# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 03:19:19 2021
#   Inital geometry file: a 75 line input string
#   Ligand name: 1-[3-(4-chlorophenoxy)propyl]-1H-imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(OCCCn2ccnc2)cc1
#
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
 P9Y  P9Y  1-[3-(4-chlorophenoxy)propyl]-1H-imidazole  ligand  29  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P9Y
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
 P9Y  C1    C   CR6   0   0.396   1.2604   8.4889   -7.7730
 P9Y  C2    C   CR16  0  -0.385   0.7880   7.3667   -8.4492
 P9Y  C3    C   CR16  0  -0.349   0.3909   9.2072   -6.9492
 P9Y  C11   C   CH2   0  -0.301   5.8329   8.2681   -9.4117
 P9Y  C13   C   CR15  0  -0.108   7.5268  10.0590   -9.9182
 P9Y  C14   C   CR15  0   0.094   8.1589   8.4906   -8.5386
 P9Y  C15   C   CR15  0  -0.218   8.7999  10.2861   -9.4784
 P9Y  C5    C   CR16  0  -0.197  -0.5360   6.9712   -8.3008
 P9Y  C6    C   CR16  0  -0.198  -0.9252   8.8122   -6.8021
 P9Y  C7    C   CH2   0  -0.178   3.4525   8.2564   -8.6661
 P9Y  C8    C   CR6   0  -0.066  -1.3848   7.6918   -7.4817
 P9Y  C9    C   CH2   0  -0.470   4.7833   8.9724   -8.5612
 P9Y  N12   N   NR5   0  -0.399   7.1309   8.9008   -9.3106
 P9Y  N16   N   N     0  -0.457   9.1851   9.2984   -8.6166
 P9Y  O4    O   O2    0  -0.471   2.5224   8.9484   -7.8511
 P9Y  CL10  CL  CL    0  -0.140  -3.0381   7.1946   -7.3011
 P9Y  H1    H   HCR6  0   0.290   1.4273   6.7844   -9.0976
 P9Y  H2    H   HCR6  0   0.273   0.7531  10.0807   -6.4220
 P9Y  H3    H   HCH2  0   0.269   5.5356   8.2537  -10.4610
 P9Y  H4    H   HCH2  0   0.269   5.9487   7.2306   -9.0966
 P9Y  H6    H   HCR5  0   0.279   8.1024   7.5877   -7.9480
 P9Y  H7    H   HCR5  0   0.250   9.4558  11.1008   -9.7447
 P9Y  H8    H   HCR6  0   0.282  -0.8922   6.0978   -8.8300
 P9Y  H9    H   HCR6  0   0.281  -1.5868   9.3759   -6.1586
 P9Y  H10   H   HCH2  0   0.231   3.1090   8.2389   -9.7070
 P9Y  H11   H   HCH2  0   0.230   3.5546   7.2168   -8.3333
 P9Y  H12   H   HCH2  0   0.251   5.1132   8.9906   -7.5199
 P9Y  H13   H   HCH2  0   0.252   4.6722  10.0076   -8.8931
 P9Y  H5    H   HCR5  0   0.289   6.8883  10.6012  -10.5957

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
 P9Y  C13  C15   aromatic  1.366  0.020  1.366
 P9Y  C13  N12   aromatic  1.367  0.020  1.367
 P9Y  C15  N16   aromatic  1.366  0.020  1.366
 P9Y  N12  C11   single    1.448  0.020  1.448
 P9Y  N12  C14   aromatic  1.349  0.020  1.349
 P9Y  C11  C9    single    1.523  0.020  1.523
 P9Y  N16  C14   aromatic  1.308  0.020  1.308
 P9Y  C7   C9    single    1.515  0.020  1.515
 P9Y  C7   O4    single    1.417  0.020  1.417
 P9Y  C2   C5    aromatic  1.390  0.020  1.390
 P9Y  C2   C1    aromatic  1.393  0.020  1.393
 P9Y  C5   C8    aromatic  1.382  0.020  1.382
 P9Y  O4   C1    single    1.345  0.020  1.345
 P9Y  C1   C3    aromatic  1.397  0.020  1.397
 P9Y  C8   CL10  single    1.736  0.020  1.736
 P9Y  C8   C6    aromatic  1.389  0.020  1.389
 P9Y  C3   C6    aromatic  1.382  0.020  1.382
 P9Y  C2   H1    single    0.930  0.020  1.080
 P9Y  C3   H2    single    0.930  0.020  1.080
 P9Y  C11  H3    single    0.970  0.020  1.090
 P9Y  C11  H4    single    0.970  0.020  1.090
 P9Y  C13  H5    single    0.930  0.020  1.080
 P9Y  C14  H6    single    0.930  0.020  1.080
 P9Y  C15  H7    single    0.930  0.020  1.080
 P9Y  C5   H8    single    0.930  0.020  1.080
 P9Y  C6   H9    single    0.930  0.020  1.080
 P9Y  C7   H10   single    0.970  0.020  1.090
 P9Y  C7   H11   single    0.970  0.020  1.090
 P9Y  C9   H12   single    0.970  0.020  1.090
 P9Y  C9   H13   single    0.970  0.020  1.090

