# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 16:45:26 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: 1-(4-methoxy-3-methylbenzyl)-1,5,6,7-tetrahydroindeno[5,6-d]imidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cn2cnc3cc4CCCc4cc23)cc1C
#
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
 1JN  1JN  1-(4-methoxy-3-methylbenzyl)-1,5,6,7-tetrahydroindeno[5,6-d]imidazole  ligand  42  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1JN
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
 1JN  C4   C  CR16  0  -0.373  -2.8431   1.3980   1.1471
 1JN  C5   C  CR6   0   0.021  -3.1944  -0.2701  -0.5780
 1JN  C6   C  CH3   0  -0.712  -3.8800  -0.7158  -1.8352
 1JN  C7   C  CR16  0  -0.318  -2.2711  -1.0767   0.0632
 1JN  C8   C  CR16  0  -0.314  -1.9166   0.5608   1.7623
 1JN  C10  C  CR56  0   0.115   2.2696  -1.7699  -0.2916
 1JN  C13  C  CR56  0   0.348   1.4743  -1.0257   0.5975
 1JN  C15  C  CH2   0  -0.463   4.2679   2.4352  -0.7917
 1JN  C17  C  CH2   0  -0.488   3.3589   2.2723   0.4368
 1JN  C20  C  CR16  0  -0.367   1.7310   0.3079   0.9091
 1JN  C22  C  CH2   0  -0.414  -0.6150  -1.5916   1.8876
 1JN  C1   C  CH3   0  -0.436  -4.7121   3.0106  -0.1832
 1JN  O2   O  O2    0  -0.463  -4.3829   1.7314  -0.6852
 1JN  C3   C  CR6   0   0.342  -3.4785   0.9889  -0.0187
 1JN  C9   C  CR6   0   0.115  -1.6193  -0.6811   1.2319
 1JN  N11  N  N     0  -0.476   1.7767  -3.0505  -0.4015
 1JN  C12  C  CR15  0   0.095   0.7375  -3.0738   0.3828
 1JN  C14  C  CR16  0  -0.392   3.3724  -1.1776  -0.9129
 1JN  C16  C  CH2   0  -0.487   4.7488   1.0140  -1.1231
 1JN  C18  C  CR56  0   0.069   3.6306   0.1441  -0.6126
 1JN  C19  C  CR56  0   0.069   2.8257   0.8732   0.2852
 1JN  N21  N  NR5   0  -0.498   0.5006  -1.8972   1.0169
 1JN  H1   H  HCR6  0   0.279  -3.0486   2.3639   1.5883
 1JN  H2   H  HCH3  0   0.243  -4.9640  -0.7512  -1.7142
 1JN  H3   H  HCH3  0   0.244  -3.6753  -0.0408  -2.6679
 1JN  H4   H  HCH3  0   0.242  -3.5456  -1.7113  -2.1231
 1JN  H5   H  HCR6  0   0.245  -2.0524  -2.0500  -0.3642
 1JN  H6   H  HCR6  0   0.255  -1.4256   0.8953   2.6687
 1JN  H7   H  HCH2  0   0.235   3.6813   2.8239  -1.6269
 1JN  H8   H  HCH2  0   0.236   5.0891   3.1307  -0.6201
 1JN  H9   H  HCH2  0   0.243   3.9371   2.3555   1.3629
 1JN  H10  H  HCH2  0   0.246   2.5732   3.0276   0.4857
 1JN  H11  H  HCR6  0   0.255   1.1095   0.8737   1.5922
 1JN  H12  H  HCH2  0   0.282  -0.2362  -1.1413   2.8068
 1JN  H13  H  HCH2  0   0.288  -1.0729  -2.5418   2.1665
 1JN  H14  H  HCH3  0   0.228  -5.1533   2.9561   0.8154
 1JN  H15  H  HCH3  0   0.228  -3.8412   3.6701  -0.1461
 1JN  H16  H  HCH3  0   0.260  -5.4441   3.4326  -0.8672
 1JN  H17  H  HCR5  0   0.288   0.0975  -3.9299   0.5460
