# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:02:56 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-(diphenylmethyl)sulfinyl-~{N}-oxidanyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)C[S@@](=O)C(c1ccccc1)c2ccccc2
#
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
 RNW  RNW  2-(diphenylmethyl)sulfinyl-~{N}-oxidanyl-ethanamide  ligand  35  20  .  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_RNW
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
 RNW  C10   C  CR16  0  -0.236  11.0677  -4.9909  25.6746
 RNW  C13   C  CR16  0  -0.302   9.2765  -2.8809  25.7954
 RNW  C17   C  C     0   0.538   7.1387  -4.0451  21.4161
 RNW  C01   C  CR16  0  -0.263  13.5738   0.2519  22.8593
 RNW  C02   C  CR16  0  -0.238  12.5035   0.7997  23.5529
 RNW  C03   C  CR16  0  -0.300  11.3488   0.0557  23.7516
 RNW  C04   C  CR6   0   0.209  11.2513  -1.2472  23.2712
 RNW  C05   C  CR16  0  -0.314  12.3285  -1.7885  22.5727
 RNW  C06   C  CR16  0  -0.237  13.4812  -1.0434  22.3681
 RNW  C07   C  CH1   0  -0.651   9.9920  -2.0249  23.5552
 RNW  C08   C  CR6   0   0.163  10.1022  -3.0144  24.6819
 RNW  C09   C  CR16  0  -0.287  10.9984  -4.0808  24.6296
 RNW  C11   C  CR16  0  -0.261  10.2460  -4.8466  26.7847
 RNW  C12   C  CR16  0  -0.239   9.3502  -3.7878  26.8435
 RNW  C16   C  CH2   0  -0.727   7.8304  -3.4012  22.5965
 RNW  N19   N  NH1   0  -0.359   5.9139  -3.5541  21.1904
 RNW  O15   O  O     0  -0.757   9.2461  -1.8663  20.9666
 RNW  O18   O  O     0  -0.463   7.6777  -4.9060  20.7465
 RNW  O20   O  OH1   0  -0.537   5.1043  -4.1404  20.2704
 RNW  S14   S  S3    0   0.769   9.4843  -2.9154  22.0177
 RNW  H101  H  HCR6  0   0.263  11.7667  -5.8149  25.6201
 RNW  H131  H  HCR6  0   0.263   8.5701  -2.0609  25.8445
 RNW  H011  H  HCR6  0   0.260  14.4729   0.8323  22.6981
 RNW  H021  H  HCR6  0   0.261  12.5644   1.8096  23.9368
 RNW  H031  H  HCR6  0   0.259  10.5167   0.4926  24.2904
 RNW  H051  H  HCR6  0   0.259  12.2824  -2.7951  22.1751
 RNW  H061  H  HCR6  0   0.262  14.3070  -1.4774  21.8199
 RNW  H071  H  HCH1  0   0.333   9.1858  -1.3164  23.7633
 RNW  H091  H  HCR6  0   0.261  11.6533  -4.2101  23.7771
 RNW  H111  H  HCR6  0   0.262  10.3044  -5.5559  27.5997
 RNW  H121  H  HCR6  0   0.262   8.7060  -3.6665  27.7045
 RNW  H161  H  HCH2  0   0.314   7.3145  -2.5207  22.9832
 RNW  H162  H  HCH2  0   0.330   7.9373  -4.1366  23.3952
 RNW  H191  H  HNH1  0   0.425   5.4570  -2.9090  21.8192
 RNW  H201  H  HOH1  0   0.482   5.1995  -3.6244  19.4586

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
 RNW  O20  N19   single    1.359  0.020  1.359
 RNW  N19  C17   single    1.339  0.020  1.339
 RNW  O15  S14   double    1.504  0.020  1.504
 RNW  C06  C05   aromatic  1.388  0.020  1.388
