   C4   110.19  3.000
 3U7  H3   C5   C4   110.20  3.000
 3U7  C6   C5   C4   109.90  3.000
 3U7  H6   C6   H5   107.87  3.000
 3U7  H6   C6   O7   110.01  3.000
 3U7  H5   C6   O7   110.03  3.000
 3U7  H6   C6   C5   110.62  3.000
 3U7  H5   C6   C5   110.58  3.000
 3U7  O7   C6   C5   107.74  3.000
 3U7  C13  C8   O7   116.38  3.000
 3U7  C13  C8   C9   118.62  3.000
 3U7  O7   C8   C9   124.99  3.000
 3U7  H7   C9   C10  118.97  3.000
 3U7  H7   C9   C8   121.18  3.000
 3U7  C10  C9   C8   119.85  3.000
 3U7  H8   C10  C11  119.88  3.000
 3U7  H8   C10  C9   117.62  3.000
 3U7  C11  C10  C9   122.48  3.000
 3U7  C16  C11  C12  122.67  3.000
 3U7  C16  C11  C10  119.81  3.000
 3U7  C12  C11  C10  117.47  3.000
 3U7  CL2  C12  C13  117.93  3.000
 3U7  CL2  C12  C11  121.33  3.000
 3U7  C13  C12  C11  120.68  3.000
 3U7  H9   O2   C3   109.96  3.000
 3U7  C8   O7   C6   119.12  3.000
 3U7  CL1  C13  C12  121.17  3.000
 3U7  CL1  C13  C8   117.96  3.000
 3U7  C12  C13  C8   120.87  3.000
 3U7  C18  C16  O17  122.08  3.000
 3U7  C18  C16  C11  116.86  3.000
 3U7  O17  C16  C11  121.06  3.000
 3U7  H17  C18  H16  104.90  3.000
 3U7  H17  C18  C19  109.91  3.000
 3U7  H16  C18  C19  110.93  3.000
 3U7  H17  C18  C16  109.62  3.000
 3U7  H16  C18  C16  107.93  3.000
 3U7  C19  C18  C16  113.20  3.000
 3U7  H19  C19  H18  106.02  3.000
 3U7  H19  C19  C20  109.26  3.000
 3U7  H18  C19  C20  109.44  3.000
 3U7  H19  C19  C18  110.07  3.000
 3U7  H18  C19  C18  110.24  3.000
 3U7  C20  C19  C18  111.65  3.000
 3U7  N24  C20  N21  110.69  3.000
 3U7  N24  C20  C19  126.69  3.000
 3U7  N21  C20  C19  122.60  3.000
 3U7  H20  N21  C22  125.70  3.000
 3U7  H20  N21  C20  126.16  3.000
 3U7  C22  N21  C20  108.14  3.000
 3U7  H21  C22  C23  132.52  3.000
 3U7  H21  C22  N21  122.49  3.000
 3U7  C23  C22  N21  104.99  3.000
 3U7  H22  C23  N24  121.85  3.000
 3U7  H22  C23  C22  127.95  3.000
 3U7  N24  C23  C22  110.20  3.000
 3U7  C23  N24  C20  105.98  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
 3U7  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 3U7  CONST_02  C11  C12  C13  C8      0.00   0.0  0
 3U7  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 3U7  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 3U7  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 3U7  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 3U7  CONST_07  C23  C22  N21  C20     0.00   0.0  0
 3U7  CONST_08  C22  C23  N24  C20     0.00   0.0  0
 3U7  CONST_09  C23  N24  C20  N21     0.00   0.0  0
 3U7  CONST_10  N24  C23  C22  N21     0.00   0.0  0
 3U7  CONST_11  N24  C20  N21  C22     0.00   0.0  0
 3U7  CONST_12  CL2  C12  C13  C8    180.00   0.0  0
 3U7  CONST_13  CL1  C13  C8   C9    180.00   0.0  0
 3U7  CONST_14  C16  C11  C10  C9    180.00   0.0  0
 3U7  CONST_15  O7   C8   C9   C10   180.00   0.0  0
 3U7  CONST_16  CL2  C12  C11  C10   180.00   0.0  0
 3U7  CONST_17  CL1  C13  C12  C11   180.00   0.0  0
 3U7  CONST_18  O7   C8   C13  C12   180.00   0.0  0
 3U7  CONST_19  C16  C11  C12  C13   180.00   0.0  0
 3U7  CONST_20  C22  N21  C20  C19   180.00   0.0  0
 3U7  CONST_21  C23  N24  C20  C19   180.00   0.0  0
 3U7  CONST_22  H8   C10  C9   C8    180.00   0.0  0
 3U7  CONST_23  H7   C9   C10  C11   180.00   0.0  0
 3U7  CONST_24  H21  C22  N21  C20   180.00   0.0  0
 3U7  CONST_25  H22  C23  N24  C20   180.00   0.0  0
 3U7  CONST_26  H20  N21  C22  C23   180.00   0.0  0
 3U7  CONST_27  H9   O2   C3   C4    180.00   0.0  0
 3U7  Var_01    C9   C8   O7   C6      0.17  30.0  2
 3U7  Var_02    O17  C16  C11  C10   142.20  30.0  2
 3U7  Var_03    N21  C20  C19  C18   162.68  30.0  2
 3U7  Var_04    C19  C18  C16  C11  -178.95  30.0  3
 3U7  Var_05    C20  C19  C18  C16   177.89  30.0  3
 3U7  Var_06    H5   C6   O7   C8     59.00  30.0  2
 3U7  Var_07    C6   C5   C4   C3    179.59  30.0  3
 3U7  Var_08    O7   C6   C5   C4    179.59  30.0  3
 3U7  Var_09    O1   C3   C4   C5      1.56  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
 3U7  plan-1  C19  0.020
 3U7  plan-1  C20  0.020
 3U7  plan-1  N21  0.020
 3U7  plan-1  C22  0.020
 3U7  plan-1  C23  0.020
 3U7  plan-1  N24  0.020
 3U7  plan-1  H20  0.020
 3U7  plan-1  H21  0.020
 3U7  plan-1  H22  0.020
 3U7  plan-2  C8   0.020
 3U7  plan-2  C9   0.020
 3U7  plan-2  C10  0.020
 3U7  plan-2  C11  0.020
 3U7  plan-2  C12  0.020
 3U7  plan-2  O7   0.020
 3U7  plan-2  C13  0.020
 3U7  plan-2  CL1  0.020
 3U7  plan-2  CL2  0.020
 3U7  plan-2  C16  0.020
 3U7  plan-2  H7   0.020
 3U7  plan-2  H8   0.020
 3U7  plan-3  C11  0.020
 3U7  plan-3  C16  0.020
 3U7  plan-3  O17  0.020
 3U7  plan-3  C18  0.020
 3U7  plan-4  C3   0.020
 3U7  plan-4  C4   0.020
 3U7  plan-4  O1   0.020
 3U7  plan-4  O2   0.020
 3U7  plan-4  H9   0.020

