# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:23:32 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: (2~{R})-2-azanyl-3-(1-benzothiophen-3-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cc1csc2ccccc12)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
 EXR  EXR  '(2~{R})-2-azanyl-3-(1-benzothiophen-3-yl)propanoic acid'  ligand  26  15  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EXR
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
 EXR  C4   C  CR56  0  -0.216   8.6679  135.2870   -8.2468
 EXR  C5   C  CR16  0  -0.250   5.9244  135.5674   -8.2764
 EXR  C6   C  CR16  0  -0.271   6.5101  134.3987   -7.7738
 EXR  C7   C  CR16  0  -0.274   7.8835  134.2485   -7.7516
 EXR  C8   C  CR16  0  -0.345   6.7061  136.5938   -8.7673
 EXR  C9   C  CR56  0   0.182   8.1001  136.4644   -8.7630
 EXR  N    N  NH2   0  -0.783   8.0082  139.8347  -11.9719
 EXR  CA   C  CH1   0  -0.192   8.2917  138.5714  -11.3213
 EXR  C1   C  CR5   0   0.205   9.0992  137.4011   -9.2130
 EXR  C2   C  CR15  0  -0.551  10.3507  136.9223   -9.0249
 EXR  S3   S  S2    0   0.202  10.3988  135.3449   -8.3161
 EXR  C    C  C     0   0.553   9.3560  137.8462  -12.1200
 EXR  O1   O  O     0  -0.445  10.3739  138.3717  -12.4982
 EXR  O2   O  OH1   0  -0.581   9.0648  136.5733  -12.3333
 EXR  H1   H  HCR6  0   0.259   4.8469  135.6655   -8.2791
 EXR  H2   H  HCR6  0   0.261   5.8814  133.6035   -7.3951
 EXR  H3   H  HCR6  0   0.269   8.3356  133.3480   -7.3573
 EXR  H4   H  HCR6  0   0.252   6.2404  137.4946   -9.1480
 EXR  H5   H  HNH2  0   0.348   8.8142  140.4449  -11.9059
 EXR  H8   H  HCH1  0   0.269   7.3784  137.9733  -11.3312
 EXR  H11  H  HCR5  0   0.297  11.2780  137.4194   -9.2706
 EXR  H12  H  HOH1  0   0.479   9.7945  136.1384  -12.8012
 EXR  CB   C  CH2   0  -0.555   8.7845  138.7100   -9.8628
 EXR  H7   H  HNH2  0   0.360   7.2595  140.3012  -11.4753
 EXR  H10  H  HCH2  0   0.263   9.6685  139.3520   -9.8533
 EXR  H9   H  HCH2  0   0.265   8.0060  139.2357   -9.3026

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
 EXR  O1  C    double    1.206  0.020  1.206
 EXR  C   O2   single    1.323  0.020  1.323
 EXR  C   CA   single    1.515  0.020  1.515
 EXR  N   CA   single    1.449  0.020  1.449
 EXR  CA  CB   single    1.546  0.020  1.546
 EXR  CB  C1   single    1.495  0.020  1.495
 EXR  C1  C2   aromatic  1.353  0.020  1.353
 EXR  C1  C9   aromatic  1.442  0.020  1.442
 EXR  C2  S3   aromatic  1.730  0.020  1.730
 EXR  C8  C9   aromatic  1.400  0.020  1.400
 EXR  C8  C5   aromatic  1.380  0.020  1.380
 EXR  C9  C4   aromatic  1.405  0.020  1.405
 EXR  S3  C4   aromatic  1.733  0.020  1.733
 EXR  C5  C6   aromatic  1.401  0.020  1.401
 EXR  C4  C7   aromatic  1.393  0.020  1.393
 EXR  C6  C7   aromatic  1.382  0.020  1.382
 EXR  C5  H1   single    0.930  0.020  1.080
 EXR  C6  H2   single    0.930  0.020  1.080
 EXR  C7  H3   single    0.930  0.020  1.080
 EXR  C8  H4   single    0.930  0.020  1.080
 EXR  N   H7   single    0.890  0.020  1.040
 EXR  N   H5   single    0.890  0.020  1.040
 EXR  CA  H8   single    0.970  0.020  1.090
 EXR  CB  H10  single    0.970  0.020  1.090
 EXR  CB  H9   single    0.970  0.020  1.090
 EXR  C2  H11  single    0.930  0.020  1.080
 EXR  O2  H12  single    0.850  0.020  0.980

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
 EXR  S3   C4  C9   111.15  3.000
 EXR  S3   C4  C7   126.99  3.000
