# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 22:54:35 2021
#   Inital geometry file: a 68 line input string
#   Ligand name: ~{N}-methyl-~{N}-(2-sulfanylethyl)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CCS)C(=O)c1ccccc1
#
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
 O3W  O3W  ~{N}-methyl-~{N}-(2-sulfanylethyl)benzamide  ligand  26  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_O3W
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
 O3W  C02  C  CH2   0  -0.544  15.2063  18.5837   3.4677
 O3W  C03  C  CH2   0  -0.331  16.1902  18.6774   2.3093
 O3W  C05  C  CH3   0  -0.536  14.5780  19.6048   0.6995
 O3W  C06  C  C     0   0.517  16.4761  20.9335   1.3270
 O3W  C07  C  CR6   0  -0.070  17.8425  21.0557   1.9243
 O3W  C08  C  CR16  0  -0.263  18.8950  20.2498   1.4983
 O3W  C09  C  CR16  0  -0.244  20.1751  20.4551   1.9939
 O3W  C10  C  CR16  0  -0.253  20.4085  21.4580   2.9256
 O3W  C11  C  CR16  0  -0.247  19.3606  22.2656   3.3497
 O3W  C12  C  CR16  0  -0.264  18.0846  22.0750   2.8401
 O3W  N04  N  NT    0  -0.432  15.8592  19.7319   1.3688
 O3W  O13  O  O     0  -0.484  15.9714  21.9061   0.7822
 O3W  S01  S  S2    0  -0.256  15.1572  20.1789   4.3498
 O3W  H1   H  HCH2  0   0.275  14.2063  18.3283   3.1190
 O3W  H2   H  HCH2  0   0.287  15.5396  17.7967   4.1433
 O3W  H3   H  HCH2  0   0.276  16.1939  17.7193   1.7845
 O3W  H4   H  HCH2  0   0.280  17.1929  18.8281   2.6997
 O3W  H5   H  HCH3  0   0.250  14.3492  18.5476   0.5773
 O3W  H6   H  HCH3  0   0.240  13.7684  20.0707   1.2658
 O3W  H7   H  HCH3  0   0.259  14.6136  20.0602  -0.2870
 O3W  H8   H  HCR6  0   0.268  18.7215  19.4653   0.7717
 O3W  H9   H  HCR6  0   0.262  20.9891  19.8293   1.6524
 O3W  H10  H  HCR6  0   0.262  21.4052  21.6114   3.3184
 O3W  H11  H  HCR6  0   0.261  19.5373  23.0504   4.0735
 O3W  H12  H  HCR6  0   0.259  17.2730  22.7132   3.1656
 O3W  H13  H  HSH1  0   0.230  14.2666  19.8239   5.2817

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
 O3W  O13  C06  double    1.224  0.020  1.224
 O3W  C05  N04  single    1.451  0.020  1.451
 O3W  C06  N04  single    1.351  0.020  1.351
 O3W  C06  C07  single    1.496  0.020  1.496
 O3W  N04  C03  single    1.451  0.020  1.451
 O3W  C08  C07  aromatic  1.392  0.020  1.392
 O3W  C08  C09  aromatic  1.388  0.020  1.388
 O3W  C07  C12  aromatic  1.391  0.020  1.391
 O3W  C09  C10  aromatic  1.389  0.020  1.389
 O3W  C03  C02  single    1.523  0.020  1.523
 O3W  C12  C11  aromatic  1.387  0.020  1.387
 O3W  C10  C11  aromatic  1.389  0.020  1.389
 O3W  C02  S01  single    1.823  0.020  1.823
 O3W  C02  H1   single    0.970  0.020  1.090
 O3W  C02  H2   single    0.970  0.020  1.090
 O3W  C03  H3   single    0.970  0.020  1.090
 O3W  C03  H4   single    0.970  0.020  1.090
 O3W  C05  H5   single    0.970  0.020  1.090
 O3W  C05  H6   single    0.970  0.020  1.090
 O3W  C05  H7   single    0.970  0.020  1.090
 O3W  C08  H8   single    0.930  0.020  1.080
 O3W  C09  H9   single    0.930  0.020  1.080
 O3W  C10  H10  single    0.930  0.020  1.080
 O3W  C11  H11  single    0.930  0.020  1.080
 O3W  C12  H12  single    0.930  0.020  1.080
