# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 01:08:10 2022
#   Inital geometry file: a 79 line input string
#   Ligand name: (5-ethyl-2-methyl-1H-indol-3-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1ccc2[nH]c(C)c(CC(O)=O)c2c1
#
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
 2JI  2JI  "(5-ethyl-2-methyl-1H-indol-3-yl)acetic acid"  ligand  30  16  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2JI
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
 2JI  C4   C  CR16   0  -0.330  -19.7394  -12.6247   1.6224
 2JI  C14  C  CH2    0  -0.664  -22.9147  -15.4921   4.7943
 2JI  C5   C  CR16   0  -0.300  -20.2253  -13.7416   0.9674
 2JI  C6   C  CR56   0   0.316  -21.0757  -14.5858   1.6763
 2JI  C7   C  CR56   0   0.083  -21.4362  -14.3225   3.0140
 2JI  C8   C  CR16   0  -0.438  -20.9181  -13.1887   3.6497
 2JI  C9   C  CR5    0  -0.023  -22.3173  -15.3719   3.4335
 2JI  C10  C  CR5    0   0.271  -22.4515  -16.2156   2.3626
 2JI  C13  C  CH3    0  -0.739  -23.2128  -17.4859   2.2352
 2JI  C3   C  CR6    0   0.116  -20.0747  -12.3335   2.9590
 2JI  C1   C  CH3    0  -0.651  -20.3816   -9.8464   3.2356
 2JI  C15  C  C      0   0.396  -21.9188  -16.0405   5.8496
 2JI  C2   C  CH2    0  -0.498  -19.5516  -11.0758   3.6016
 2JI  N11  N  NR15   0  -0.730  -21.7032  -15.7408   1.3108
 2JI  O16  O  O      0  -0.610  -21.7451  -15.3520   6.8752
 2JI  O17  O  OC    -1  -0.604  -21.3852  -17.1350   5.5839
 2JI  H1   H  HCR6   0   0.233  -19.0735  -11.9529   1.0923
 2JI  H2   H  HCH2   0   0.207  -23.3030  -14.5210   5.1128
 2JI  H3   H  HCH2   0   0.229  -23.7740  -16.1708   4.7630
 2JI  H4   H  HCR6   0   0.246  -19.9472  -13.9506  -0.0583
 2JI  H5   H  HCR6   0   0.224  -21.1726  -12.9813   4.6842
 2JI  H6   H  HCH3   0   0.248  -22.5507  -18.3544   2.2536
 2JI  H7   H  HCH3   0   0.251  -23.9208  -17.5976   3.0544
 2JI  H8   H  HCH3   0   0.244  -23.7744  -17.5256   1.3005
 2JI  H9   H  HCH3   0   0.224  -19.9805   -8.9458   3.7027
 2JI  H10  H  HCH3   0   0.221  -20.3921   -9.6852   2.1567
 2JI  H11  H  HCH3   0   0.221  -21.4156   -9.9618   3.5638
 2JI  H12  H  HCH2   0   0.229  -18.5137  -10.9105   3.3009
 2JI  H13  H  HCH2   0   0.231  -19.5429  -11.1934   4.6877
 2JI  H14  H  HNR5   0   0.397  -21.6406  -16.1776   0.4062

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
 2JI  C5   C6   aromatic  1.392  0.020  1.392
 2JI  C5   C4   aromatic  1.383  0.020  1.383
 2JI  N11  C6   aromatic  1.364  0.020  1.364
 2JI  N11  C10  aromatic  1.375  0.020  1.375
 2JI  C6   C7   aromatic  1.410  0.020  1.410
 2JI  C4   C3   aromatic  1.408  0.020  1.408
 2JI  C13  C10  single    1.486  0.020  1.486
 2JI  C10  C9   aromatic  1.370  0.020  1.370
 2JI  C1   C2   single    1.528  0.020  1.528
 2JI  C7   C9   aromatic  1.433  0.020  1.433
 2JI  C7   C8   aromatic  1.399  0.020  1.399
 2JI  C3   C8   aromatic  1.386  0.020  1.386
 2JI  C3   C2   single    1.506  0.020  1.506
 2JI  C9   C14  single    1.491  0.020  1.491
 2JI  C14  C15  single    1.551  0.020  1.551
 2JI  C15  O16  deloc     1.247  0.020  1.247
 2JI  C15  O17  deloc     1.246  0.020  1.246
 2JI  C4   H1   single    0.930  0.020  1.080
