# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 09:18:49 2021
#   Inital geometry file: a 60 line input string
#   Ligand name: 4-(methylsulfonyl)benzaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc(C=O)cc1
#
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
 L3Y  L3Y  4-(methylsulfonyl)benzaldehyde  ligand  20  12  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L3Y
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
 L3Y  C01  C  CH3   0  -0.791  -14.5841  -19.4229   0.5140
 L3Y  S02  S  S     0   1.218  -15.9442  -20.3884  -0.0982
 L3Y  O03  O  OS    0  -0.663  -15.4520  -21.7166  -0.4543
 L3Y  C04  C  CR6   0  -0.198  -17.0061  -20.5560   1.3221
 L3Y  C05  C  CR16  0  -0.215  -18.0206  -19.6319   1.5185
 L3Y  C06  C  CR16  0  -0.262  -18.8388  -19.7713   2.6287
 L3Y  C07  C  CR6   0  -0.001  -18.6391  -20.8203   3.5192
 L3Y  C08  C  C1    0   0.129  -19.5352  -20.9382   4.6877
 L3Y  C09  C  CR16  0  -0.250  -17.6148  -21.7412   3.3044
 L3Y  C10  C  CR16  0  -0.216  -16.7937  -21.6134   2.1999
 L3Y  O11  O  OS    0  -0.663  -16.6541  -19.6073  -1.1073
 L3Y  H1   H  HCH3  0   0.299  -14.1018  -19.9535   1.3317
 L3Y  H2   H  HCH3  0   0.315  -13.8840  -19.2919  -0.3110
 L3Y  H3   H  HCH3  0   0.299  -14.9503  -18.4559   0.8506
 L3Y  H4   H  HCR6  0   0.294  -18.1787  -18.8188   0.8235
 L3Y  H5   H  HCR6  0   0.286  -19.6384  -19.0603   2.7966
 L3Y  H6   H  H     0   0.209  -20.3057  -20.1514   4.7581
 L3Y  H9   H  HCR6  0   0.283  -17.4629  -22.5586   3.9968
 L3Y  H10  H  HCR6  0   0.294  -16.0033  -22.3310   2.0278
 L3Y  O1   O  O     0  -0.367  -19.4569  -21.8134   5.5144

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
 L3Y  O11  S02  double    1.460  0.020  1.460
 L3Y  O03  S02  double    1.460  0.020  1.460
 L3Y  S02  C01  single    1.777  0.020  1.777
 L3Y  S02  C04  single    1.781  0.020  1.781
 L3Y  C04  C05  aromatic  1.386  0.020  1.386
 L3Y  C04  C10  aromatic  1.391  0.020  1.391
 L3Y  C05  C06  aromatic  1.386  0.020  1.386
 L3Y  C10  C09  aromatic  1.382  0.020  1.382
 L3Y  C06  C07  aromatic  1.390  0.020  1.390
 L3Y  C09  C07  aromatic  1.394  0.020  1.394
 L3Y  C07  C08  single    1.477  0.020  1.477
 L3Y  C01  H1   single    0.970  0.020  1.090
 L3Y  C01  H2   single    0.970  0.020  1.090
 L3Y  C01  H3   single    0.970  0.020  1.090
 L3Y  C05  H4   single    0.930  0.020  1.080
 L3Y  C06  H5   single    0.930  0.020  1.080
 L3Y  C08  H6   single    0.930  0.020  1.080
 L3Y  C09  H9   single    0.930  0.020  1.080
 L3Y  C10  H10  single    0.930  0.020  1.080
 L3Y  C08  O1   double    1.206  0.020  1.206

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
 L3Y  H3   C01  H2   110.10  3.000
 L3Y  H3   C01  H1   110.51  3.000
 L3Y  H2   C01  H1   110.06  3.000
 L3Y  H3   C01  S02  109.39  3.000
 L3Y  H2   C01  S02  107.24  3.000
 L3Y  H1   C01  S02  109.48  3.000
 L3Y  O11  S02  C04  108.15  3.000
 L3Y  C04  S02  O03  108.04  3.000
 L3Y  O11  S02  O03  118.80  3.000
 L3Y  C04  S02  C01  103.46  3.000
 L3Y  O03  S02  C01  108.68  3.000
 L3Y  O11  S02  C01  108.64  3.000
 L3Y  C10  C04  C05  121.95  3.000
 L3Y  C10  C04  S02  118.94  3.000
 L3Y  C05  C04  S02  119.11  3.000
 L3Y  H4   C05  C06  120.27  3.000
 L3Y  H4   C05  C04  121.15  3.000
 L3Y  C06  C05  C04  118.58  3.000
 L3Y  H5   C06  C07  120.13  3.000
 L3Y  H5   C06  C05  119.60  3.000
 L3Y  C07  C06  C05  120.27  3.000
 L3Y  C09  C07  C08  120.99  3.000
 L3Y  C08  C07  C06  118.67  3.000
 L3Y  C09  C07  C06  120.34  3.000
 L3Y  O1   C08  H6   121.25  3.000
 L3Y  O1   C08  C07  124.09  3.000
 L3Y  H6   C08  C07  114.65  3.000
 L3Y  H9   C09  C10  119.86  3.000
 L3Y  H9   C09  C07  120.24  3.000
 L3Y  C10  C09  C07  119.90  3.000
 L3Y  H10  C10  C09  120.00  3.000
 L3Y  H10  C10  C04  121.05  3.000
 L3Y  C09  C10  C04  118.95  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
 L3Y  CONST_01  C07  C06  C05  C04    0.00   0.0  0
 L3Y  CONST_02  C07  C09  C10  C04    0.00   0.0  0
 L3Y  CONST_03  C09  C10  C04  C05    0.00   0.0  0
 L3Y  CONST_04  C09  C07  C06  C05    0.00   0.0  0
 L3Y  CONST_05  C10  C04  C05  C06    0.00   0.0  0
 L3Y  CONST_06  C10  C09  C07  C06    0.00   0.0  0
 L3Y  CONST_07  C06  C05  C04  S02  180.00   0.0  0
 L3Y  CONST_08  C09  C10  C04  S02  180.00   0.0  0
 L3Y  CONST_09  C08  C07  C06  C05  180.00   0.0  0
 L3Y  CONST_10  C10  C09  C07  C08  180.00   0.0  0
 L3Y  CONST_11  H5   C06  C05  C04  180.00   0.0  0
 L3Y  CONST_12  H9   C09  C10  C04  180.00   0.0  0
 L3Y  CONST_13  H10  C10  C04  C05  180.00   0.0  0
 L3Y  CONST_14  H4   C05  C06  C07  180.00   0.0  0
 L3Y  Var_01    C05  C04  S02  C01   92.43  30.0  2
 L3Y  Var_02    O1   C08  C07  C06  179.42  30.0  2
 L3Y  Var_03    H1   C01  S02  C04   59.98  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
 L3Y  plan-1  S02  0.020
 L3Y  plan-1  C04  0.020
 L3Y  plan-1  C05  0.020
 L3Y  plan-1  C06  0.020
 L3Y  plan-1  C07  0.020
 L3Y  plan-1  C08  0.020
 L3Y  plan-1  C09  0.020
 L3Y  plan-1  C10  0.020
 L3Y  plan-1  H4   0.020
 L3Y  plan-1  H5   0.020
 L3Y  plan-1  H9   0.020
 L3Y  plan-1  H10  0.020
 L3Y  plan-2  C07  0.020
 L3Y  plan-2  C08  0.020
 L3Y  plan-2  H6   0.020
 L3Y  plan-2  O1   0.020

