# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 03:29:35 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 1H-indole-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1c[nH]c2ccccc12
#
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
 C2Y  C2Y  'methyl 1H-indole-3-carboxylate'  ligand  22  13  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C2Y
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
 C2Y  C4  C  CR56  0   0.350  -1.6197  -0.8721  -0.0155
 C2Y  C5  C  CR56  0   0.085  -0.7305   0.2208  -0.0128
 C2Y  C6  C  CR16  0  -0.369  -1.2545   1.5182  -0.0200
 C2Y  C7  C  CR16  0  -0.258  -2.6266   1.6803  -0.0281
 C2Y  C8  C  CR16  0  -0.281  -3.4927   0.5760  -0.0304
 C2Y  C9  C  CR16  0  -0.296  -3.0027  -0.7157  -0.0244
 C2Y  N   N  NR15  0  -0.674  -0.8642  -2.0177  -0.0068
 C2Y  O   O  O     0  -0.465   1.9222   1.6122  -0.0069
 C2Y  C1  C  CH3   0  -0.421   4.1918   0.2213   0.0290
 C2Y  C2  C  CR5   0  -0.194   0.5940  -0.3362  -0.0020
 C2Y  C3  C  CR15  0   0.004   0.4459  -1.7054   0.0013
 C2Y  O1  O  O2    0  -0.468   2.9075  -0.3967   0.0236
 C2Y  H1  H  HCR6  0   0.248  -0.5988   2.3775  -0.0188
 C2Y  H2  H  HCR6  0   0.251  -3.0448   2.6788  -0.0329
 C2Y  H3  H  HCR6  0   0.255  -4.5626   0.7380  -0.0371
 C2Y  H4  H  HCR6  0   0.267  -3.6675  -1.5695  -0.0269
 C2Y  H5  H  HNR5  0   0.422  -1.2260  -2.9581  -0.0090
 C2Y  H6  H  HCH3  0   0.249   4.9128  -0.5900   0.0675
 C2Y  H7  H  HCH3  0   0.235   4.3580   0.8088  -0.8739
 C2Y  H8  H  HCH3  0   0.235   4.3258   0.8624   0.9004
 C2Y  H9  H  HCR5  0   0.303   1.1946  -2.4807   0.0082
 C2Y  C   C  C     0   0.522   1.8428   0.4031   0.0045

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
 C2Y  C7  C8  aromatic  1.403  0.020  1.403
 C2Y  C7  C6  aromatic  1.382  0.020  1.382
 C2Y  C8  C9  aromatic  1.382  0.020  1.382
 C2Y  C6  C5  aromatic  1.399  0.020  1.399
 C2Y  C9  C4  aromatic  1.392  0.020  1.392
 C2Y  C5  C4  aromatic  1.409  0.020  1.409
 C2Y  C5  C2  aromatic  1.437  0.020  1.437
 C2Y  O1  C1  single    1.425  0.020  1.425
 C2Y  O1  C   single    1.332  0.020  1.332
 C2Y  C4  N   aromatic  1.372  0.020  1.372
 C2Y  C2  C   single    1.451  0.020  1.451
 C2Y  C2  C3  aromatic  1.377  0.020  1.377
 C2Y  C   O   double    1.212  0.020  1.212
 C2Y  N   C3  aromatic  1.347  0.020  1.347
 C2Y  C6  H1  single    0.930  0.020  1.080
 C2Y  C7  H2  single    0.930  0.020  1.080
 C2Y  C8  H3  single    0.930  0.020  1.080
 C2Y  C9  H4  single    0.930  0.020  1.080
 C2Y  N   H5  single    0.860  0.020  1.020
 C2Y  C1  H6  single    0.970  0.020  1.090
 C2Y  C1  H7  single    0.970  0.020  1.090
 C2Y  C1  H8  single    0.970  0.020  1.090
 C2Y  C3  H9  single    0.930  0.020  1.080

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
 C2Y  N   C4  C9  129.86  3.000
 C2Y  N   C4  C5  107.46  3.000
 C2Y  C9  C4  C5  122.68  3.000
 C2Y  C2  C5  C6  134.80  3.000
 C2Y  C2  C5  C4  106.33  3.000
 C2Y  C6  C5  C4  118.87  3.000
