# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 23:19:29 2022
#   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  27  15  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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   0.417  51.0889   4.9526  43.4822
 R8Y  C5   C  C      0   0.535  51.7521   9.4877  45.0361
 R8Y  C6   C  CR5    0  -0.320  51.2541   8.8873  46.3057
 R8Y  C7   C  CR15   0  -0.190  51.6954   9.2476  47.5473
 R8Y  C8   C  CR15   0  -0.184  50.9799   8.6167  48.5960
 R8Y  C9   C  CR15   0  -0.452  49.9846   7.8102  48.1330
 R8Y  O2   O  O      0  -0.485  51.9127  10.7025  44.9958
 R8Y  N    N  NT     0  -0.444  52.0026   8.6840  43.9860
 R8Y  C2   C  CH2    0  -0.316  52.1257   7.2312  44.0559
 R8Y  C3   C  CH2    0  -0.583  50.9939   6.4892  43.3629
 R8Y  O1   O  OC    -1  -0.602  51.9031   4.4981  44.3104
 R8Y  O    O  O      0  -0.614  50.3238   4.2992  42.7466
 R8Y  C1   C  CH2    0  -0.317  52.4362   9.2983  42.7378
 R8Y  C    C  CH3    0  -0.659  53.9303   9.5847  42.6964
 R8Y  S    S  S2     0   0.237  49.9269   7.7947  46.4250
 R8Y  H1   H  HCR5   0   0.267  52.5132   9.9367  47.7044
 R8Y  H2   H  HCR5   0   0.269  51.1907   8.7624  49.6455
 R8Y  H3   H  HCR5   0   0.300  49.2794   7.2266  48.7049
 R8Y  H4   H  HCH2   0   0.252  52.2046   6.9222  45.0948
 R8Y  H5   H  HCH2   0   0.248  53.0802   6.9625  43.5960
 R8Y  H6   H  HCH2   0   0.228  50.9504   6.7619  42.3043
 R8Y  H7   H  HCH2   0   0.228  50.0324   6.8058  43.7815
 R8Y  H9   H  HCH2   0   0.248  51.8716  10.2149  42.5723
 R8Y  H10  H  HCH2   0   0.247  52.1679   8.6171  41.9295
 R8Y  H11  H  HCH3   0   0.232  54.2021  10.0060  41.7281
 R8Y  H12  H  HCH3   0   0.231  54.2185  10.2982  43.4667
 R8Y  H13  H  HCH3   0   0.227  54.5160   8.6750  42.8355

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   deloc     1.246  0.020  1.246
 R8Y  C   C1   single    1.522  0.020  1.522
 R8Y  C1  N    single    1.457  0.020  1.457
 R8Y  C4  C3   single    1.544  0.020  1.544
 R8Y  C4  O1   deloc     1.247  0.020  1.247
 R8Y  C3  C2   single    1.520  0.020  1.520
 R8Y  C2  N    single    1.460  0.020  1.460
 R8Y  N   C5   single    1.346  0.020  1.346
 R8Y  O2  C5   double    1.226  0.020  1.226
 R8Y  C5  C6   single    1.490  0.020  1.490
 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  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   126.98  3.000
 R8Y  O1   C4  C3   117.01  3.000
 R8Y  O    C4  C3   116.00  3.000
 R8Y  N    C5  O2   122.79  3.000
 R8Y  O2   C5  C6   118.10  3.000
 R8Y  N    C5  C6   119.10  3.000
 R8Y  S    C6  C7   110.68  3.000
 R8Y  C7   C6  C5   124.07  3.000
 R8Y  S    C6  C5   124.88  3.000
 R8Y  H1   C7  C8   123.92  3.000
 R8Y  H1   C7  C6   123.00  3.000
 R8Y  C8   C7  C6   113.07  3.000
 R8Y  H2   C8  C9   123.54  3.000
 R8Y  H2   C8  C7   124.07  3.000
 R8Y  C9   C8  C7   112.39  3.000
 R8Y  H3   C9  S    120.17  3.000
 R8Y  H3   C9  C8   128.13  3.000
 R8Y  S    C9  C8   111.70  3.000
 R8Y  C1   N   C2   115.81  3.000
 R8Y  C2   N   C5   124.94  3.000
 R8Y  C1   N   C5   118.17  3.000
 R8Y  H5   C2  H4   105.60  3.000
 R8Y  H5   C2  C3   109.77  3.000
 R8Y  H4   C2  C3   110.55  3.000
 R8Y  H5   C2  N    107.35  3.000
 R8Y  H4   C2  N    109.57  3.000
 R8Y  C3   C2  N    113.64  3.000
 R8Y  H7   C3  H6   105.24  3.000
 R8Y  H7   C3  C2   109.77  3.000
 R8Y  H6   C3  C2   110.43  3.000
 R8Y  H7   C3  C4   108.18  3.000
 R8Y  H6   C3  C4   108.98  3.000
 R8Y  C2   C3  C4   113.86  3.000
 R8Y  H10  C1  H9   106.59  3.000
 R8Y  H10  C1  C    109.81  3.000
 R8Y  H9   C1  C    110.27  3.000
 R8Y  H10  C1  N    107.36  3.000
 R8Y  H9   C1  N    109.31  3.000
 R8Y  C    C1  N    113.25  3.000
 R8Y  H13  C   H12  108.30  3.000
 R8Y  H13  C   H11  107.56  3.000
 R8Y  H12  C   H11  108.00  3.000
 R8Y  H13  C   C1   111.52  3.000
 R8Y  H12  C   C1   111.34  3.000
 R8Y  H11  C   C1   109.98  3.000
 R8Y  C9   S   C6    92.15  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_12  C2   N   C5  C6     0.00   0.0  0
 R8Y  CONST_13  C1   N   C5  O2     0.00   0.0  0
 R8Y  CONST_14  C2   N   C5  O2   180.00   0.0  0
 R8Y  Var_01    N    C5  C6  C7   137.55  30.0  2
 R8Y  Var_02    N    C2  C3  C4  -177.68  30.0  3
 R8Y  Var_03    C    C1  N   C5    83.28  30.0  2
 R8Y  Var_04    C3   C2  N   C5   111.80  30.0  2
 R8Y  Var_05    O    C4  C3  C2  -168.15  30.0  2
 R8Y  Var_06    H11  C   C1  N    177.80  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