 1JN  H18  H  HCR6  0   0.244   3.9900  -1.7388  -1.6041
 1JN  H19  H  HCH2  0   0.245   4.9473   0.8724  -2.1867
 1JN  H20  H  HCH2  0   0.241   5.6799   0.7815  -0.5962

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
 1JN  O2   C3   single    1.347  0.020  1.347
 1JN  O2   C1   single    1.413  0.020  1.413
 1JN  C6   C5   single    1.500  0.020  1.500
 1JN  C3   C5   aromatic  1.407  0.020  1.407
 1JN  C3   C4   aromatic  1.389  0.020  1.389
 1JN  C5   C7   aromatic  1.384  0.020  1.384
 1JN  C4   C8   aromatic  1.392  0.020  1.392
 1JN  C7   C9   aromatic  1.395  0.020  1.395
 1JN  C8   C9   aromatic  1.383  0.020  1.383
 1JN  C9   C22  single    1.506  0.020  1.506
 1JN  C22  N21  single    1.448  0.020  1.448
 1JN  C17  C19  single    1.505  0.020  1.505
 1JN  C17  C15  single    1.537  0.020  1.537
 1JN  C20  C19  aromatic  1.381  0.020  1.381
 1JN  C20  C13  aromatic  1.393  0.020  1.393
 1JN  C19  C18  aromatic  1.409  0.020  1.409
 1JN  N21  C13  aromatic  1.372  0.020  1.372
 1JN  N21  C12  aromatic  1.357  0.020  1.357
 1JN  C13  C10  aromatic  1.406  0.020  1.406
 1JN  C15  C16  single    1.537  0.020  1.537
 1JN  C12  N11  aromatic  1.302  0.020  1.302
 1JN  C18  C16  single    1.506  0.020  1.506
 1JN  C18  C14  aromatic  1.380  0.020  1.380
 1JN  C10  C14  aromatic  1.398  0.020  1.398
 1JN  C10  N11  aromatic  1.377  0.020  1.377
 1JN  C4   H1   single    0.930  0.020  1.080
 1JN  C6   H2   single    0.970  0.020  1.090
 1JN  C6   H3   single    0.970  0.020  1.090
 1JN  C6   H4   single    0.970  0.020  1.090
 1JN  C7   H5   single    0.930  0.020  1.080
 1JN  C8   H6   single    0.930  0.020  1.080
 1JN  C15  H7   single    0.970  0.020  1.090
 1JN  C15  H8   single    0.970  0.020  1.090
 1JN  C17  H9   single    0.970  0.020  1.090
 1JN  C17  H10  single    0.970  0.020  1.090
 1JN  C20  H11  single    0.930  0.020  1.080
 1JN  C22  H12  single    0.970  0.020  1.090
 1JN  C22  H13  single    0.970  0.020  1.090
 1JN  C1   H14  single    0.970  0.020  1.090
 1JN  C1   H15  single    0.970  0.020  1.090
 1JN  C1   H16  single    0.970  0.020  1.090
 1JN  C12  H17  single    0.930  0.020  1.080
 1JN  C14  H18  single    0.930  0.020  1.080
 1JN  C16  H19  single    0.970  0.020  1.090
 1JN  C16  H20  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
 1JN  H1   C4   C3   121.22  3.000
 1JN  H1   C4   C8   118.90  3.000
 1JN  C3   C4   C8   119.88  3.000
 1JN  C3   C5   C7   118.19  3.000
 1JN  C7   C5   C6   121.35  3.000
 1JN  C3   C5   C6   120.46  3.000
 1JN  H4   C6   H3   107.83  3.000
 1JN  H4   C6   H2   107.74  3.000
 1JN  H3   C6   H2   106.91  3.000
 1JN  H4   C6   C5   110.67  3.000
 1JN  H3   C6   C5   111.72  3.000
 1JN  H2   C6   C5   111.76  3.000
 1JN  H5   C7   C9   119.33  3.000
