# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 19:54:17 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 1-[5-(2,4-dichlorophenoxy)pentyl]-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(OCCCCCn2ccnc2)c(Cl)c1
#
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
 5G8  5G8  1-[5-(2,4-dichlorophenoxy)pentyl]-1H-imidazole  ligand  35  19  .  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_5G8
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
 5G8  C1   C   CR6   0   0.474   2.4117  -0.0252  -0.0052
 5G8  C2   C   CR6   0  -0.163   3.3958   0.9703  -0.0228
 5G8  C3   C   CR16  0  -0.163   4.7422   0.6601  -0.0273
 5G8  C4   C   CR6   0  -0.073   5.1247  -0.6729  -0.0137
 5G8  C5   C   CR16  0  -0.193   4.1768  -1.6788   0.0042
 5G8  C6   C   CR16  0  -0.396   2.8273  -1.3539   0.0081
 5G8  C7   C   CH2   0  -0.175   0.1019  -0.5918   0.0055
 5G8  C8   C   CH2   0  -0.457  -1.2257   0.1349   0.0016
 5G8  CL2  CL  CL    0  -0.100   2.9046   2.6253  -0.0417
 5G8  CL4  CL  CL    0  -0.126   6.8109  -1.0696  -0.0199
 5G8  O1   O   O2    0  -0.457   1.1397   0.3818  -0.0031
 5G8  C9   C   CH2   0  -0.438  -2.3896  -0.8488   0.0111
 5G8  C10  C   CH2   0  -0.428  -3.7406  -0.1462   0.0034
 5G8  C11  C   CH2   0  -0.298  -4.8879  -1.1466   0.0206
 5G8  N12  N   NR5   0  -0.397  -6.1871  -0.5037   0.0167
 5G8  C16  C   CR15  0  -0.109  -6.8417   0.0028  -1.0702
 5G8  C15  C   CR15  0  -0.220  -7.9804   0.5758  -0.5793
 5G8  N14  N   N     0  -0.458  -8.0312   0.4356   0.7786
 5G8  C13  C   CR15  0   0.093  -6.9387  -0.2112   1.0982
 5G8  H1   H   HCR6  0   0.301   5.4796   1.4504  -0.0411
 5G8  H2   H   HCR6  0   0.288   4.4743  -2.7183   0.0140
 5G8  H3   H   HCR6  0   0.300   2.1079  -2.1601   0.0209
 5G8  H4   H   HCH2  0   0.229   0.1861  -1.2270   0.8946
 5G8  H5   H   HCH2  0   0.229   0.1841  -1.2389  -0.8752
 5G8  H6   H   HCH2  0   0.236  -1.2890   0.7885   0.8760
 5G8  H7   H   HCH2  0   0.236  -1.2907   0.7739  -0.8834
 5G8  H8   H   HCH2  0   0.228  -2.3175  -1.5105  -0.8583
 5G8  H9   H   HCH2  0   0.228  -2.3183  -1.4929   0.8936
 5G8  H10  H   HCH2  0   0.234  -3.8237   0.5125   0.8729
 5G8  H11  H   HCH2  0   0.235  -3.8237   0.4888  -0.8838
 5G8  H12  H   HCH2  0   0.262  -4.8310  -1.8079  -0.8448
 5G8  H13  H   HCH2  0   0.263  -4.8306  -1.7767   0.9089
 5G8  H14  H   HCR5  0   0.286  -6.4544  -0.0930  -2.0711
 5G8  H15  H   HCR5  0   0.248  -8.7623   1.0727  -1.1329
 5G8  H16  H   HCR5  0   0.277  -6.6411  -0.5010   2.0954

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
 5G8  C13  N14  aromatic  1.309  0.020  1.309
 5G8  C13  N12  aromatic  1.349  0.020  1.349
 5G8  N14  C15  aromatic  1.366  0.020  1.366
 5G8  N12  C11  single    1.450  0.020  1.450
 5G8  N12  C16  aromatic  1.366  0.020  1.366
 5G8  C15  C16  aromatic  1.366  0.020  1.366
 5G8  C11  C10  single    1.522  0.020  1.522
