# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 13:46:14 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-{3-[(naphthalen-1-yl)oxy]propyl}-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1[nH]c2ccccc2c1CCCOc3cccc4ccccc34
#
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
 CJY  CJY  '3-{3-[(naphthalen-1-yl)oxy]propyl}-1H-indole-2-carboxylic acid'  ligand  44  26  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CJY
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
 CJY  C4   C  CR16   0  -0.287   5.6301   2.8911   0.2400
 CJY  C5   C  CR16   0  -0.244  -4.8989  -0.3077  -2.4065
 CJY  C6   C  CR16   0  -0.317  -6.6097   0.4331   0.7984
 CJY  C7   C  CR16   0  -0.287  -3.9479   0.4495   1.6279
 CJY  C8   C  CR16   0  -0.373   3.5819   2.2463  -0.8881
 CJY  C10  C  CR16   0  -0.312   5.7740   1.6393   0.8057
 CJY  C13  C  CR66   0  -0.020  -4.2420   0.1918   0.2687
 CJY  C15  C  CR5    0   0.021   2.9113  -0.2238  -0.4147
 CJY  C17  C  CR6    0   0.368  -3.2173  -0.0610  -0.6944
 CJY  C20  C  CH2    0  -0.178  -0.8745  -0.2618  -1.0929
 CJY  C1   C  CR16   0  -0.252  -6.2996   0.6785   2.1085
 CJY  C2   C  CR16   0  -0.257  -4.9546   0.6866   2.5263
 CJY  C3   C  CR16   0  -0.272   4.5440   3.1938  -0.6010
 CJY  C9   C  CR16   0  -0.347  -5.9042  -0.0714  -1.5141
 CJY  C11  C  CR16   0  -0.410  -3.5461  -0.3059  -2.0059
 CJY  C12  C  CR66   0   0.127  -5.5954   0.1837  -0.1555
 CJY  C14  C  CR56   0   0.033   3.6994   0.9668  -0.3295
 CJY  C16  C  CR56   0   0.344   4.7992   0.6836   0.5140
 CJY  C23  C  CR5    0   0.091   3.5407  -1.1617   0.3697
 CJY  C18  C  CH2    0  -0.521   1.6346  -0.3553  -1.1789
 CJY  C19  C  CH2    0  -0.452   0.4060  -0.1397  -0.2956
 CJY  N22  N  NR15   0  -0.720   4.6719  -0.6062   0.9150
 CJY  O25  O  OC    -1  -0.605   4.0010  -3.1858   1.4322
 CJY  O26  O  O      0  -0.577   2.1536  -3.0452   0.1824
 CJY  O21  O  O2     0  -0.467  -1.9655  -0.0359  -0.2134
 CJY  H1   H  HCR6   0   0.246   6.3675   3.6557   0.4487
 CJY  H4   H  HCR6   0   0.254  -2.9203   0.4617   1.9644
 CJY  H5   H  HCR6   0   0.237   2.7476   2.4906  -1.5358
 CJY  H6   H  HCR6   0   0.254   6.6117   1.4106   1.4527
 CJY  H7   H  HCH2   0   0.220  -0.8911   0.4692  -1.9104
 CJY  H8   H  HCH2   0   0.221  -0.9505  -1.2590  -1.5422
 CJY  H9   H  HCR6   0   0.257  -7.0868   0.8670   2.8269
 CJY  H10  H  HCR6   0   0.257  -4.7161   0.8812   3.5637
 CJY  H11  H  HCR6   0   0.242   4.4657   4.1863  -1.0264
 CJY  H12  H  HCR6   0   0.249  -6.9397  -0.0776  -1.8312
 CJY  H13  H  HCR6   0   0.280  -2.7852  -0.4989  -2.7496
 CJY  H14  H  HCH2   0   0.225   1.6268   0.3757  -1.9939
 CJY  H15  H  HCH2   0   0.237   1.5746  -1.3413  -1.6406
 CJY  H16  H  HCH2   0   0.229   0.4540   0.8484   0.1705
 CJY  H17  H  HCH2   0   0.239   0.4148  -0.8818   0.5056
 CJY  H18  H  HNR5   0   0.391   5.2922  -1.1121   1.5253
 CJY  C24  C  C      0   0.365   3.1969  -2.5901   0.6862
 CJY  H2   H  HCR6   0   0.258  -5.1294  -0.5023  -3.4460
 CJY  H3   H  HCR6   0   0.254  -7.6433   0.4257   0.4735

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