 1JN  H5   C7   C5   118.35  3.000
 1JN  C9   C7   C5   122.32  3.000
 1JN  H6   C8   C9   120.04  3.000
 1JN  H6   C8   C4   119.04  3.000
 1JN  C9   C8   C4   120.91  3.000
 1JN  C14  C10  N11  129.89  3.000
 1JN  N11  C10  C13  109.90  3.000
 1JN  C14  C10  C13  120.21  3.000
 1JN  N21  C13  C20  132.08  3.000
 1JN  N21  C13  C10  104.97  3.000
 1JN  C20  C13  C10  122.95  3.000
 1JN  H8   C15  H7   107.34  3.000
 1JN  H8   C15  C16  112.86  3.000
 1JN  H7   C15  C16  109.41  3.000
 1JN  H8   C15  C17  112.80  3.000
 1JN  H7   C15  C17  109.35  3.000
 1JN  C16  C15  C17  105.04  3.000
 1JN  H10  C17  H9   106.84  3.000
 1JN  H10  C17  C19  113.14  3.000
 1JN  H9   C17  C19  110.06  3.000
 1JN  H10  C17  C15  112.86  3.000
 1JN  H9   C17  C15  110.84  3.000
 1JN  C19  C17  C15  103.16  3.000
 1JN  H11  C20  C19  121.73  3.000
 1JN  H11  C20  C13  122.37  3.000
 1JN  C19  C20  C13  115.90  3.000
 1JN  H13  C22  H12  106.84  3.000
 1JN  H13  C22  N21  107.06  3.000
 1JN  H12  C22  N21  109.03  3.000
 1JN  H13  C22  C9   110.98  3.000
 1JN  H12  C22  C9   110.41  3.000
 1JN  N21  C22  C9   112.32  3.000
 1JN  H16  C1   H15  108.89  3.000
 1JN  H16  C1   H14  108.81  3.000
 1JN  H15  C1   H14  108.70  3.000
 1JN  H16  C1   O2   106.54  3.000
 1JN  H15  C1   O2   111.88  3.000
 1JN  H14  C1   O2   111.93  3.000
 1JN  C3   O2   C1   118.67  3.000
 1JN  O2   C3   C5   115.62  3.000
 1JN  C5   C3   C4   120.32  3.000
 1JN  O2   C3   C4   124.06  3.000
 1JN  C22  C9   C8   121.30  3.000
 1JN  C22  C9   C7   120.32  3.000
 1JN  C8   C9   C7   118.39  3.000
 1JN  C12  N11  C10  104.73  3.000
 1JN  H17  C12  N21  120.83  3.000
 1JN  H17  C12  N11  125.27  3.000
 1JN  N21  C12  N11  113.90  3.000
 1JN  H18  C14  C18  121.89  3.000
 1JN  H18  C14  C10  120.92  3.000
 1JN  C18  C14  C10  117.19  3.000
 1JN  H20  C16  H19  106.67  3.000
 1JN  H20  C16  C18  110.22  3.000
 1JN  H19  C16  C18  112.99  3.000
 1JN  H20  C16  C15  111.02  3.000
 1JN  H19  C16  C15  112.78  3.000
 1JN  C18  C16  C15  103.23  3.000
 1JN  C19  C18  C16  109.95  3.000
 1JN  C16  C18  C14  128.21  3.000
 1JN  C19  C18  C14  121.83  3.000
 1JN  C18  C19  C20  121.92  3.000
 1JN  C18  C19  C17  110.05  3.000
 1JN  C20  C19  C17  128.02  3.000
 1JN  C12  N21  C22  126.75  3.000
 1JN  C12  N21  C13  106.49  3.000
 1JN  C22  N21  C13  126.61  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
 1JN  CONST_01  C7   C5   C3   C4      0.00   0.0  0
 1JN  CONST_02  C7   C9   C8   C4      0.00   0.0  0
 1JN  CONST_03  C8   C4   C3   C5      0.00   0.0  0
 1JN  CONST_04  C8   C9   C7   C5      0.00   0.0  0
 1JN  CONST_05  C19  C20  C13  C10     0.00   0.0  0
 1JN  CONST_06  C12  N21  C13  C10     0.00   0.0  0
 1JN  CONST_07  C19  C18  C14  C10     0.00   0.0  0
