# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 02:55:06 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R)-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
 4Z9  4Z9  '(2R)-2-hydroxy-3-(1H-indol-3-yl)propanoic acid'  ligand  25  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_4Z9
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
 4Z9  C8   C  CR56   0   0.351   2.5091   0.6933  -0.0275
 4Z9  C5   C  CR16   0  -0.270   2.7737  -2.0304   0.3018
 4Z9  C9   C  CR56   0   0.025   1.3932  -0.1475  -0.2443
 4Z9  C10  C  C      0   0.387  -3.3527  -0.4291   0.0160
 4Z9  O11  O  OC    -1  -0.596  -3.4840  -1.4851  -0.6215
 4Z9  C13  C  CH1    0  -0.070  -1.9195   0.0264   0.3675
 4Z9  O14  O  OH1    0  -0.692  -1.9746   1.1899   1.1509
 4Z9  C3   C  CR5    0   0.038   0.2956   0.6919  -0.6264
 4Z9  C2   C  CR15   0  -0.091   0.7803   1.9682  -0.6174
 4Z9  N1   N  NR15   0  -0.688   2.1032   1.9726  -0.2635
 4Z9  C7   C  CR16   0  -0.307   3.7537   0.1920   0.3520
 4Z9  C6   C  CR16   0  -0.287   3.8690  -1.1757   0.5129
 4Z9  C4   C  CR16   0  -0.375   1.5419  -1.5289  -0.0725
 4Z9  H1   H  HCR6   0   0.243   2.9014  -3.0968   0.4364
 4Z9  H3   H  HCH1   0   0.200  -1.4361  -0.7818   0.9367
 4Z9  H4   H  HOH1   0   0.424  -2.9298   1.3873   1.1552
 4Z9  H7   H  HCR5   0   0.274   0.2731   2.8925  -0.8455
 4Z9  H8   H  HNR5   0   0.405   2.6768   2.7947  -0.1815
 4Z9  H9   H  HCR6   0   0.256   4.5986   0.8493   0.5159
 4Z9  H10  H  HCR6   0   0.246   4.8214  -1.5969   0.8081
 4Z9  H11  H  HCR6   0   0.237   0.7045  -2.1983  -0.2298
 4Z9  C15  C  CH2    0  -0.563  -1.1020   0.2589  -0.9096
 4Z9  H5   H  HCH2   0   0.231  -1.1018  -0.6654  -1.4920
 4Z9  H6   H  HCH2   0   0.232  -1.6071   1.0132  -1.5211
 4Z9  O12  O  O      0  -0.609  -4.2603   0.3391   0.4119

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
 4Z9  C6   C5   aromatic  1.405  0.020  1.405
 4Z9  C6   C7   aromatic  1.382  0.020  1.382
 4Z9  C5   C4   aromatic  1.382  0.020  1.382
 4Z9  C7   C8   aromatic  1.394  0.020  1.394
 4Z9  C4   C9   aromatic  1.400  0.020  1.400
 4Z9  C8   C9   aromatic  1.414  0.020  1.414
 4Z9  C8   N1   aromatic  1.363  0.020  1.363
 4Z9  C9   C3   aromatic  1.434  0.020  1.434
 4Z9  O14  C13  single    1.404  0.020  1.404
 4Z9  N1   C2   aromatic  1.369  0.020  1.369
 4Z9  C3   C15  single    1.490  0.020  1.490
 4Z9  C3   C2   aromatic  1.365  0.020  1.365
 4Z9  C13  C15  single    1.534  0.020  1.534
 4Z9  C13  C10  single    1.544  0.020  1.544
 4Z9  O12  C10  deloc     1.253  0.020  1.253
 4Z9  C10  O11  deloc     1.240  0.020  1.240
 4Z9  C5   H1   single    0.930  0.020  1.080
 4Z9  C13  H3   single    0.970  0.020  1.090
 4Z9  O14  H4   single    0.850  0.020  0.980
 4Z9  C15  H5   single    0.970  0.020  1.090
 4Z9  C15  H6   single    0.970  0.020  1.090
 4Z9  C2   H7   single    0.930  0.020  1.080
 4Z9  N1   H8   single    0.860  0.020  1.020
 4Z9  C7   H9   single    0.930  0.020  1.080
 4Z9  C6   H10  single    0.930  0.020  1.080
 4Z9  C4   H11  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
 4Z9  C7   C8   N1   130.58  3.000
 4Z9  N1   C8   C9   107.26  3.000
 4Z9  C7   C8   C9   122.16  3.000
 4Z9  H1   C5   C4   119.76  3.000
 4Z9  H1   C5   C6   119.24  3.000
 4Z9  C4   C5   C6   120.99  3.000
 4Z9  C4   C9   C3   133.77  3.000
