# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 11:39:46 2022
#   Inital geometry file: a 68 line input string
#   Ligand name: 5-(2-methoxyethoxy)-1~{H}-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1ccc2[nH]ccc2c1
#
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
 EY9  EY9  5-(2-methoxyethoxy)-1~{H}-indole  ligand  27  14  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EY9
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
 EY9  C10  C  CR56  0   0.080  1.0679  30.2320  22.3722
 EY9  C13  C  CR15  0  -0.023  0.8204  28.8490  24.1206
 EY9  C01  C  CH3   0  -0.393  5.5429  35.4435  19.4096
 EY9  C03  C  CH2   0  -0.163  3.6965  34.0358  19.6627
 EY9  C04  C  CH2   0  -0.237  2.1757  34.0764  19.7168
 EY9  C06  C  CR6   0   0.384  1.6115  32.1995  21.1086
 EY9  C07  C  CR16  0  -0.393  2.0337  32.8410  22.2892
 EY9  C08  C  CR16  0  -0.290  1.9791  32.1926  23.5099
 EY9  C09  C  CR56  0   0.329  1.4953  30.8911  23.5458
 EY9  C11  C  CR16  0  -0.460  1.1306  30.9011  21.1464
 EY9  C12  C  CR15  0  -0.424  0.6398  28.9270  22.7681
 EY9  N14  N  NR15  0  -0.680  1.3319  30.0220  24.5900
 EY9  O02  O  O2    0  -0.481  4.1437  35.3537  19.4863
 EY9  O05  O  O2    0  -0.492  1.6218  32.7894  19.8824
 EY9  H1   H  HCR5  0   0.278  0.6182  28.0322  24.7951
 EY9  H2   H  HCH3  0   0.233  5.8065  36.4918  19.2737
 EY9  H3   H  HCH3  0   0.204  6.0282  35.0802  20.3233
 EY9  H4   H  HCH3  0   0.204  5.9459  34.8727  18.5647
 EY9  H5   H  HCH2  0   0.207  4.1114  33.5991  20.5823
 EY9  H6   H  HCH2  0   0.208  4.0156  33.3909  18.8316
 EY9  H7   H  HCH2  0   0.226  1.8353  34.7710  20.4918
 EY9  H8   H  HCH2  0   0.256  1.7874  34.4433  18.7655
 EY9  H9   H  HCR6  0   0.270  2.4139  33.8528  22.2699
 EY9  H10  H  HCR6  0   0.261  2.3094  32.6979  24.4085
 EY9  H11  H  HCR6  0   0.246  0.8099  30.4169  20.2317
 EY9  H12  H  HCR5  0   0.243  0.2510  28.1467  22.1336
 EY9  H13  H  HNR5  0   0.407  1.5519  30.2138  25.5529

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
 EY9  C03  C04  single    1.522  0.020  1.522
 EY9  C03  O02  single    1.403  0.020  1.403
 EY9  C04  O05  single    1.411  0.020  1.411
 EY9  O05  C06  single    1.361  0.020  1.361
 EY9  O02  C01  single    1.404  0.020  1.404
 EY9  C06  C11  aromatic  1.385  0.020  1.385
 EY9  C06  C07  aromatic  1.408  0.020  1.408
 EY9  C11  C10  aromatic  1.398  0.020  1.398
 EY9  C07  C08  aromatic  1.383  0.020  1.383
 EY9  C10  C12  aromatic  1.429  0.020  1.429
 EY9  C10  C09  aromatic  1.412  0.020  1.412
 EY9  C12  C13  aromatic  1.367  0.020  1.367
 EY9  C08  C09  aromatic  1.389  0.020  1.389
 EY9  C09  N14  aromatic  1.368  0.020  1.368
 EY9  C13  N14  aromatic  1.363  0.020  1.363
 EY9  C13  H1   single    0.930  0.020  1.080
 EY9  C01  H2   single    0.970  0.020  1.090
 EY9  C01  H3   single    0.970  0.020  1.090
 EY9  C01  H4   single    0.970  0.020  1.090
 EY9  C03  H5   single    0.970  0.020  1.090
 EY9  C03  H6   single    0.970  0.020  1.090
 EY9  C04  H7   single    0.970  0.020  1.090
 EY9  C04  H8   single    0.970  0.020  1.090
 EY9  C07  H9   single    0.930  0.020  1.080
 EY9  C08  H10  single    0.930  0.020  1.080
 EY9  C11  H11  single    0.930  0.020  1.080
 EY9  C12  H12  single    0.930  0.020  1.080
 EY9  N14  H13  single    0.860  0.020  1.020

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
 EY9  C12  C10  C11  133.89  3.000
 EY9  C12  C10  C09  106.66  3.000
 EY9  C11  C10  C09  119.45  3.000
 EY9  H1   C13  N14  120.45  3.000
 EY9  H1   C13  C12  129.60  3.000
