# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 06:50:01 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  39  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 PERFECT
;

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   0.417   7.2856  -2.0745   0.0939
 3U7  C4   C   CH2    0  -0.593   5.7567  -2.1209  -0.0841
 3U7  C5   C   CH2    0  -0.451   5.0307  -0.8020   0.1298
 3U7  C6   C   CH2    0  -0.178   3.5414  -0.9877  -0.0530
 3U7  C8   C   CR6    0   0.480   1.5778   0.3462   0.0238
 3U7  C9   C   CR16   0  -0.375   0.7428  -0.7300  -0.2582
 3U7  C10  C   CR16   0  -0.290  -0.6212  -0.5363  -0.3467
 3U7  C11  C   CR6    0   0.021  -1.2194   0.7112  -0.1848
 3U7  C12  C   CR6    0  -0.033  -0.3732   1.7937   0.1044
 3U7  O1   O   O      0  -0.606   7.8139  -0.9655   0.3018
 3U7  O2   O   OC    -1  -0.630   7.8739  -3.1719   0.0033
 3U7  O7   O   O2     0  -0.448   2.8971   0.2751   0.1370
 3U7  C13  C   CR6    0  -0.112   0.9973   1.6099   0.2160
 3U7  CL1  CL  CL     0  -0.069   2.0434   2.9206   0.5919
 3U7  CL2  CL  CL     0  -0.078  -0.9870   3.3723   0.4000
 3U7  C16  C   C      0   0.389  -2.6952   0.8421  -0.3538
 3U7  O17  O   O      0  -0.388  -3.2141   1.8955  -0.6469
 3U7  C18  C   CH2    0  -0.591  -3.5216  -0.4050  -0.1425
 3U7  C19  C   CH2    0  -0.530  -5.0199  -0.1369  -0.1249
 3U7  C20  C   CR5    0   0.475  -5.7909  -1.4042   0.0324
 3U7  N21  N   NR15   0  -0.609  -6.8755  -1.5148   0.8286
 3U7  C22  C   CR15   0  -0.113  -7.3593  -2.7874   0.7149
 3U7  C23  C   CR15   0  -0.224  -6.5200  -3.4054  -0.1650
 3U7  N24  N   N      0  -0.465  -5.5495  -2.5370  -0.5826
 3U7  H1   H   HCH2   0   0.228   5.5484  -2.4978  -1.0923
 3U7  H2   H   HCH2   0   0.225   5.3542  -2.8834   0.5918
 3U7  H3   H   HCH2   0   0.227   5.2294  -0.4217   1.1344
 3U7  H4   H   HCH2   0   0.227   5.3968  -0.0520  -0.5744
 3U7  H5   H   HCH2   0   0.231   3.3171  -1.3664  -1.0558
 3U7  H6   H   HCH2   0   0.231   3.1531  -1.7108   0.6719
 3U7  H7   H   HCR6   0   0.303   1.1423  -1.7220  -0.4122
 3U7  H8   H   HCR6   0   0.284  -1.2327  -1.4002  -0.5649
 3U7  H16  H   HCH2   0   0.286  -3.2956  -1.1233  -0.9356
 3U7  H17  H   HCH2   0   0.284  -3.2065  -0.8859   0.7873
 3U7  H18  H   HCH2   0   0.262  -5.2747   0.5493   0.6848
 3U7  H19  H   HCH2   0   0.267  -5.3223   0.3552  -1.0527
 3U7  H20  H   HNR5   0   0.415  -7.2627  -0.7878   1.4093
 3U7  H21  H   HCR5   0   0.281  -8.2236  -3.1292   1.2581
 3U7  H22  H   HCR5   0   0.245  -6.5626  -4.4246  -0.5171

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    1.540  0.020  1.540
 3U7  C3   O1   deloc     1.246  0.020  1.246
 3U7  C3   O2   deloc     1.248  0.020  1.248
 3U7  C4   C5   single    1.521  0.020  1.521
 3U7  C5   C6   single    1.512  0.020  1.512
 3U7  C6   O7   single    1.430  0.020  1.430
 3U7  C8   C9   aromatic  1.391  0.020  1.391
 3U7  C8   O7   single    1.326  0.020  1.326
 3U7  C8   C13  aromatic  1.404  0.020  1.404
 3U7  C9   C10  aromatic  1.381  0.020  1.381
 3U7  C10  C11  aromatic  1.393  0.020  1.393
 3U7  C11  C12  aromatic  1.404  0.020  1.404
 3U7  C11  C16  single    1.491  0.020  1.491
 3U7  C12  C13  aromatic  1.387  0.020  1.387
 3U7  C16  O17  double    1.210  0.020  1.210
 3U7  C16  C18  single    1.511  0.020  1.511
 3U7  C18  C19  single    1.522  0.020  1.522
 3U7  C19  C20  single    1.492  0.020  1.492