 5G8  C10  C9   single    1.523  0.020  1.523
 5G8  CL4  C4   single    1.732  0.020  1.732
 5G8  C5   C6   aromatic  1.388  0.020  1.388
 5G8  C5   C4   aromatic  1.382  0.020  1.382
 5G8  C6   C1   aromatic  1.392  0.020  1.392
 5G8  C4   C3   aromatic  1.387  0.020  1.387
 5G8  C9   C8   single    1.524  0.020  1.524
 5G8  C8   C7   single    1.513  0.020  1.513
 5G8  C7   O1   single    1.423  0.020  1.423
 5G8  C1   O1   single    1.336  0.020  1.336
 5G8  C1   C2   aromatic  1.400  0.020  1.400
 5G8  C3   C2   aromatic  1.382  0.020  1.382
 5G8  C2   CL2  single    1.727  0.020  1.727
 5G8  C3   H1   single    0.930  0.020  1.080
 5G8  C5   H2   single    0.930  0.020  1.080
 5G8  C6   H3   single    0.930  0.020  1.080
 5G8  C7   H4   single    0.970  0.020  1.090
 5G8  C7   H5   single    0.970  0.020  1.090
 5G8  C8   H6   single    0.970  0.020  1.090
 5G8  C8   H7   single    0.970  0.020  1.090
 5G8  C9   H8   single    0.970  0.020  1.090
 5G8  C9   H9   single    0.970  0.020  1.090
 5G8  C10  H10  single    0.970  0.020  1.090
 5G8  C10  H11  single    0.970  0.020  1.090
 5G8  C11  H12  single    0.970  0.020  1.090
 5G8  C11  H13  single    0.970  0.020  1.090
 5G8  C16  H14  single    0.930  0.020  1.080
 5G8  C15  H15  single    0.930  0.020  1.080
 5G8  C13  H16  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
 5G8  O1   C1   C6   125.11  3.000
 5G8  O1   C1   C2   116.92  3.000
 5G8  C6   C1   C2   117.97  3.000
 5G8  CL2  C2   C3   119.50  3.000
 5G8  CL2  C2   C1   118.80  3.000
 5G8  C3   C2   C1   121.70  3.000
 5G8  H1   C3   C4   120.98  3.000
 5G8  H1   C3   C2   120.04  3.000
 5G8  C4   C3   C2   118.98  3.000
 5G8  CL4  C4   C5   120.06  3.000
 5G8  C5   C4   C3   120.69  3.000
 5G8  CL4  C4   C3   119.25  3.000
 5G8  H2   C5   C6   119.50  3.000
 5G8  H2   C5   C4   120.73  3.000
 5G8  C6   C5   C4   119.76  3.000
 5G8  H3   C6   C5   118.21  3.000
 5G8  H3   C6   C1   120.89  3.000
 5G8  C5   C6   C1   120.90  3.000
 5G8  H5   C7   H4   107.70  3.000
 5G8  H5   C7   O1   110.14  3.000
 5G8  H4   C7   O1   110.21  3.000
 5G8  H5   C7   C8   110.32  3.000
 5G8  H4   C7   C8   110.35  3.000
 5G8  O1   C7   C8   108.13  3.000
 5G8  H7   C8   H6   107.12  3.000
 5G8  H7   C8   C9   109.68  3.000
 5G8  H6   C8   C9   109.67  3.000
 5G8  H7   C8   C7   109.57  3.000
 5G8  H6   C8   C7   109.62  3.000
 5G8  C9   C8   C7   111.10  3.000
 5G8  C7   O1   C1   119.08  3.000
 5G8  H9   C9   H8   106.27  3.000
 5G8  H9   C9   C10  109.47  3.000
 5G8  H8   C9   C10  109.46  3.000
 5G8  H9   C9   C8   109.57  3.000
 5G8  H8   C9   C8   109.56  3.000
 5G8  C10  C9   C8   112.32  3.000
 5G8  H11  C10  H10  106.81  3.000
 5G8  H11  C10  C11  109.47  3.000
 5G8  H10  C10  C11  109.24  3.000
 5G8  H11  C10  C9   109.83  3.000
 5G8  H10  C10  C9   109.95  3.000
 5G8  C11  C10  C9   111.43  3.000
 5G8  H13  C11  H12  107.05  3.000
 5G8  H13  C11  N12  107.79  3.000
