# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 17:10:32 2021
#   Inital geometry file: a 73 line input string
#   Ligand name: N-ethyl-N-(thiophene-2-carbonyl)-beta-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(CCC(O)=O)C(=O)c1sccc1
#
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
 R8Y  R8Y  N-ethyl-N-(thiophene-2-carbonyl)-beta-alanine  ligand  28  15  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_R8Y
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
 R8Y  C4   C  C     0   0.544  51.0511   5.0366  43.2850
 R8Y  C5   C  C     0   0.547  51.7449   9.4891  45.0127
 R8Y  C6   C  CR5   0  -0.329  51.2489   8.8772  46.2747
 R8Y  C7   C  CR15  0  -0.186  51.7325   9.1712  47.5177
 R8Y  C8   C  CR15  0  -0.185  51.0122   8.5295  48.5567
 R8Y  C9   C  CR15  0  -0.449  49.9750   7.7824  48.0862
 R8Y  O2   O  O     0  -0.478  51.9342  10.6972  44.9829
 R8Y  N    N  NT    0  -0.451  51.9631   8.6940  43.9428
 R8Y  C2   C  CH2   0  -0.334  52.0892   7.2479  44.0059
 R8Y  C3   C  CH2   0  -0.561  50.9372   6.5375  43.2943
 R8Y  O1   O  OH1   0  -0.589  51.4440   4.5524  44.4568
 R8Y  O    O  O     0  -0.443  50.7924   4.3392  42.3362
 R8Y  C1   C  CH2   0  -0.321  52.4035   9.3159  42.6986
 R8Y  C    C  CH3   0  -0.661  53.8987   9.5914  42.6610
 R8Y  S    S  S2    0   0.237  49.8792   7.8378  46.3806
 R8Y  H1   H  HCR5  0   0.273  52.5831   9.8178  47.6807
 R8Y  H2   H  HCR5  0   0.274  51.2507   8.6252  49.6059
 R8Y  H3   H  HCR5  0   0.305  49.2569   7.2071  48.6500
 R8Y  H4   H  HCH2  0   0.280  52.1627   6.9305  45.0429
 R8Y  H5   H  HCH2  0   0.276  53.0366   6.9709  43.5355
 R8Y  H6   H  HCH2  0   0.279  50.8569   6.8687  42.2589
 R8Y  H7   H  HCH2  0   0.282  49.9881   6.7917  43.7762
 R8Y  H8   H  HOH1  0   0.484  51.4862   3.5845  44.4203
 R8Y  H9   H  HCH2  0   0.256  51.8424  10.2353  42.5393
 R8Y  H10  H  HCH2  0   0.250  52.1305   8.6439  41.8845
 R8Y  H11  H  HCH3  0   0.237  54.1778   9.9867  41.6842
 R8Y  H12  H  HCH3  0   0.235  54.1861  10.3214  43.4157
 R8Y  H13  H  HCH3  0   0.227  54.4779   8.6819  42.8259

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
 R8Y  O   C4   double    1.206  0.020  1.206
 R8Y  C   C1   single    1.521  0.020  1.521
 R8Y  C1  N    single    1.459  0.020  1.459
 R8Y  C4  C3   single    1.505  0.020  1.505
 R8Y  C4  O1   single    1.327  0.020  1.327
 R8Y  C3  C2   single    1.529  0.020  1.529
 R8Y  C2  N    single    1.453  0.020  1.453
 R8Y  N   C5   single    1.351  0.020  1.351
 R8Y  O2  C5   double    1.223  0.020  1.223
 R8Y  C5  C6   single    1.488  0.020  1.488
 R8Y  C6  S    aromatic  1.723  0.020  1.723
 R8Y  C6  C7   aromatic  1.366  0.020  1.366
 R8Y  S   C9   aromatic  1.709  0.020  1.709
 R8Y  C7  C8   aromatic  1.418  0.020  1.418
 R8Y  C9  C8   aromatic  1.362  0.020  1.362
 R8Y  C7  H1   single    0.930  0.020  1.080
 R8Y  C8  H2   single    0.930  0.020  1.080
 R8Y  C9  H3   single    0.930  0.020  1.080
 R8Y  C2  H4   single    0.970  0.020  1.090
 R8Y  C2  H5   single    0.970  0.020  1.090
 R8Y  C3  H6   single    0.970  0.020  1.090
 R8Y  C3  H7   single    0.970  0.020  1.090
 R8Y  O1  H8   single    0.850  0.020  0.980
 R8Y  C1  H9   single    0.970  0.020  1.090
 R8Y  C1  H10  single    0.970  0.020  1.090