 4Z9  C3   C9   C8   107.27  3.000
 4Z9  C4   C9   C8   118.96  3.000
 4Z9  C13  C10  O11  117.79  3.000
 4Z9  O11  C10  O12  127.41  3.000
 4Z9  C13  C10  O12  114.79  3.000
 4Z9  H3   C13  C15  107.93  3.000
 4Z9  H3   C13  O14  109.71  3.000
 4Z9  C15  C13  O14  111.10  3.000
 4Z9  H3   C13  C10  107.98  3.000
 4Z9  C15  C13  C10  110.47  3.000
 4Z9  O14  C13  C10  109.57  3.000
 4Z9  H4   O14  C13  102.04  3.000
 4Z9  C2   C3   C15  127.29  3.000
 4Z9  C2   C3   C9   105.89  3.000
 4Z9  C15  C3   C9   126.77  3.000
 4Z9  H7   C2   N1   120.40  3.000
 4Z9  H7   C2   C3   129.24  3.000
 4Z9  N1   C2   C3   110.35  3.000
 4Z9  H8   N1   C2   125.07  3.000
 4Z9  H8   N1   C8   125.69  3.000
 4Z9  C2   N1   C8   109.23  3.000
 4Z9  H9   C7   C6   121.20  3.000
 4Z9  H9   C7   C8   121.29  3.000
 4Z9  C6   C7   C8   117.52  3.000
 4Z9  H10  C6   C7   119.36  3.000
 4Z9  H10  C6   C5   119.35  3.000
 4Z9  C7   C6   C5   121.29  3.000
 4Z9  H11  C4   C9   120.64  3.000
 4Z9  H11  C4   C5   120.28  3.000
 4Z9  C9   C4   C5   119.08  3.000
 4Z9  H6   C15  H5   106.57  3.000
 4Z9  H6   C15  C3   109.80  3.000
 4Z9  H5   C15  C3   110.30  3.000
 4Z9  H6   C15  C13  108.88  3.000
 4Z9  H5   C15  C13  108.40  3.000
 4Z9  C3   C15  C13  112.68  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
 4Z9  CONST_01  C5   C6   C7  C8     0.00   0.0  0
 4Z9  CONST_02  C5   C4   C9  C8     0.00   0.0  0
 4Z9  CONST_03  C2   C3   C9  C8     0.00   0.0  0
 4Z9  CONST_04  C3   C2   N1  C8     0.00   0.0  0
 4Z9  CONST_05  C3   C9   C4  C5   180.00   0.0  0
 4Z9  CONST_06  C6   C5   C4  C9     0.00   0.0  0
 4Z9  CONST_07  C6   C7   C8  C9     0.00   0.0  0
 4Z9  CONST_08  C2   N1   C8  C9     0.00   0.0  0
 4Z9  CONST_09  N1   C2   C3  C9     0.00   0.0  0
 4Z9  CONST_10  C7   C8   C9  C3   180.00   0.0  0
 4Z9  CONST_11  N1   C8   C9  C3     0.00   0.0  0
 4Z9  CONST_12  C7   C8   N1  C2   180.00   0.0  0
 4Z9  CONST_13  C4   C9   C3  C2   180.00   0.0  0
 4Z9  CONST_14  C6   C7   C8  N1   180.00   0.0  0
 4Z9  CONST_15  C4   C9   C8  N1   180.00   0.0  0
 4Z9  CONST_16  C4   C5   C6  C7     0.00   0.0  0
 4Z9  CONST_17  C4   C9   C8  C7     0.00   0.0  0
 4Z9  CONST_18  C15  C3   C9  C8   180.00   0.0  0
 4Z9  CONST_19  C4   C9   C3  C15    0.00   0.0  0
 4Z9  CONST_20  N1   C2   C3  C15  180.00   0.0  0
 4Z9  CONST_21  H10  C6   C7  C8   180.00   0.0  0
 4Z9  CONST_22  H11  C4   C9  C8   180.00   0.0  0
 4Z9  CONST_23  H7   C2   N1  C8   180.00   0.0  0
 4Z9  CONST_24  H9   C7   C6  C5   180.00   0.0  0
 4Z9  CONST_25  H1   C5   C4  C9   180.00   0.0  0
 4Z9  CONST_26  H8   N1   C8  C9   180.00   0.0  0
 4Z9  Var_01    C13  C15  C3  C9    79.60  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
 4Z9  chir_01  C13  O14  C15  C10  positiv

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
 4Z9  plan-1  C8   0.020
 4Z9  plan-1  C5   0.020
 4Z9  plan-1  C9   0.020
 4Z9  plan-1  C3   0.020
 4Z9  plan-1  C2   0.020
 4Z9  plan-1  N1   0.020
 4Z9  plan-1  C7   0.020
 4Z9  plan-1  C6   0.020
 4Z9  plan-1  C4   0.020
 4Z9  plan-1  H1   0.020
 4Z9  plan-1  H7   0.020
 4Z9  plan-1  H8   0.020
 4Z9  plan-1  H9   0.020
 4Z9  plan-1  H10  0.020
 4Z9  plan-1  H11  0.020
 4Z9  plan-1  C15  0.020
 4Z9  plan-2  C10  0.020
 4Z9  plan-2  O11  0.020
 4Z9  plan-2  C13  0.020
 4Z9  plan-2  O12  0.020