 O3W  S01  H13  single    1.200  0.020  1.300

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
 O3W  H2   C02  H1   108.06  3.000
 O3W  H2   C02  S01  109.89  3.000
 O3W  H1   C02  S01  109.59  3.000
 O3W  H2   C02  C03  108.57  3.000
 O3W  H1   C02  C03  111.35  3.000
 O3W  S01  C02  C03  109.37  3.000
 O3W  H4   C03  H3   106.92  3.000
 O3W  H4   C03  N04  110.03  3.000
 O3W  H3   C03  N04  109.07  3.000
 O3W  H4   C03  C02  109.36  3.000
 O3W  H3   C03  C02  108.29  3.000
 O3W  N04  C03  C02  112.98  3.000
 O3W  H7   C05  H6   108.41  3.000
 O3W  H7   C05  H5   108.17  3.000
 O3W  H6   C05  H5   108.47  3.000
 O3W  H7   C05  N04  110.67  3.000
 O3W  H6   C05  N04  112.21  3.000
 O3W  H5   C05  N04  108.81  3.000
 O3W  O13  C06  N04  122.15  3.000
 O3W  N04  C06  C07  118.50  3.000
 O3W  O13  C06  C07  119.31  3.000
 O3W  C12  C07  C08  119.59  3.000
 O3W  C12  C07  C06  118.78  3.000
 O3W  C08  C07  C06  121.39  3.000
 O3W  H8   C08  C09  119.63  3.000
 O3W  H8   C08  C07  120.22  3.000
 O3W  C09  C08  C07  120.15  3.000
 O3W  H9   C09  C10  120.20  3.000
 O3W  H9   C09  C08  119.71  3.000
 O3W  C10  C09  C08  120.09  3.000
 O3W  H10  C10  C11  120.10  3.000
 O3W  H10  C10  C09  120.04  3.000
 O3W  C11  C10  C09  119.86  3.000
 O3W  H11  C11  C12  119.71  3.000
 O3W  H11  C11  C10  120.17  3.000
 O3W  C12  C11  C10  120.12  3.000
 O3W  H12  C12  C11  119.88  3.000
 O3W  H12  C12  C07  119.95  3.000
 O3W  C11  C12  C07  120.16  3.000
 O3W  C06  N04  C05  117.82  3.000
 O3W  C06  N04  C03  124.20  3.000
 O3W  C05  N04  C03  115.89  3.000
 O3W  H13  S01  C02   97.05  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
 O3W  CONST_01  C10  C09  C08  C07     0.00   0.0  0
 O3W  CONST_02  C10  C11  C12  C07     0.00   0.0  0
 O3W  CONST_03  C11  C12  C07  C08     0.00   0.0  0
 O3W  CONST_04  C11  C10  C09  C08     0.00   0.0  0
 O3W  CONST_05  C12  C07  C08  C09     0.00   0.0  0
 O3W  CONST_06  C12  C11  C10  C09     0.00   0.0  0
 O3W  CONST_07  C09  C08  C07  C06   180.00   0.0  0
 O3W  CONST_08  C11  C12  C07  C06   180.00   0.0  0
 O3W  CONST_09  H9   C09  C08  C07   180.00   0.0  0
 O3W  CONST_10  H11  C11  C12  C07   180.00   0.0  0
 O3W  CONST_11  H12  C12  C07  C08   180.00   0.0  0
 O3W  CONST_12  H10  C10  C09  C08   180.00   0.0  0
 O3W  CONST_13  H8   C08  C09  C10   180.00   0.0  0
 O3W  CONST_15  C07  C06  N04  C05   180.00   0.0  0
 O3W  CONST_17  O13  C06  N04  C05     0.00   0.0  0
 O3W  Var_01    O13  C06  C07  C08  -120.75  30.0  2
 O3W  Var_02    C05  N04  C03  C02   -61.49  30.0  1
 O3W  Var_03    S01  C02  C03  N04   -58.20  30.0  3
 O3W  Var_04    H5   C05  N04  C03   -31.54  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
 O3W  plan-1  C06  0.020
 O3W  plan-1  C07  0.020
 O3W  plan-1  C08  0.020
 O3W  plan-1  C09  0.020
 O3W  plan-1  C10  0.020
 O3W  plan-1  C11  0.020
 O3W  plan-1  C12  0.020
 O3W  plan-1  H8   0.020
 O3W  plan-1  H9   0.020
 O3W  plan-1  H10  0.020
 O3W  plan-1  H11  0.020
 O3W  plan-1  H12  0.020
 O3W  plan-2  C03  0.020
 O3W  plan-2  C05  0.020
 O3W  plan-2  C06  0.020
 O3W  plan-2  C07  0.020
 O3W  plan-2  N04  0.020
 O3W  plan-2  O13  0.020