 3U7  C20  N21  aromatic  1.350  0.020  1.350
 3U7  C20  N24  aromatic  1.311  0.020  1.311
 3U7  N21  C22  aromatic  1.366  0.020  1.366
 3U7  C22  C23  aromatic  1.364  0.020  1.364
 3U7  C23  N24  aromatic  1.368  0.020  1.368
 3U7  C12  CL2  single    1.719  0.020  1.719
 3U7  C13  CL1  single    1.719  0.020  1.719
 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  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   126.50  3.000
 3U7  O2   C3   C4   115.65  3.000
 3U7  O1   C3   C4   117.85  3.000
 3U7  H2   C4   H1   104.97  3.000
 3U7  H2   C4   C5   109.97  3.000
 3U7  H1   C4   C5   109.69  3.000
 3U7  H2   C4   C3   108.32  3.000
 3U7  H1   C4   C3   107.78  3.000
 3U7  C5   C4   C3   115.57  3.000
 3U7  H4   C5   H3   107.04  3.000
 3U7  H4   C5   C6   109.67  3.000
 3U7  H3   C5   C6   109.45  3.000
 3U7  H4   C5   C4   110.18  3.000
 3U7  H3   C5   C4   110.15  3.000
 3U7  C6   C5   C4   110.29  3.000
 3U7  H6   C6   H5   107.77  3.000
 3U7  H6   C6   O7   109.60  3.000
 3U7  H5   C6   O7   109.55  3.000
 3U7  H6   C6   C5   110.51  3.000
 3U7  H5   C6   C5   110.78  3.000
 3U7  O7   C6   C5   108.62  3.000
 3U7  C13  C8   O7   116.62  3.000
 3U7  C13  C8   C9   118.43  3.000
 3U7  O7   C8   C9   124.96  3.000
 3U7  H7   C9   C10  119.01  3.000
 3U7  H7   C9   C8   121.15  3.000
 3U7  C10  C9   C8   119.83  3.000
 3U7  H8   C10  C11  119.77  3.000
 3U7  H8   C10  C9   117.37  3.000
 3U7  C11  C10  C9   122.85  3.000
 3U7  C16  C11  C12  123.51  3.000
 3U7  C16  C11  C10  119.37  3.000
 3U7  C12  C11  C10  117.10  3.000
 3U7  CL2  C12  C13  117.41  3.000
 3U7  CL2  C12  C11  121.88  3.000
 3U7  C13  C12  C11  120.66  3.000
 3U7  C8   O7   C6   118.96  3.000
 3U7  CL1  C13  C12  121.19  3.000
 3U7  CL1  C13  C8   117.69  3.000
 3U7  C12  C13  C8   121.11  3.000
 3U7  C18  C16  O17  121.19  3.000
 3U7  C18  C16  C11  116.93  3.000
 3U7  O17  C16  C11  121.88  3.000
 3U7  H17  C18  H16  105.56  3.000
 3U7  H17  C18  C19  110.57  3.000
 3U7  H16  C18  C19  109.11  3.000
 3U7  H17  C18  C16  108.93  3.000
 3U7  H16  C18  C16  109.13  3.000
 3U7  C19  C18  C16  113.24  3.000
 3U7  H19  C19  H18  106.38  3.000
 3U7  H19  C19  C20  109.21  3.000
 3U7  H18  C19  C20  109.59  3.000
 3U7  H19  C19  C18  109.99  3.000
 3U7  H18  C19  C18  110.43  3.000
 3U7  C20  C19  C18  111.12  3.000
 3U7  N24  C20  N21  110.72  3.000
 3U7  N24  C20  C19  126.10  3.000
 3U7  N21  C20  C19  123.17  3.000
 3U7  H20  N21  C22  125.72  3.000
 3U7  H20  N21  C20  126.12  3.000
 3U7  C22  N21  C20  108.16  3.000
 3U7  H21  C22  C23  132.51  3.000
 3U7  H21  C22  N21  122.55  3.000
 3U7  C23  C22  N21  104.94  3.000
 3U7  H22  C23  N24  121.87  3.000
 3U7  H22  C23  C22  127.89  3.000
 3U7  N24  C23  C22  110.24  3.000
 3U7  C23  N24  C20  105.94  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  Var_01    C9   C8   O7   C6      0.66  30.0  2
 3U7  Var_02    O17  C16  C11  C10  -156.08  30.0  2
 3U7  Var_03    N21  C20  C19  C18   138.63  30.0  2
 3U7  Var_04    C19  C18  C16  C11   171.20  30.0  3
 3U7  Var_05    C20  C19  C18  C16   177.77  30.0  3
 3U7  Var_06    H5   C6   O7   C8     58.94  30.0  1
 3U7  Var_07    C6   C5   C4   C3   -179.14  30.0  3
 3U7  Var_08    O7   C6   C5   C4   -179.19  30.0  3
 3U7  Var_09    O1   C3   C4   C5     -4.90  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