 R8Y  C   H11  single    0.970  0.020  1.090
 R8Y  C   H12  single    0.970  0.020  1.090
 R8Y  C   H13  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
 R8Y  O    C4  O1   123.18  3.000
 R8Y  O1   C4  C3   112.38  3.000
 R8Y  O    C4  C3   124.43  3.000
 R8Y  N    C5  O2   122.48  3.000
 R8Y  O2   C5  C6   118.59  3.000
 R8Y  N    C5  C6   118.93  3.000
 R8Y  S    C6  C7   110.83  3.000
 R8Y  C7   C6  C5   124.43  3.000
 R8Y  S    C6  C5   124.43  3.000
 R8Y  H1   C7  C8   124.06  3.000
 R8Y  H1   C7  C6   123.01  3.000
 R8Y  C8   C7  C6   112.93  3.000
 R8Y  H2   C8  C9   123.52  3.000
 R8Y  H2   C8  C7   124.02  3.000
 R8Y  C9   C8  C7   112.46  3.000
 R8Y  H3   C9  S    120.08  3.000
 R8Y  H3   C9  C8   128.22  3.000
 R8Y  S    C9  C8   111.69  3.000
 R8Y  C1   N   C2   115.79  3.000
 R8Y  C2   N   C5   124.44  3.000
 R8Y  C1   N   C5   118.25  3.000
 R8Y  H5   C2  H4   106.13  3.000
 R8Y  H5   C2  C3   109.56  3.000
 R8Y  H4   C2  C3   111.06  3.000
 R8Y  H5   C2  N    107.98  3.000
 R8Y  H4   C2  N    109.75  3.000
 R8Y  C3   C2  N    112.14  3.000
 R8Y  H7   C3  H6   106.49  3.000
 R8Y  H7   C3  C2   109.91  3.000
 R8Y  H6   C3  C2   110.88  3.000
 R8Y  H7   C3  C4   107.45  3.000
 R8Y  H6   C3  C4   107.62  3.000
 R8Y  C2   C3  C4   114.15  3.000
 R8Y  H8   O1  C4   110.11  3.000
 R8Y  H10  C1  H9   106.39  3.000
 R8Y  H10  C1  C    109.83  3.000
 R8Y  H9   C1  C    110.49  3.000
 R8Y  H10  C1  N    107.37  3.000
 R8Y  H9   C1  N    109.22  3.000
 R8Y  C    C1  N    113.27  3.000
 R8Y  H13  C   H12  108.31  3.000
 R8Y  H13  C   H11  107.57  3.000
 R8Y  H12  C   H11  108.09  3.000
 R8Y  H13  C   C1   111.55  3.000
 R8Y  H12  C   C1   111.33  3.000
 R8Y  H11  C   C1   109.85  3.000
 R8Y  C9   S   C6    92.08  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
 R8Y  CONST_01  C8   C9  S   C6     0.00   0.0  0
 R8Y  CONST_02  C9   C8  C7  C6     0.00   0.0  0
 R8Y  CONST_03  C9   S   C6  C7     0.00   0.0  0
 R8Y  CONST_04  S    C9  C8  C7     0.00   0.0  0
 R8Y  CONST_05  S    C6  C7  C8     0.00   0.0  0
 R8Y  CONST_06  C9   S   C6  C5   180.00   0.0  0
 R8Y  CONST_07  C8   C7  C6  C5   180.00   0.0  0
 R8Y  CONST_08  H3   C9  S   C6   180.00   0.0  0
 R8Y  CONST_09  H2   C8  C7  C6   180.00   0.0  0
 R8Y  CONST_10  H1   C7  C8  C9   180.00   0.0  0
 R8Y  CONST_11  C1   N   C5  C6   180.00   0.0  0
 R8Y  CONST_13  C1   N   C5  O2     0.00   0.0  0
 R8Y  CONST_15  H8   O1  C4  C3   180.00   0.0  0
 R8Y  Var_01    N    C5  C6  C7   135.72  30.0  2
 R8Y  Var_02    N    C2  C3  C4   177.71  30.0  3
 R8Y  Var_03    C    C1  N   C5    81.82  30.0  2
 R8Y  Var_04    C3   C2  N   C5   113.71  30.0  3
 R8Y  Var_05    O    C4  C3  C2  -138.69  30.0  3
 R8Y  Var_06    H11  C   C1  N    175.88  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
 R8Y  plan-1  C5  0.020
 R8Y  plan-1  C6  0.020
 R8Y  plan-1  C7  0.020
 R8Y  plan-1  C8  0.020
 R8Y  plan-1  C9  0.020
 R8Y  plan-1  S   0.020
 R8Y  plan-1  H1  0.020
 R8Y  plan-1  H2  0.020
 R8Y  plan-1  H3  0.020
 R8Y  plan-2  C5  0.020
 R8Y  plan-2  C6  0.020
 R8Y  plan-2  O2  0.020
 R8Y  plan-2  N   0.020
 R8Y  plan-2  C2  0.020
 R8Y  plan-2  C1  0.020
 R8Y  plan-3  C4  0.020
 R8Y  plan-3  C3  0.020
 R8Y  plan-3  O1  0.020
 R8Y  plan-3  O   0.020
 R8Y  plan-3  H8  0.020