 2JI  C14  H2   single    0.970  0.020  1.090
 2JI  C14  H3   single    0.970  0.020  1.090
 2JI  C5   H4   single    0.930  0.020  1.080
 2JI  C8   H5   single    0.930  0.020  1.080
 2JI  C13  H6   single    0.970  0.020  1.090
 2JI  C13  H7   single    0.970  0.020  1.090
 2JI  C13  H8   single    0.970  0.020  1.090
 2JI  C1   H9   single    0.970  0.020  1.090
 2JI  C1   H10  single    0.970  0.020  1.090
 2JI  C1   H11  single    0.970  0.020  1.090
 2JI  C2   H12  single    0.970  0.020  1.090
 2JI  C2   H13  single    0.970  0.020  1.090
 2JI  N11  H14  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
 2JI  H1   C4   C3   118.82  3.000
 2JI  H1   C4   C5   118.99  3.000
 2JI  C3   C4   C5   122.19  3.000
 2JI  H3   C14  H2   106.26  3.000
 2JI  H3   C14  C15  107.70  3.000
 2JI  H2   C14  C15  110.11  3.000
 2JI  H3   C14  C9   109.76  3.000
 2JI  H2   C14  C9   109.67  3.000
 2JI  C15  C14  C9   113.09  3.000
 2JI  H4   C5   C6   121.47  3.000
 2JI  H4   C5   C4   120.93  3.000
 2JI  C6   C5   C4   117.59  3.000
 2JI  N11  C6   C7   107.13  3.000
 2JI  C7   C6   C5   121.73  3.000
 2JI  N11  C6   C5   131.13  3.000
 2JI  C9   C7   C8   133.47  3.000
 2JI  C8   C7   C6   119.18  3.000
 2JI  C9   C7   C6   107.35  3.000
 2JI  H5   C8   C3   120.00  3.000
 2JI  H5   C8   C7   120.07  3.000
 2JI  C3   C8   C7   119.94  3.000
 2JI  C10  C9   C7   106.40  3.000
 2JI  C7   C9   C14  124.93  3.000
 2JI  C10  C9   C14  128.65  3.000
 2JI  N11  C10  C13  120.54  3.000
 2JI  C13  C10  C9   130.05  3.000
 2JI  N11  C10  C9   109.39  3.000
 2JI  H8   C13  H7   107.83  3.000
 2JI  H8   C13  H6   107.31  3.000
 2JI  H7   C13  H6   107.46  3.000
 2JI  H8   C13  C10  111.60  3.000
 2JI  H7   C13  C10  110.87  3.000
 2JI  H6   C13  C10  111.57  3.000
 2JI  C2   C3   C8   120.94  3.000
 2JI  C2   C3   C4   119.66  3.000
 2JI  C8   C3   C4   119.37  3.000
 2JI  H11  C1   H10  107.70  3.000
 2JI  H11  C1   H9   107.88  3.000
 2JI  H10  C1   H9   107.76  3.000
 2JI  H11  C1   C2   110.96  3.000
 2JI  H10  C1   C2   111.16  3.000
 2JI  H9   C1   C2   111.22  3.000
 2JI  O17  C15  O16  126.90  3.000
 2JI  O17  C15  C14  116.12  3.000
 2JI  O16  C15  C14  116.98  3.000
 2JI  H13  C2   H12  106.40  3.000
 2JI  H13  C2   C1   109.21  3.000
 2JI  H12  C2   C1   109.16  3.000
 2JI  H13  C2   C3   109.69  3.000
 2JI  H12  C2   C3   109.80  3.000
 2JI  C1   C2   C3   112.40  3.000
 2JI  H14  N11  C10  124.85  3.000
 2JI  H14  N11  C6   125.42  3.000
 2JI  C10  N11  C6   109.73  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
 2JI  CONST_01  N11  C6   C5   C4    180.00   0.0  0
 2JI  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 2JI  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 2JI  CONST_04  C10  N11  C6   C5    180.00   0.0  0
 2JI  CONST_05  C9   C7   C6   C5    180.00   0.0  0
 2JI  CONST_06  C8   C7   C6   C5      0.00   0.0  0
 2JI  CONST_07  C8   C3   C4   C5      0.00   0.0  0
 2JI  CONST_08  C3   C4   C5   C6      0.00   0.0  0
 2JI  CONST_09  C9   C10  N11  C6      0.00   0.0  0
 2JI  CONST_10  C10  C9   C7   C6      0.00   0.0  0
 2JI  CONST_11  C3   C8   C7   C6      0.00   0.0  0
 2JI  CONST_12  C10  N11  C6   C7      0.00   0.0  0