 5G8  H12  C11  N12  108.28  3.000
 5G8  H13  C11  C10  110.44  3.000
 5G8  H12  C11  C10  110.50  3.000
 5G8  N12  C11  C10  112.58  3.000
 5G8  C13  N12  C16  106.89  3.000
 5G8  C16  N12  C11  126.58  3.000
 5G8  C13  N12  C11  126.39  3.000
 5G8  H14  C16  C15  132.13  3.000
 5G8  H14  C16  N12  122.26  3.000
 5G8  C15  C16  N12  105.61  3.000
 5G8  H15  C15  N14  122.02  3.000
 5G8  H15  C15  C16  127.79  3.000
 5G8  N14  C15  C16  110.19  3.000
 5G8  C13  N14  C15  105.21  3.000
 5G8  H16  C13  N14  126.00  3.000
 5G8  H16  C13  N12  121.90  3.000
 5G8  N14  C13  N12  112.10  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
 5G8  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 5G8  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 5G8  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 5G8  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 5G8  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 5G8  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 5G8  CONST_07  C15  N14  C13  N12     0.00   0.0  0
 5G8  CONST_08  N14  C15  C16  N12     0.00   0.0  0
 5G8  CONST_09  N14  C13  N12  C16     0.00   0.0  0
 5G8  CONST_10  C13  N14  C15  C16     0.00   0.0  0
 5G8  CONST_11  C13  N12  C16  C15     0.00   0.0  0
 5G8  CONST_12  CL4  C4   C3   C2    180.00   0.0  0
 5G8  CONST_13  O1   C1   C2   C3    180.00   0.0  0
 5G8  CONST_14  CL2  C2   C3   C4    180.00   0.0  0
 5G8  CONST_15  O1   C1   C6   C5    180.00   0.0  0
 5G8  CONST_16  CL4  C4   C5   C6    180.00   0.0  0
 5G8  CONST_17  CL2  C2   C1   C6    180.00   0.0  0
 5G8  CONST_18  N14  C13  N12  C11   180.00   0.0  0
 5G8  CONST_19  C15  C16  N12  C11   180.00   0.0  0
 5G8  CONST_20  H2   C5   C6   C1    180.00   0.0  0
 5G8  CONST_21  H1   C3   C2   C1    180.00   0.0  0
 5G8  CONST_22  H3   C6   C1   C2    180.00   0.0  0
 5G8  CONST_23  H15  C15  C16  N12   180.00   0.0  0
 5G8  CONST_24  H16  C13  N12  C16   180.00   0.0  0
 5G8  CONST_25  H14  C16  C15  N14   180.00   0.0  0
 5G8  Var_01    C13  N12  C11  C10   -94.52  30.0  2
 5G8  Var_02    C8   C7   O1   C1   -179.82  30.0  1
 5G8  Var_03    N12  C11  C10  C9    179.87  30.0  1
 5G8  Var_04    C10  C9   C8   C7   -179.84  30.0  1
 5G8  Var_05    C11  C10  C9   C8   -179.70  30.0  1
 5G8  Var_06    C9   C8   C7   O1   -179.97  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
 5G8  plan-1  C11  0.020
 5G8  plan-1  N12  0.020
 5G8  plan-1  C16  0.020
 5G8  plan-1  C15  0.020
 5G8  plan-1  N14  0.020
 5G8  plan-1  C13  0.020
 5G8  plan-1  H14  0.020
 5G8  plan-1  H15  0.020
 5G8  plan-1  H16  0.020
 5G8  plan-2  C1   0.020
 5G8  plan-2  C2   0.020
 5G8  plan-2  C3   0.020
 5G8  plan-2  C4   0.020
 5G8  plan-2  C5   0.020
 5G8  plan-2  C6   0.020
 5G8  plan-2  CL2  0.020
 5G8  plan-2  CL4  0.020
 5G8  plan-2  O1   0.020
 5G8  plan-2  H1   0.020
 5G8  plan-2  H2   0.020
 5G8  plan-2  H3   0.020