 C2Y  H1  C6  C7  120.60  3.000
 C2Y  H1  C6  C5  120.66  3.000
 C2Y  C7  C6  C5  118.73  3.000
 C2Y  H2  C7  C8  119.17  3.000
 C2Y  H2  C7  C6  119.46  3.000
 C2Y  C8  C7  C6  121.37  3.000
 C2Y  H3  C8  C9  119.39  3.000
 C2Y  H3  C8  C7  119.50  3.000
 C2Y  C9  C8  C7  121.12  3.000
 C2Y  H4  C9  C8  121.32  3.000
 C2Y  H4  C9  C4  121.45  3.000
 C2Y  C8  C9  C4  117.23  3.000
 C2Y  H5  N   C3  124.45  3.000
 C2Y  H5  N   C4  125.55  3.000
 C2Y  C3  N   C4  109.99  3.000
 C2Y  H8  C1  H7  109.05  3.000
 C2Y  H8  C1  H6  109.24  3.000
 C2Y  H7  C1  H6  109.31  3.000
 C2Y  H8  C1  O1  111.64  3.000
 C2Y  H7  C1  O1  111.59  3.000
 C2Y  H6  C1  O1  105.92  3.000
 C2Y  C3  C2  C   126.80  3.000
 C2Y  C3  C2  C5  106.63  3.000
 C2Y  C   C2  C5  126.57  3.000
 C2Y  H9  C3  C2  129.82  3.000
 C2Y  H9  C3  N   120.59  3.000
 C2Y  C2  C3  N   109.58  3.000
 C2Y  C1  O1  C   117.39  3.000
 C2Y  O1  C   C2  112.46  3.000
 C2Y  C2  C   O   124.38  3.000
 C2Y  O1  C   O   123.16  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
 C2Y  CONST_01  C7  C8  C9  C4    0.00   0.0  0
 C2Y  CONST_02  C7  C6  C5  C4    0.00   0.0  0
 C2Y  CONST_03  C3  C2  C5  C4    0.00   0.0  0
 C2Y  CONST_04  C2  C3  N   C4    0.00   0.0  0
 C2Y  CONST_05  C8  C7  C6  C5    0.00   0.0  0
 C2Y  CONST_06  C8  C9  C4  C5    0.00   0.0  0
 C2Y  CONST_07  C3  N   C4  C5    0.00   0.0  0
 C2Y  CONST_08  N   C3  C2  C5    0.00   0.0  0
 C2Y  CONST_09  C9  C8  C7  C6    0.00   0.0  0
 C2Y  CONST_10  C9  C4  C5  C6    0.00   0.0  0
 C2Y  CONST_11  N   C4  C5  C6  180.00   0.0  0
 C2Y  CONST_12  C3  C2  C5  C6  180.00   0.0  0
 C2Y  CONST_13  C2  C5  C6  C7  180.00   0.0  0
 C2Y  CONST_14  N   C4  C9  C8  180.00   0.0  0
 C2Y  CONST_15  C2  C5  C4  C9  180.00   0.0  0
 C2Y  CONST_16  C3  N   C4  C9  180.00   0.0  0
 C2Y  CONST_17  C2  C5  C4  N     0.00   0.0  0
 C2Y  CONST_18  C   C2  C5  C4  180.00   0.0  0
 C2Y  CONST_19  C   C2  C5  C6    0.00   0.0  0
 C2Y  CONST_20  C   C2  C3  N   180.00   0.0  0
 C2Y  CONST_21  H3  C8  C9  C4  180.00   0.0  0
 C2Y  CONST_22  H1  C6  C5  C4  180.00   0.0  0
 C2Y  CONST_23  H9  C3  N   C4  180.00   0.0  0
 C2Y  CONST_24  H2  C7  C6  C5  180.00   0.0  0
 C2Y  CONST_25  H4  C9  C4  C5  180.00   0.0  0
 C2Y  CONST_26  H5  N   C4  C5  180.00   0.0  0
 C2Y  Var_01    O1  C   C2  C5  179.56  30.0  2
 C2Y  Var_02    C2  C   O1  C1  179.88  30.0  3
 C2Y  Var_03    H6  C1  O1  C   178.76  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
 C2Y  plan-1  C4  0.020
 C2Y  plan-1  C5  0.020
 C2Y  plan-1  C6  0.020
 C2Y  plan-1  C7  0.020
 C2Y  plan-1  C8  0.020
 C2Y  plan-1  C9  0.020
 C2Y  plan-1  N   0.020
 C2Y  plan-1  C2  0.020
 C2Y  plan-1  C3  0.020
 C2Y  plan-1  H1  0.020
 C2Y  plan-1  H2  0.020
 C2Y  plan-1  H3  0.020
 C2Y  plan-1  H4  0.020
 C2Y  plan-1  H5  0.020
 C2Y  plan-1  H9  0.020
 C2Y  plan-1  C   0.020
 C2Y  plan-2  O   0.020
 C2Y  plan-2  C2  0.020
 C2Y  plan-2  O1  0.020
 C2Y  plan-2  C   0.020