 CJY  C9   C5   aromatic  1.365  0.020  1.365
 CJY  C9   C12  aromatic  1.416  0.020  1.416
 CJY  C6   C12  aromatic  1.415  0.020  1.415
 CJY  C6   C1   aromatic  1.369  0.020  1.369
 CJY  C5   C11  aromatic  1.411  0.020  1.411
 CJY  C12  C13  aromatic  1.418  0.020  1.418
 CJY  C1   C2   aromatic  1.408  0.020  1.408
 CJY  C11  C17  aromatic  1.374  0.020  1.374
 CJY  C13  C17  aromatic  1.429  0.020  1.429
 CJY  C13  C7   aromatic  1.414  0.020  1.414
 CJY  C2   C7   aromatic  1.370  0.020  1.370
 CJY  C17  O21  single    1.341  0.020  1.341
 CJY  O21  C20  single    1.419  0.020  1.419
 CJY  C3   C4   aromatic  1.407  0.020  1.407
 CJY  C3   C8   aromatic  1.381  0.020  1.381
 CJY  C4   C10  aromatic  1.381  0.020  1.381
 CJY  C20  C19  single    1.513  0.020  1.513
 CJY  C8   C14  aromatic  1.401  0.020  1.401
 CJY  C10  C16  aromatic  1.396  0.020  1.396
 CJY  C14  C16  aromatic  1.415  0.020  1.415
 CJY  C14  C15  aromatic  1.430  0.020  1.430
 CJY  C19  C18  single    1.528  0.020  1.528
 CJY  C16  N22  aromatic  1.357  0.020  1.357
 CJY  C15  C18  single    1.494  0.020  1.494
 CJY  C15  C23  aromatic  1.375  0.020  1.375
 CJY  N22  C23  aromatic  1.373  0.020  1.373
 CJY  C23  C24  single    1.503  0.020  1.503
 CJY  C24  O26  deloc     1.245  0.020  1.245
 CJY  C24  O25  deloc     1.248  0.020  1.248
 CJY  C4   H1   single    0.930  0.020  1.080
 CJY  C5   H2   single    0.930  0.020  1.080
 CJY  C6   H3   single    0.930  0.020  1.080
 CJY  C7   H4   single    0.930  0.020  1.080
 CJY  C8   H5   single    0.930  0.020  1.080
 CJY  C10  H6   single    0.930  0.020  1.080
 CJY  C20  H7   single    0.970  0.020  1.090
 CJY  C20  H8   single    0.970  0.020  1.090
 CJY  C1   H9   single    0.930  0.020  1.080
 CJY  C2   H10  single    0.930  0.020  1.080
 CJY  C3   H11  single    0.930  0.020  1.080
 CJY  C9   H12  single    0.930  0.020  1.080
 CJY  C11  H13  single    0.930  0.020  1.080
 CJY  C18  H14  single    0.970  0.020  1.090
 CJY  C18  H15  single    0.970  0.020  1.090
 CJY  C19  H16  single    0.970  0.020  1.090
 CJY  C19  H17  single    0.970  0.020  1.090
 CJY  N22  H18  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
 CJY  H1   C4   C3   119.29  3.000
 CJY  H1   C4   C10  119.35  3.000
 CJY  C3   C4   C10  121.36  3.000
 CJY  H2   C5   C11  118.50  3.000
 CJY  H2   C5   C9   120.14  3.000
 CJY  C11  C5   C9   121.36  3.000
 CJY  H3   C6   C12  118.73  3.000
 CJY  H3   C6   C1   120.30  3.000
 CJY  C12  C6   C1   120.98  3.000
 CJY  H4   C7   C2   119.49  3.000
 CJY  H4   C7   C13  119.91  3.000
 CJY  C2   C7   C13  120.60  3.000
 CJY  H5   C8   C14  120.57  3.000
 CJY  H5   C8   C3   120.39  3.000
 CJY  C14  C8   C3   119.04  3.000
 CJY  H6   C10  C16  121.36  3.000
 CJY  H6   C10  C4   121.11  3.000
 CJY  C16  C10  C4   117.52  3.000
 CJY  C12  C13  C17  118.80  3.000
 CJY  C17  C13  C7   122.07  3.000
 CJY  C12  C13  C7   119.14  3.000
 CJY  C18  C15  C23  128.54  3.000
 CJY  C23  C15  C14  106.35  3.000
 CJY  C18  C15  C14  125.08  3.000
 CJY  O21  C17  C11  124.68  3.000
