# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:44:05 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 2-butylthiophene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCc1sccc1
#
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
 Y8G  Y8G  '2-butylthiophene         '  ligand  21  9  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y8G
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
 Y8G  C01  C  CH3   0  -0.664  24.3356  -23.7458  -0.9700
 Y8G  C02  C  CH2   0  -0.434  25.0480  -24.3199  -2.1876
 Y8G  C03  C  CH2   0  -0.414  24.7199  -23.5973  -3.4899
 Y8G  C04  C  CH2   0  -0.511  23.2461  -23.6445  -3.9132
 Y8G  C05  C  CR5   0  -0.138  22.7438  -25.0265  -4.1891
 Y8G  C06  C  CR15  0  -0.237  22.8472  -25.7433  -5.3454
 Y8G  C07  C  CR15  0  -0.181  22.2935  -27.0504  -5.2521
 Y8G  C08  C  CR15  0  -0.474  21.7739  -27.3122  -4.0220
 Y8G  S09  S  S2    0   0.191  21.9572  -25.9663  -2.9751
 Y8G  H1   H  HCH3  0   0.229  24.6570  -24.2448  -0.0552
 Y8G  H2   H  HCH3  0   0.217  24.5456  -22.6803  -0.8571
 Y8G  H3   H  HCH3  0   0.216  23.2524  -23.8597  -1.0351
 Y8G  H4   H  HCH2  0   0.216  24.8157  -25.3839  -2.2835
 Y8G  H5   H  HCH2  0   0.226  26.1281  -24.2640  -2.0296
 Y8G  H6   H  HCH2  0   0.227  25.3267  -24.0141  -4.2981
 Y8G  H7   H  HCH2  0   0.224  25.0100  -22.5460  -3.3982
 Y8G  H8   H  HCH2  0   0.259  23.1295  -23.0536  -4.8243
 Y8G  H9   H  HCH2  0   0.248  22.6223  -23.1580  -3.1600
 Y8G  H10  H  HCR5  0   0.254  23.3030  -25.3439  -6.2417
 Y8G  H11  H  HCR5  0   0.260  22.2780  -27.7596  -6.0676
 Y8G  H12  H  HCR5  0   0.288  21.2898  -28.2137  -3.6797

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
 Y8G  C06  C07  aromatic  1.423  0.020  1.423
 Y8G  C06  C05  aromatic  1.364  0.020  1.364
 Y8G  C07  C08  aromatic  1.361  0.020  1.361
 Y8G  C05  C04  single    1.496  0.020  1.496
 Y8G  C05  S09  aromatic  1.725  0.020  1.725
 Y8G  C08  S09  aromatic  1.715  0.020  1.715
 Y8G  C04  C03  single    1.534  0.020  1.534
 Y8G  C03  C02  single    1.525  0.020  1.525
 Y8G  C02  C01  single    1.523  0.020  1.523
 Y8G  C01  H1   single    0.970  0.020  1.090
 Y8G  C01  H2   single    0.970  0.020  1.090
 Y8G  C01  H3   single    0.970  0.020  1.090
 Y8G  C02  H4   single    0.970  0.020  1.090
 Y8G  C02  H5   single    0.970  0.020  1.090
 Y8G  C03  H6   single    0.970  0.020  1.090
 Y8G  C03  H7   single    0.970  0.020  1.090
 Y8G  C04  H8   single    0.970  0.020  1.090
 Y8G  C04  H9   single    0.970  0.020  1.090
 Y8G  C06  H10  single    0.930  0.020  1.080
 Y8G  C07  H11  single    0.930  0.020  1.080
 Y8G  C08  H12  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
 Y8G  H3   C01  H2   107.40  3.000
 Y8G  H3   C01  H1   107.15  3.000
 Y8G  H2   C01  H1   107.65  3.000
 Y8G  H3   C01  C02  112.16  3.000
 Y8G  H2   C01  C02  111.13  3.000
 Y8G  H1   C01  C02  111.12  3.000
 Y8G  H5   C02  H4   105.81  3.000
 Y8G  H5   C02  C03  108.17  3.000
 Y8G  H4   C02  C03  109.91  3.000
 Y8G  H5   C02  C01  109.11  3.000
 Y8G  H4   C02  C01  109.72  3.000
 Y8G  C03  C02  C01  113.79  3.000
 Y8G  H7   C03  H6   106.32  3.000
 Y8G  H7   C03  C04  107.90  3.000
 Y8G  H6   C03  C04  108.51  3.000
 Y8G  H7   C03  C02  109.06  3.000
 Y8G  H6   C03  C02  109.34  3.000
 Y8G  C04  C03  C02  115.32  3.000
 Y8G  H9   C04  H8   105.86  3.000
 Y8G  H9   C04  C05  110.30  3.000
 Y8G  H8   C04  C05  108.06  3.000
 Y8G  H9   C04  C03  110.16  3.000
 Y8G  H8   C04  C03  108.42  3.000
 Y8G  C05  C04  C03  113.69  3.000
 Y8G  S09  C05  C06  110.17  3.000
 Y8G  S09  C05  C04  121.77  3.000
 Y8G  C06  C05  C04  128.04  3.000
 Y8G  H10  C06  C07  123.88  3.000
 Y8G  H10  C06  C05  122.69  3.000
 Y8G  C07  C06  C05  113.43  3.000
 Y8G  H11  C07  C08  123.39  3.000
 Y8G  H11  C07  C06  123.99  3.000
 Y8G  C08  C07  C06  112.62  3.000
 Y8G  H12  C08  S09  120.66  3.000
 Y8G  H12  C08  C07  128.23  3.000
 Y8G  S09  C08  C07  111.10  3.000
 Y8G  C08  S09  C05   92.68  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
 Y8G  CONST_01  C08  C07  C06  C05     0.00   0.0  0
 Y8G  CONST_02  C07  C08  S09  C05     0.00   0.0  0
 Y8G  CONST_03  S09  C08  C07  C06     0.00   0.0  0
 Y8G  CONST_04  C08  S09  C05  C06     0.00   0.0  0
 Y8G  CONST_05  S09  C05  C06  C07     0.00   0.0  0
 Y8G  CONST_06  C07  C06  C05  C04   180.00   0.0  0
 Y8G  CONST_07  C08  S09  C05  C04   180.00   0.0  0
 Y8G  CONST_08  H11  C07  C06  C05   180.00   0.0  0
 Y8G  CONST_09  H12  C08  S09  C05   180.00   0.0  0
 Y8G  CONST_10  H10  C06  C07  C08   180.00   0.0  0
 Y8G  Var_01    C06  C05  C04  C03   -84.40  30.0  1
 Y8G  Var_02    C05  C04  C03  C02   -62.68  30.0  1
 Y8G  Var_03    C04  C03  C02  C01   -61.89  30.0  1
 Y8G  Var_04    H1   C01  C02  C03  -175.77  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
 Y8G  plan-1  C04  0.020
 Y8G  plan-1  C05  0.020
 Y8G  plan-1  C06  0.020
 Y8G  plan-1  C07  0.020
 Y8G  plan-1  C08  0.020
 Y8G  plan-1  S09  0.020
 Y8G  plan-1  H10  0.020
 Y8G  plan-1  H11  0.020
 Y8G  plan-1  H12  0.020