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
 P9Y  O4    C1   C3   116.26  3.000
 P9Y  C3    C1   C2   119.32  3.000
 P9Y  O4    C1   C2   124.42  3.000
 P9Y  H1    C2   C5   118.31  3.000
 P9Y  H1    C2   C1   121.65  3.000
 P9Y  C5    C2   C1   120.04  3.000
 P9Y  H2    C3   C6   119.83  3.000
 P9Y  H2    C3   C1   119.60  3.000
 P9Y  C6    C3   C1   120.57  3.000
 P9Y  H4    C11  H3   107.12  3.000
 P9Y  H4    C11  N12  107.48  3.000
 P9Y  H3    C11  N12  108.50  3.000
 P9Y  H4    C11  C9   110.59  3.000
 P9Y  H3    C11  C9   110.82  3.000
 P9Y  N12   C11  C9   112.13  3.000
 P9Y  H5    C13  N12  122.31  3.000
 P9Y  H5    C13  C15  132.16  3.000
 P9Y  N12   C13  C15  105.53  3.000
 P9Y  H6    C14  N16  126.13  3.000
 P9Y  H6    C14  N12  121.80  3.000
 P9Y  N16   C14  N12  112.07  3.000
 P9Y  H7    C15  N16  122.00  3.000
 P9Y  H7    C15  C13  127.77  3.000
 P9Y  N16   C15  C13  110.23  3.000
 P9Y  H8    C5   C8   120.58  3.000
 P9Y  H8    C5   C2   119.43  3.000
 P9Y  C8    C5   C2   119.99  3.000
 P9Y  H9    C6   C8   120.62  3.000
 P9Y  H9    C6   C3   119.80  3.000
 P9Y  C8    C6   C3   119.58  3.000
 P9Y  H11   C7   H10  107.59  3.000
 P9Y  H11   C7   O4   110.46  3.000
 P9Y  H10   C7   O4   110.38  3.000
 P9Y  H11   C7   C9   110.20  3.000
 P9Y  H10   C7   C9   110.40  3.000
 P9Y  O4    C7   C9   107.82  3.000
 P9Y  CL10  C8   C6   119.69  3.000
 P9Y  C6    C8   C5   120.49  3.000
 P9Y  CL10  C8   C5   119.81  3.000
 P9Y  H13   C9   H12  107.72  3.000
 P9Y  H13   C9   C7   109.72  3.000
 P9Y  H12   C9   C7   109.82  3.000
 P9Y  H13   C9   C11  109.79  3.000
 P9Y  H12   C9   C11  109.37  3.000
 P9Y  C7    C9   C11  110.37  3.000
 P9Y  C14   N12  C13  106.94  3.000
 P9Y  C14   N12  C11  126.17  3.000
 P9Y  C13   N12  C11  126.81  3.000
 P9Y  C15   N16  C14  105.23  3.000
 P9Y  C7    O4   C1   118.83  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
 P9Y  CONST_01  C8    C5   C2   C1      0.00   0.0  0
 P9Y  CONST_02  C8    C6   C3   C1      0.00   0.0  0
 P9Y  CONST_03  C6    C8   C5   C2      0.00   0.0  0
 P9Y  CONST_04  C6    C3   C1   C2      0.00   0.0  0
 P9Y  CONST_05  C5    C2   C1   C3      0.00   0.0  0
 P9Y  CONST_06  C5    C8   C6   C3      0.00   0.0  0
 P9Y  CONST_07  C14   N16  C15  C13     0.00   0.0  0
 P9Y  CONST_08  N16   C14  N12  C13     0.00   0.0  0
 P9Y  CONST_09  C15   C13  N12  C14     0.00   0.0  0
 P9Y  CONST_10  N12   C14  N16  C15     0.00   0.0  0
 P9Y  CONST_11  N16   C15  C13  N12     0.00   0.0  0
 P9Y  CONST_12  CL10  C8   C5   C2    180.00   0.0  0
 P9Y  CONST_13  CL10  C8   C6   C3    180.00   0.0  0
 P9Y  CONST_14  C15   C13  N12  C11   180.00   0.0  0
 P9Y  CONST_15  N16   C14  N12  C11   180.00   0.0  0
 P9Y  CONST_16  O4    C1   C2   C5    180.00   0.0  0
 P9Y  CONST_17  O4    C1   C3   C6    180.00   0.0  0
 P9Y  CONST_18  H8    C5   C2   C1    180.00   0.0  0
 P9Y  CONST_19  H9    C6   C3   C1    180.00   0.0  0
 P9Y  CONST_20  H2    C3   C1   C2    180.00   0.0  0
 P9Y  CONST_21  H1    C2   C1   C3    180.00   0.0  0
 P9Y  CONST_22  H6    C14  N12  C13   180.00   0.0  0
 P9Y  CONST_23  H5    C13  N12  C14   180.00   0.0  0
 P9Y  CONST_24  H7    C15  N16  C14   180.00   0.0  0
 P9Y  Var_01    C9    C11  N12  C13   -76.77  30.0  2
 P9Y  Var_02    C9    C7   O4   C1   -179.47  30.0  1
 P9Y  Var_03    N12   C11  C9   C7   -178.43  30.0  1
 P9Y  Var_04    O4    C7   C9   C11   179.62  30.0  1

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
 P9Y  plan-1  C11   0.020
 P9Y  plan-1  C13   0.020
 P9Y  plan-1  C14   0.020
 P9Y  plan-1  C15   0.020
 P9Y  plan-1  N12   0.020
 P9Y  plan-1  N16   0.020
 P9Y  plan-1  H6    0.020
 P9Y  plan-1  H7    0.020
 P9Y  plan-1  H5    0.020
 P9Y  plan-2  C1    0.020
 P9Y  plan-2  C2    0.020
 P9Y  plan-2  C3    0.020
 P9Y  plan-2  C5    0.020
 P9Y  plan-2  C6    0.020
 P9Y  plan-2  C8    0.020
 P9Y  plan-2  O4    0.020
 P9Y  plan-2  CL10  0.020
 P9Y  plan-2  H1    0.020
 P9Y  plan-2  H2    0.020
 P9Y  plan-2  H8    0.020
 P9Y  plan-2  H9    0.020