 EY9  N14  C13  C12  109.95  3.000
 EY9  H4   C01  H3   107.87  3.000
 EY9  H4   C01  H2   108.42  3.000
 EY9  H3   C01  H2   108.40  3.000
 EY9  H4   C01  O02  112.03  3.000
 EY9  H3   C01  O02  111.98  3.000
 EY9  H2   C01  O02  108.03  3.000
 EY9  H6   C03  H5   106.85  3.000
 EY9  H6   C03  O02  111.32  3.000
 EY9  H5   C03  O02  110.98  3.000
 EY9  H6   C03  C04  109.42  3.000
 EY9  H5   C03  C04  110.97  3.000
 EY9  O02  C03  C04  107.33  3.000
 EY9  H8   C04  H7   107.04  3.000
 EY9  H8   C04  O05  105.63  3.000
 EY9  H7   C04  O05  111.94  3.000
 EY9  H8   C04  C03  109.48  3.000
 EY9  H7   C04  C03  110.65  3.000
 EY9  O05  C04  C03  111.84  3.000
 EY9  O05  C06  C11  115.69  3.000
 EY9  C11  C06  C07  120.54  3.000
 EY9  O05  C06  C07  123.76  3.000
 EY9  H9   C07  C08  117.93  3.000
 EY9  H9   C07  C06  121.12  3.000
 EY9  C08  C07  C06  120.96  3.000
 EY9  H10  C08  C09  121.48  3.000
 EY9  H10  C08  C07  120.11  3.000
 EY9  C09  C08  C07  118.41  3.000
 EY9  N14  C09  C08  131.03  3.000
 EY9  N14  C09  C10  107.55  3.000
 EY9  C08  C09  C10  121.42  3.000
 EY9  H11  C11  C06  119.91  3.000
 EY9  H11  C11  C10  120.87  3.000
 EY9  C06  C11  C10  119.22  3.000
 EY9  H12  C12  C13  126.06  3.000
 EY9  H12  C12  C10  127.28  3.000
 EY9  C13  C12  C10  106.65  3.000
 EY9  H13  N14  C09  125.67  3.000
 EY9  H13  N14  C13  125.15  3.000
 EY9  C09  N14  C13  109.19  3.000
 EY9  C03  O02  C01  112.62  3.000
 EY9  C06  O05  C04  120.27  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
 EY9  CONST_01  C07  C06  C11  C10     0.00   0.0  0
 EY9  CONST_02  N14  C13  C12  C10     0.00   0.0  0
 EY9  CONST_03  C07  C08  C09  C10     0.00   0.0  0
 EY9  CONST_04  C13  N14  C09  C10     0.00   0.0  0
 EY9  CONST_05  C11  C10  C12  C13   180.00   0.0  0
 EY9  CONST_06  C09  C10  C12  C13     0.00   0.0  0
 EY9  CONST_07  C08  C09  N14  C13   180.00   0.0  0
 EY9  CONST_08  C12  C10  C11  C06   180.00   0.0  0
 EY9  CONST_09  C09  C10  C11  C06     0.00   0.0  0
 EY9  CONST_10  C09  C08  C07  C06     0.00   0.0  0
 EY9  CONST_11  N14  C09  C08  C07   180.00   0.0  0
 EY9  CONST_12  C11  C06  C07  C08     0.00   0.0  0
 EY9  CONST_13  C11  C10  C09  C08     0.00   0.0  0
 EY9  CONST_14  C12  C10  C09  C08   180.00   0.0  0
 EY9  CONST_15  C12  C13  N14  C09     0.00   0.0  0
 EY9  CONST_16  N14  C09  C10  C11   180.00   0.0  0
 EY9  CONST_17  N14  C09  C10  C12     0.00   0.0  0
 EY9  CONST_18  O05  C06  C11  C10   180.00   0.0  0
 EY9  CONST_19  O05  C06  C07  C08   180.00   0.0  0
 EY9  CONST_20  H1   C13  C12  C10   180.00   0.0  0
 EY9  CONST_21  H10  C08  C09  C10   180.00   0.0  0
 EY9  CONST_22  H13  N14  C09  C10   180.00   0.0  0
 EY9  CONST_23  H11  C11  C06  C07   180.00   0.0  0
 EY9  CONST_24  H12  C12  C10  C09   180.00   0.0  0
 EY9  CONST_25  H9   C07  C08  C09   180.00   0.0  0
 EY9  Var_01    C11  C06  O05  C04  -175.68  30.0  2
 EY9  Var_02    H7   C04  O05  C06   -46.30  30.0  2
 EY9  Var_03    C04  C03  O02  C01  -179.49  30.0  1
 EY9  Var_04    O05  C04  C03  O02   179.51  30.0  3
 EY9  Var_05    H2   C01  O02  C03  -180.00  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
 EY9  plan-1  C10  0.020
 EY9  plan-1  C13  0.020
 EY9  plan-1  C06  0.020
 EY9  plan-1  C07  0.020
 EY9  plan-1  C08  0.020
 EY9  plan-1  C09  0.020
 EY9  plan-1  C11  0.020
 EY9  plan-1  C12  0.020
 EY9  plan-1  N14  0.020
 EY9  plan-1  O05  0.020
 EY9  plan-1  H1   0.020
 EY9  plan-1  H9   0.020
 EY9  plan-1  H10  0.020
 EY9  plan-1  H11  0.020
 EY9  plan-1  H12  0.020
 EY9  plan-1  H13  0.020