 EXR  C9   C4  C7   121.86  3.000
 EXR  H1   C5  C8   119.71  3.000
 EXR  H1   C5  C6   119.53  3.000
 EXR  C8   C5  C6   120.75  3.000
 EXR  H2   C6  C7   119.47  3.000
 EXR  H2   C6  C5   119.73  3.000
 EXR  C7   C6  C5   120.80  3.000
 EXR  H3   C7  C6   120.77  3.000
 EXR  H3   C7  C4   120.99  3.000
 EXR  C6   C7  C4   118.24  3.000
 EXR  H4   C8  C9   120.40  3.000
 EXR  H4   C8  C5   119.99  3.000
 EXR  C9   C8  C5   119.61  3.000
 EXR  C1   C9  C8   128.98  3.000
 EXR  C8   C9  C4   118.75  3.000
 EXR  C1   C9  C4   112.27  3.000
 EXR  H5   N   H7   106.19  3.000
 EXR  H5   N   CA   109.89  3.000
 EXR  H7   N   CA   109.04  3.000
 EXR  H8   CA  C    108.70  3.000
 EXR  H8   CA  CB   108.93  3.000
 EXR  C    CA  CB   108.44  3.000
 EXR  H8   CA  N    108.05  3.000
 EXR  CB   CA  N    114.07  3.000
 EXR  C    CA  N    108.54  3.000
 EXR  C2   C1  CB   124.40  3.000
 EXR  C2   C1  C9   111.57  3.000
 EXR  CB   C1  C9   123.97  3.000
 EXR  H11  C2  S3   119.26  3.000
 EXR  H11  C2  C1   126.83  3.000
 EXR  S3   C2  C1   113.91  3.000
 EXR  C2   S3  C4    91.09  3.000
 EXR  O2   C   O1   123.66  3.000
 EXR  O2   C   CA   113.00  3.000
 EXR  O1   C   CA   123.32  3.000
 EXR  H12  O2  C    110.09  3.000
 EXR  H9   CB  H10  106.80  3.000
 EXR  H9   CB  C1   110.37  3.000
 EXR  H10  CB  C1   109.90  3.000
 EXR  H9   CB  CA   107.42  3.000
 EXR  H10  CB  CA   108.59  3.000
 EXR  C1   CB  CA   113.50  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
 EXR  CONST_01  C2   C1  C9  C4    0.00   0.0  0
 EXR  CONST_02  C5   C8  C9  C4    0.00   0.0  0
 EXR  CONST_03  C1   C2  S3  C4    0.00   0.0  0
 EXR  CONST_04  C5   C6  C7  C4    0.00   0.0  0
 EXR  CONST_05  C1   C9  C8  C5  180.00   0.0  0
 EXR  CONST_06  C9   C8  C5  C6    0.00   0.0  0
 EXR  CONST_07  C9   C4  C7  C6    0.00   0.0  0
 EXR  CONST_08  S3   C4  C7  C6  180.00   0.0  0
 EXR  CONST_09  C1   C9  C4  C7  180.00   0.0  0
 EXR  CONST_10  C8   C9  C4  C7    0.00   0.0  0
 EXR  CONST_11  C2   S3  C4  C7  180.00   0.0  0
 EXR  CONST_12  C8   C5  C6  C7    0.00   0.0  0
 EXR  CONST_13  C2   C1  C9  C8  180.00   0.0  0
 EXR  CONST_14  S3   C4  C9  C8  180.00   0.0  0
 EXR  CONST_15  S3   C2  C1  C9    0.00   0.0  0
 EXR  CONST_16  C2   S3  C4  C9    0.00   0.0  0
 EXR  CONST_17  S3   C4  C9  C1    0.00   0.0  0
 EXR  CONST_18  CB   C1  C9  C4  180.00   0.0  0
 EXR  CONST_19  CB   C1  C9  C8    0.00   0.0  0
 EXR  CONST_20  S3   C2  C1  CB  180.00   0.0  0
 EXR  CONST_21  H4   C8  C9  C4  180.00   0.0  0
 EXR  CONST_22  H11  C2  S3  C4  180.00   0.0  0
 EXR  CONST_23  H2   C6  C7  C4  180.00   0.0  0
 EXR  CONST_24  H3   C7  C6  C5  180.00   0.0  0
 EXR  CONST_25  H1   C5  C6  C7  180.00   0.0  0
 EXR  CONST_26  H12  O2  C   CA  180.00   0.0  0
 EXR  Var_01    CA   CB  C1  C9  -74.16  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
 EXR  chir_01  CA  C  N  CB  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
 EXR  plan-1  C4   0.020
 EXR  plan-1  C5   0.020
 EXR  plan-1  C6   0.020
 EXR  plan-1  C7   0.020
 EXR  plan-1  C8   0.020
 EXR  plan-1  C9   0.020
 EXR  plan-1  C1   0.020
 EXR  plan-1  C2   0.020
 EXR  plan-1  S3   0.020
 EXR  plan-1  H1   0.020
 EXR  plan-1  H2   0.020
 EXR  plan-1  H3   0.020
 EXR  plan-1  H4   0.020
 EXR  plan-1  H11  0.020
 EXR  plan-1  CB   0.020
 EXR  plan-2  CA   0.020
 EXR  plan-2  C    0.020
 EXR  plan-2  O1   0.020
 EXR  plan-2  O2   0.020
 EXR  plan-2  H12  0.020