 1JN  CONST_08  N21  C12  N11  C10     0.00   0.0  0
 1JN  CONST_09  C18  C19  C20  C13     0.00   0.0  0
 1JN  CONST_10  N11  C12  N21  C13     0.00   0.0  0
 1JN  CONST_11  C18  C14  C10  C13     0.00   0.0  0
 1JN  CONST_12  C12  N11  C10  C13     0.00   0.0  0
 1JN  CONST_13  C14  C18  C19  C20     0.00   0.0  0
 1JN  CONST_14  C12  N21  C13  C20   180.00   0.0  0
 1JN  CONST_15  C14  C10  C13  C20     0.00   0.0  0
 1JN  CONST_16  N11  C10  C13  C20   180.00   0.0  0
 1JN  CONST_17  C9   C7   C5   C3      0.00   0.0  0
 1JN  CONST_18  C9   C8   C4   C3      0.00   0.0  0
 1JN  CONST_19  N21  C13  C10  N11     0.00   0.0  0
 1JN  CONST_20  C18  C14  C10  N11   180.00   0.0  0
 1JN  CONST_21  C14  C10  N11  C12   180.00   0.0  0
 1JN  CONST_22  N21  C13  C10  C14   180.00   0.0  0
 1JN  CONST_23  N21  C13  C20  C19   180.00   0.0  0
 1JN  CONST_24  C6   C5   C3   C4    180.00   0.0  0
 1JN  CONST_25  C22  C9   C8   C4    180.00   0.0  0
 1JN  CONST_26  C22  C9   C7   C5    180.00   0.0  0
 1JN  CONST_27  C9   C7   C5   C6    180.00   0.0  0
 1JN  CONST_28  O2   C3   C5   C7    180.00   0.0  0
 1JN  CONST_29  O2   C3   C4   C8    180.00   0.0  0
 1JN  CONST_30  C22  N21  C13  C10   180.00   0.0  0
 1JN  CONST_31  C22  N21  C13  C20     0.00   0.0  0
 1JN  CONST_32  N11  C12  N21  C22   180.00   0.0  0
 1JN  CONST_33  H1   C4   C3   C5    180.00   0.0  0
 1JN  CONST_34  H6   C8   C9   C7    180.00   0.0  0
 1JN  CONST_35  H5   C7   C9   C8    180.00   0.0  0
 1JN  CONST_36  H11  C20  C13  C10   180.00   0.0  0
 1JN  CONST_37  H17  C12  N11  C10   180.00   0.0  0
 1JN  CONST_38  H18  C14  C10  C13   180.00   0.0  0
 1JN  Var_01    C20  C19  C17  C15  -162.89  30.0  1
 1JN  Var_02    C19  C18  C16  C15   -17.45  30.0  1
 1JN  Var_03    C18  C16  C15  C17    27.91  30.0  1
 1JN  Var_04    C19  C17  C15  C16   -28.07  30.0  1
 1JN  Var_05    N21  C22  C9   C7     60.34  30.0  2
 1JN  Var_06    C9   C22  N21  C13    68.65  30.0  2
 1JN  Var_07    H2   C6   C5   C7    120.25  30.0  2
 1JN  Var_08    H14  C1   O2   C3    -61.55  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
 1JN  plan-1  C4   0.020
 1JN  plan-1  C5   0.020
 1JN  plan-1  C6   0.020
 1JN  plan-1  C7   0.020
 1JN  plan-1  C8   0.020
 1JN  plan-1  C22  0.020
 1JN  plan-1  O2   0.020
 1JN  plan-1  C3   0.020
 1JN  plan-1  C9   0.020
 1JN  plan-1  H1   0.020
 1JN  plan-1  H5   0.020
 1JN  plan-1  H6   0.020
 1JN  plan-2  C10  0.020
 1JN  plan-2  C13  0.020
 1JN  plan-2  C17  0.020
 1JN  plan-2  C20  0.020
 1JN  plan-2  C22  0.020
 1JN  plan-2  N11  0.020
 1JN  plan-2  C12  0.020
 1JN  plan-2  C14  0.020
 1JN  plan-2  C16  0.020
 1JN  plan-2  C18  0.020
 1JN  plan-2  C19  0.020
 1JN  plan-2  N21  0.020
 1JN  plan-2  H11  0.020
 1JN  plan-2  H17  0.020
 1JN  plan-2  H18  0.020