 CJY  O21  C17  C13  115.10  3.000
 CJY  C11  C17  C13  120.22  3.000
 CJY  H8   C20  H7   107.44  3.000
 CJY  H8   C20  O21  110.21  3.000
 CJY  H7   C20  O21  110.13  3.000
 CJY  H8   C20  C19  110.36  3.000
 CJY  H7   C20  C19  110.59  3.000
 CJY  O21  C20  C19  108.12  3.000
 CJY  H9   C1   C2   119.78  3.000
 CJY  H9   C1   C6   120.12  3.000
 CJY  C2   C1   C6   120.09  3.000
 CJY  H10  C2   C1   119.73  3.000
 CJY  H10  C2   C7   119.86  3.000
 CJY  C1   C2   C7   120.41  3.000
 CJY  H11  C3   C8   119.81  3.000
 CJY  H11  C3   C4   119.21  3.000
 CJY  C8   C3   C4   120.98  3.000
 CJY  H12  C9   C12  119.36  3.000
 CJY  H12  C9   C5   120.79  3.000
 CJY  C12  C9   C5   119.85  3.000
 CJY  H13  C11  C17  121.32  3.000
 CJY  H13  C11  C5   118.63  3.000
 CJY  C17  C11  C5   120.05  3.000
 CJY  C9   C12  C13  119.73  3.000
 CJY  C13  C12  C6   118.78  3.000
 CJY  C9   C12  C6   121.49  3.000
 CJY  C16  C14  C15  107.30  3.000
 CJY  C15  C14  C8   133.64  3.000
 CJY  C16  C14  C8   119.06  3.000
 CJY  N22  C16  C14  107.07  3.000
 CJY  N22  C16  C10  130.89  3.000
 CJY  C14  C16  C10  122.04  3.000
 CJY  N22  C23  C24  119.30  3.000
 CJY  C24  C23  C15  131.57  3.000
 CJY  N22  C23  C15  109.13  3.000
 CJY  H15  C18  H14  106.75  3.000
 CJY  H15  C18  C19  109.15  3.000
 CJY  H14  C18  C19  109.29  3.000
 CJY  H15  C18  C15  110.08  3.000
 CJY  H14  C18  C15  109.15  3.000
 CJY  C19  C18  C15  112.27  3.000
 CJY  H17  C19  H16  107.51  3.000
 CJY  H17  C19  C18  108.76  3.000
 CJY  H16  C19  C18  109.78  3.000
 CJY  H17  C19  C20  109.79  3.000
 CJY  H16  C19  C20  109.55  3.000
 CJY  C18  C19  C20  111.37  3.000
 CJY  H18  N22  C23  123.03  3.000
 CJY  H18  N22  C16  126.81  3.000
 CJY  C23  N22  C16  110.16  3.000
 CJY  C20  O21  C17  119.48  3.000
 CJY  O26  C24  O25  127.40  3.000
 CJY  O25  C24  C23  115.60  3.000
 CJY  O26  C24  C23  117.00  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
 CJY  CONST_01  C14  C8   C3   C4      0.00   0.0  0
 CJY  CONST_02  C14  C16  C10  C4      0.00   0.0  0
 CJY  CONST_03  N22  C16  C10  C4    180.00   0.0  0
 CJY  CONST_04  C6   C12  C9   C5    180.00   0.0  0
 CJY  CONST_05  C13  C12  C9   C5      0.00   0.0  0
 CJY  CONST_06  C13  C17  C11  C5      0.00   0.0  0
 CJY  CONST_07  C17  C13  C12  C6    180.00   0.0  0
 CJY  CONST_08  C7   C13  C12  C6      0.00   0.0  0
 CJY  CONST_09  C7   C2   C1   C6      0.00   0.0  0
 CJY  CONST_10  C9   C12  C13  C7    180.00   0.0  0
 CJY  CONST_11  C11  C17  C13  C7    180.00   0.0  0
 CJY  CONST_12  C10  C4   C3   C8      0.00   0.0  0
 CJY  CONST_13  C10  C16  C14  C8      0.00   0.0  0
 CJY  CONST_14  N22  C16  C14  C8    180.00   0.0  0
 CJY  CONST_15  C23  C15  C14  C8    180.00   0.0  0
 CJY  CONST_16  C15  C14  C16  C10   180.00   0.0  0
 CJY  CONST_17  C23  N22  C16  C10   180.00   0.0  0
 CJY  CONST_18  C1   C6   C12  C13     0.00   0.0  0
 CJY  CONST_19  C1   C2   C7   C13     0.00   0.0  0
 CJY  CONST_20  C3   C8   C14  C15   180.00   0.0  0
 CJY  CONST_21  N22  C16  C14  C15     0.00   0.0  0
 CJY  CONST_22  C16  N22  C23  C15     0.00   0.0  0
