# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:30:16 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (2S)-2-hydroxy-3-(1H-indol-3-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](Cc1c[nH]c2ccccc12)C(O)=O
#
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
 3IL  3IL  '(2S)-2-hydroxy-3-(1H-indol-3-yl)propanoic acid'  ligand  25  15  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3IL
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
 3IL  N1    N  NC1    0  -0.688  -2.0565  -2.0291   0.3351
 3IL  C2    C  C1     0  -0.095  -0.7217  -2.1227   0.0464
 3IL  C3    C  C      0   0.037  -0.2265  -0.9018  -0.3177
 3IL  C4    C  CR16   0  -0.360  -1.4879   1.3719  -0.5155
 3IL  C5    C  CR16   0  -0.275  -2.7353   1.9478  -0.3756
 3IL  C6    C  CR16   0  -0.286  -3.8439   1.1868   0.0349
 3IL  C7    C  CR16   0  -0.310  -3.7253  -0.1625   0.3059
 3IL  C8    C  CR6    0   0.349  -2.4648  -0.7413   0.1548
 3IL  C9    C  CR6    0   0.023  -1.3355   0.0051  -0.2526
 3IL  C10   C  C      0   0.386   3.4470   0.3258  -0.0604
 3IL  O11   O  OC    -1  -0.597   4.1286  -0.6176  -0.4902
 3IL  O12   O  O      0  -0.608   3.7799   1.5312   0.0198
 3IL  C13   C  CH1    0  -0.066   2.0151   0.0152   0.4294
 3IL  O14   O  OH1    0  -0.685   1.4310   1.1854   0.9374
 3IL  C15   C  CH2    0  -0.559   1.1816  -0.5915  -0.7047
 3IL  HN1   H  HNC1   0   0.405  -2.6417  -2.7982   0.6137
 3IL  H2    H  H      0   0.275  -0.2137  -3.0725   0.1161
 3IL  H4    H  HCR6   0   0.232  -0.6368   1.9681  -0.8174
 3IL  H5    H  HCR6   0   0.240  -2.8658   3.0035  -0.5770
 3IL  H6    H  HCR6   0   0.245  -4.8086   1.6669   0.1405
 3IL  H7    H  HCR6   0   0.254  -4.5803  -0.7476   0.6212
 3IL  H13   H  HCH1   0   0.197   2.0844  -0.7398   1.2268
 3IL  H14   H  HOH1   0   0.424   2.1144   1.8548   0.7461
 3IL  H151  H  HCH2   0   0.225   1.1865   0.0961  -1.5580
 3IL  H152  H  HCH2   0   0.237   1.6807  -1.5038  -1.0366

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
 3IL  N1   C2    aromatic  1.369  0.020  1.369
 3IL  N1   C8    aromatic  1.363  0.020  1.363
 3IL  N1   HN1   single    0.860  0.020  1.020
 3IL  C2   C3    aromatic  1.367  0.020  1.367
 3IL  C2   H2    single    0.930  0.020  1.080
 3IL  C3   C9    aromatic  1.434  0.020  1.434
 3IL  C3   C15   single    1.493  0.020  1.493
 3IL  C4   C5    aromatic  1.381  0.020  1.381
 3IL  C4   C9    aromatic  1.400  0.020  1.400
 3IL  C4   H4    single    0.930  0.020  1.080
 3IL  C5   C6    aromatic  1.406  0.020  1.406
 3IL  C5   H5    single    0.930  0.020  1.080
 3IL  C6   C7    aromatic  1.381  0.020  1.381
 3IL  C6   H6    single    0.930  0.020  1.080
 3IL  C7   C8    aromatic  1.395  0.020  1.395
 3IL  C7   H7    single    0.930  0.020  1.080
 3IL  C8   C9    aromatic  1.414  0.020  1.414
 3IL  C10  O11   deloc     1.241  0.020  1.241
 3IL  C10  O12   deloc     1.253  0.020  1.253
 3IL  C10  C13   single    1.545  0.020  1.545
 3IL  C13  O14   single    1.403  0.020  1.403
 3IL  C13  C15   single    1.533  0.020  1.533
 3IL  C13  H13   single    0.970  0.020  1.090
 3IL  O14  H14   single    0.850  0.020  0.980
 3IL  C15  H151  single    0.970  0.020  1.090
 3IL  C15  H152  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
 3IL  HN1   N1   C8    125.79  3.000
 3IL  HN1   N1   C2    124.99  3.000
 3IL  C8    N1   C2    109.20  3.000
 3IL  H2    C2   C3    129.25  3.000
 3IL  H2    C2   N1    120.36  3.000