 2JI  CONST_13  N11  C10  C9   C7      0.00   0.0  0
 2JI  CONST_14  N11  C6   C7   C8    180.00   0.0  0
 2JI  CONST_15  C10  C9   C7   C8    180.00   0.0  0
 2JI  CONST_16  N11  C6   C7   C9      0.00   0.0  0
 2JI  CONST_17  C3   C8   C7   C9    180.00   0.0  0
 2JI  CONST_18  N11  C10  C9   C14   180.00   0.0  0
 2JI  CONST_19  C6   C7   C9   C14   180.00   0.0  0
 2JI  CONST_20  C8   C7   C9   C14     0.00   0.0  0
 2JI  CONST_21  C2   C3   C4   C5    180.00   0.0  0
 2JI  CONST_22  C13  C10  N11  C6    180.00   0.0  0
 2JI  CONST_23  C13  C10  C9   C7    180.00   0.0  0
 2JI  CONST_24  C2   C3   C8   C7    180.00   0.0  0
 2JI  CONST_25  H5   C8   C3   C4    180.00   0.0  0
 2JI  CONST_26  H14  N11  C6   C5      0.00   0.0  0
 2JI  CONST_27  H1   C4   C5   C6    180.00   0.0  0
 2JI  CONST_28  H5   C8   C7   C6    180.00   0.0  0
 2JI  CONST_29  H4   C5   C6   C7    180.00   0.0  0
 2JI  CONST_30  H14  N11  C6   C7    180.00   0.0  0
 2JI  CONST_31  H1   C4   C3   C8    180.00   0.0  0
 2JI  CONST_32  H14  N11  C10  C9    180.00   0.0  0
 2JI  CONST_33  H5   C8   C7   C9      0.00   0.0  0
 2JI  CONST_34  H4   C5   C4   C3    180.00   0.0  0
 2JI  CONST_35  H4   C5   C6   N11     0.00   0.0  0
 2JI  Var_01    C1   C2   C3   C4     81.40  30.0  2
 2JI  Var_02    C15  C14  C9   C7    -77.66  30.0  2
 2JI  Var_03    C1   C2   C3   C8    -96.48  30.0  2
 2JI  Var_04    C15  C14  C9   C10   100.59  30.0  2
 2JI  Var_05    H12  C2   C3   C4    -40.31  30.0  2
 2JI  Var_06    H13  C2   C3   C4   -156.90  30.0  2
 2JI  Var_07    H2   C14  C9   C7     45.67  30.0  2
 2JI  Var_08    H3   C14  C9   C7    162.05  30.0  2
 2JI  Var_09    H12  C2   C3   C8    141.81  30.0  2
 2JI  Var_10    H13  C2   C3   C8     25.23  30.0  2
 2JI  Var_11    H6   C13  C10  C9   -104.70  30.0  2
 2JI  Var_12    H7   C13  C10  C9     15.04  30.0  2
 2JI  Var_13    H8   C13  C10  C9    135.27  30.0  2
 2JI  Var_14    H2   C14  C9   C10  -136.08  30.0  2
 2JI  Var_15    H3   C14  C9   C10   -19.70  30.0  2
 2JI  Var_16    H6   C13  C10  N11    73.37  30.0  2
 2JI  Var_17    H7   C13  C10  N11  -166.89  30.0  2
 2JI  Var_18    H8   C13  C10  N11   -46.67  30.0  2
 2JI  Var_19    O16  C15  C14  C9    125.16  30.0  3
 2JI  Var_20    O17  C15  C14  C9    -55.48  30.0  3
 2JI  Var_21    H9   C1   C2   C3   -179.43  30.0  3
 2JI  Var_22    H10  C1   C2   C3    -59.36  30.0  3
 2JI  Var_23    H11  C1   C2   C3     60.47  30.0  3
 2JI  Var_24    H2   C14  C15  O16     2.08  30.0  2
 2JI  Var_25    H3   C14  C15  O16  -113.38  30.0  2
 2JI  Var_26    H2   C14  C15  O17  -178.56  30.0  2
 2JI  Var_27    H3   C14  C15  O17    65.98  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
 2JI  plan-1  C4   0.020
 2JI  plan-1  C14  0.020
 2JI  plan-1  C5   0.020
 2JI  plan-1  C6   0.020
 2JI  plan-1  C7   0.020
 2JI  plan-1  C8   0.020
 2JI  plan-1  C9   0.020
 2JI  plan-1  C10  0.020
 2JI  plan-1  C13  0.020
 2JI  plan-1  C3   0.020
 2JI  plan-1  C2   0.020
 2JI  plan-1  N11  0.020
 2JI  plan-1  H1   0.020
 2JI  plan-1  H4   0.020
 2JI  plan-1  H5   0.020
 2JI  plan-1  H14  0.020
 2JI  plan-2  C14  0.020
 2JI  plan-2  C15  0.020
 2JI  plan-2  O16  0.020
 2JI  plan-2  O17  0.020