 CJY  CONST_23  C9   C5   C11  C17     0.00   0.0  0
 CJY  CONST_24  C9   C12  C13  C17     0.00   0.0  0
 CJY  CONST_25  C2   C7   C13  C17   180.00   0.0  0
 CJY  CONST_26  C9   C12  C6   C1    180.00   0.0  0
 CJY  CONST_27  C12  C6   C1   C2      0.00   0.0  0
 CJY  CONST_28  C12  C13  C7   C2      0.00   0.0  0
 CJY  CONST_29  C16  C10  C4   C3      0.00   0.0  0
 CJY  CONST_30  C16  C14  C8   C3      0.00   0.0  0
 CJY  CONST_31  C12  C9   C5   C11     0.00   0.0  0
 CJY  CONST_32  C12  C13  C17  C11     0.00   0.0  0
 CJY  CONST_33  C23  N22  C16  C14     0.00   0.0  0
 CJY  CONST_34  N22  C23  C15  C14     0.00   0.0  0
 CJY  CONST_35  C23  C15  C14  C16     0.00   0.0  0
 CJY  CONST_36  O21  C17  C11  C5    180.00   0.0  0
 CJY  CONST_37  O21  C17  C13  C7      0.00   0.0  0
 CJY  CONST_38  C18  C15  C14  C8      0.00   0.0  0
 CJY  CONST_39  C14  C15  C23  C24   180.00   0.0  0
 CJY  CONST_40  C16  N22  C23  C24   180.00   0.0  0
 CJY  CONST_41  O21  C17  C13  C12   180.00   0.0  0
 CJY  CONST_42  C18  C15  C14  C16   180.00   0.0  0
 CJY  CONST_43  N22  C23  C15  C18   180.00   0.0  0
 CJY  CONST_44  H5   C8   C3   C4    180.00   0.0  0
 CJY  CONST_45  H12  C9   C12  C6      0.00   0.0  0
 CJY  CONST_46  H10  C2   C1   C6    180.00   0.0  0
 CJY  CONST_47  H9   C1   C2   C7    180.00   0.0  0
 CJY  CONST_48  H1   C4   C3   C8    180.00   0.0  0
 CJY  CONST_49  H11  C3   C4   C10   180.00   0.0  0
 CJY  CONST_50  H18  N22  C16  C10     0.00   0.0  0
 CJY  CONST_51  H3   C6   C12  C13   180.00   0.0  0
 CJY  CONST_52  H13  C11  C17  C13   180.00   0.0  0
 CJY  CONST_53  H2   C5   C11  C17   180.00   0.0  0
 CJY  CONST_54  H4   C7   C13  C17     0.00   0.0  0
 CJY  CONST_55  H6   C10  C4   C3    180.00   0.0  0
 CJY  Var_01    O26  C24  C23  C15    -1.02  30.0  2
 CJY  Var_02    C11  C17  O21  C20     0.60  30.0  1
 CJY  Var_03    C19  C18  C15  C14   -95.55  30.0  2
 CJY  Var_04    C20  C19  C18  C15   179.35  30.0  1
 CJY  Var_05    C19  C20  O21  C17   178.51  30.0  3
 CJY  Var_06    O21  C20  C19  C18  -179.36  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
 CJY  plan-1  C4   0.020
 CJY  plan-1  C8   0.020
 CJY  plan-1  C10  0.020
 CJY  plan-1  C15  0.020
 CJY  plan-1  C3   0.020
 CJY  plan-1  C14  0.020
 CJY  plan-1  C16  0.020
 CJY  plan-1  C23  0.020
 CJY  plan-1  C18  0.020
 CJY  plan-1  N22  0.020
 CJY  plan-1  H1   0.020
 CJY  plan-1  H5   0.020
 CJY  plan-1  H6   0.020
 CJY  plan-1  H11  0.020
 CJY  plan-1  H18  0.020
 CJY  plan-1  C24  0.020
 CJY  plan-2  C5   0.020
 CJY  plan-2  C6   0.020
 CJY  plan-2  C7   0.020
 CJY  plan-2  C13  0.020
 CJY  plan-2  C17  0.020
 CJY  plan-2  C1   0.020
 CJY  plan-2  C2   0.020
 CJY  plan-2  C9   0.020
 CJY  plan-2  C11  0.020
 CJY  plan-2  C12  0.020
 CJY  plan-2  O21  0.020
 CJY  plan-2  H4   0.020
 CJY  plan-2  H9   0.020
 CJY  plan-2  H10  0.020
 CJY  plan-2  H12  0.020
 CJY  plan-2  H13  0.020
 CJY  plan-2  H2   0.020
 CJY  plan-2  H3   0.020
 CJY  plan-3  C23  0.020
 CJY  plan-3  O25  0.020
 CJY  plan-3  O26  0.020
 CJY  plan-3  C24  0.020