 3IL  C3    C2   N1    110.39  3.000
 3IL  C15   C3   C9    127.56  3.000
 3IL  C15   C3   C2    126.61  3.000
 3IL  C9    C3   C2    105.82  3.000
 3IL  H4    C4   C9    120.31  3.000
 3IL  H4    C4   C5    120.59  3.000
 3IL  C9    C4   C5    119.10  3.000
 3IL  H5    C5   C6    119.15  3.000
 3IL  H5    C5   C4    119.78  3.000
 3IL  C6    C5   C4    121.07  3.000
 3IL  H6    C6   C7    119.37  3.000
 3IL  H6    C6   C5    119.41  3.000
 3IL  C7    C6   C5    121.22  3.000
 3IL  H7    C7   C8    121.37  3.000
 3IL  H7    C7   C6    121.14  3.000
 3IL  C8    C7   C6    117.49  3.000
 3IL  C9    C8   C7    122.27  3.000
 3IL  C9    C8   N1    107.32  3.000
 3IL  C7    C8   N1    130.42  3.000
 3IL  C8    C9   C4    118.86  3.000
 3IL  C8    C9   C3    107.27  3.000
 3IL  C4    C9   C3    133.87  3.000
 3IL  C13   C10  O12   114.79  3.000
 3IL  C13   C10  O11   117.79  3.000
 3IL  O12   C10  O11   127.42  3.000
 3IL  H13   C13  C15   107.39  3.000
 3IL  H13   C13  O14   109.64  3.000
 3IL  C15   C13  O14   111.81  3.000
 3IL  H13   C13  C10   108.02  3.000
 3IL  C15   C13  C10   110.43  3.000
 3IL  O14   C13  C10   109.45  3.000
 3IL  H14   O14  C13   102.10  3.000
 3IL  H152  C15  H151  106.59  3.000
 3IL  H152  C15  C13   107.88  3.000
 3IL  H151  C15  C13   108.99  3.000
 3IL  H152  C15  C3    109.66  3.000
 3IL  H151  C15  C3    109.67  3.000
 3IL  C13   C15  C3    113.79  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
 3IL  CONST_01  C9   C3   C2  N1    0.00   0.0  0
 3IL  CONST_02  C6   C7   C8  N1  180.00   0.0  0
 3IL  CONST_03  C3   C9   C8  N1    0.00   0.0  0
 3IL  CONST_04  C4   C9   C8  N1  180.00   0.0  0
 3IL  CONST_05  C7   C8   N1  C2  180.00   0.0  0
 3IL  CONST_06  C9   C8   N1  C2    0.00   0.0  0
 3IL  CONST_07  C4   C9   C3  C2  180.00   0.0  0
 3IL  CONST_08  C8   C9   C3  C2    0.00   0.0  0
 3IL  CONST_09  C8   N1   C2  C3    0.00   0.0  0
 3IL  CONST_10  C5   C4   C9  C3  180.00   0.0  0
 3IL  CONST_11  C7   C8   C9  C3  180.00   0.0  0
 3IL  CONST_12  C7   C6   C5  C4    0.00   0.0  0
 3IL  CONST_13  C7   C8   C9  C4    0.00   0.0  0
 3IL  CONST_14  C8   C9   C4  C5    0.00   0.0  0
 3IL  CONST_15  C8   C7   C6  C5    0.00   0.0  0
 3IL  CONST_16  C9   C4   C5  C6    0.00   0.0  0
 3IL  CONST_17  C9   C8   C7  C6    0.00   0.0  0
 3IL  CONST_18  C15  C3   C2  N1  180.00   0.0  0
 3IL  CONST_19  C15  C3   C9  C4    0.00   0.0  0
 3IL  CONST_20  C15  C3   C9  C8  180.00   0.0  0
 3IL  CONST_21  H7   C7   C8  N1    0.00   0.0  0
 3IL  CONST_22  HN1  N1   C2  C3  180.00   0.0  0
 3IL  CONST_23  H4   C4   C9  C3    0.00   0.0  0
 3IL  CONST_24  H6   C6   C5  C4  180.00   0.0  0
 3IL  CONST_25  H5   C5   C6  C7  180.00   0.0  0
 3IL  CONST_26  H2   C2   N1  C8  180.00   0.0  0
 3IL  Var_01    C13  C15  C3  C2  -98.84  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3IL  chir_01  C13  C10  O14  C15  negativ

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
 3IL  plan-1  N1   0.020
 3IL  plan-1  C2   0.020
 3IL  plan-1  C3   0.020
 3IL  plan-1  C4   0.020
 3IL  plan-1  C5   0.020
 3IL  plan-1  C6   0.020
 3IL  plan-1  C7   0.020
 3IL  plan-1  C8   0.020
 3IL  plan-1  C9   0.020
 3IL  plan-1  C15  0.020
 3IL  plan-1  HN1  0.020
 3IL  plan-1  H2   0.020
 3IL  plan-1  H4   0.020
 3IL  plan-1  H5   0.020
 3IL  plan-1  H6   0.020
 3IL  plan-1  H7   0.020
 3IL  plan-2  C10  0.020
 3IL  plan-2  O11  0.020
 3IL  plan-2  O12  0.020
 3IL  plan-2  C13  0.020