 RNW  C06  C01   aromatic  1.388  0.020  1.388
 RNW  C17  O18   double    1.217  0.020  1.217
 RNW  C17  C16   single    1.512  0.020  1.512
 RNW  C05  C04   aromatic  1.393  0.020  1.393
 RNW  S14  C16   single    1.818  0.020  1.818
 RNW  S14  C07   single    1.848  0.020  1.848
 RNW  C01  C02   aromatic  1.388  0.020  1.388
 RNW  C04  C07   single    1.507  0.020  1.507
 RNW  C04  C03   aromatic  1.392  0.020  1.392
 RNW  C07  C08   single    1.504  0.020  1.504
 RNW  C02  C03   aromatic  1.388  0.020  1.388
 RNW  C09  C08   aromatic  1.394  0.020  1.394
 RNW  C09  C10   aromatic  1.387  0.020  1.387
 RNW  C08  C13   aromatic  1.393  0.020  1.393
 RNW  C10  C11   aromatic  1.389  0.020  1.389
 RNW  C13  C12   aromatic  1.388  0.020  1.388
 RNW  C11  C12   aromatic  1.388  0.020  1.388
 RNW  C10  H101  single    0.930  0.020  1.080
 RNW  C13  H131  single    0.930  0.020  1.080
 RNW  C01  H011  single    0.930  0.020  1.080
 RNW  C02  H021  single    0.930  0.020  1.080
 RNW  C03  H031  single    0.930  0.020  1.080
 RNW  C05  H051  single    0.930  0.020  1.080
 RNW  C06  H061  single    0.930  0.020  1.080
 RNW  C07  H071  single    0.970  0.020  1.090
 RNW  C09  H091  single    0.930  0.020  1.080
 RNW  C11  H111  single    0.930  0.020  1.080
 RNW  C12  H121  single    0.930  0.020  1.080
 RNW  C16  H161  single    0.970  0.020  1.090
 RNW  C16  H162  single    0.970  0.020  1.090
 RNW  N19  H191  single    0.860  0.020  1.020
 RNW  O20  H201  single    0.850  0.020  0.980

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
 RNW  H101  C10  C11   120.11  3.000
 RNW  H101  C10  C09   119.60  3.000
 RNW  C11   C10  C09   120.29  3.000
 RNW  H131  C13  C12   119.67  3.000
 RNW  H131  C13  C08   119.69  3.000
 RNW  C12   C13  C08   120.64  3.000
 RNW  O18   C17  N19   124.89  3.000
 RNW  O18   C17  C16   121.90  3.000
 RNW  N19   C17  C16   113.20  3.000
 RNW  H011  C01  C06   120.20  3.000
 RNW  H011  C01  C02   120.22  3.000
 RNW  C06   C01  C02   119.57  3.000
 RNW  H021  C02  C03   119.76  3.000
 RNW  H021  C02  C01   120.15  3.000
 RNW  C03   C02  C01   120.10  3.000
 RNW  H031  C03  C04   119.69  3.000
 RNW  H031  C03  C02   119.60  3.000
 RNW  C04   C03  C02   120.71  3.000
 RNW  C07   C04  C05   122.69  3.000
 RNW  C07   C04  C03   118.46  3.000
 RNW  C05   C04  C03   118.84  3.000
 RNW  H051  C05  C06   118.69  3.000
 RNW  H051  C05  C04   120.80  3.000
 RNW  C06   C05  C04   120.50  3.000
 RNW  H061  C06  C05   119.56  3.000
 RNW  H061  C06  C01   120.17  3.000
 RNW  C05   C06  C01   120.27  3.000
 RNW  H071  C07  S14   105.56  3.000
 RNW  H071  C07  C08   109.74  3.000
 RNW  S14   C07  C08   109.06  3.000
 RNW  H071  C07  C04   108.52  3.000
 RNW  C08   C07  C04   114.80  3.000
 RNW  S14   C07  C04   108.75  3.000
 RNW  C09   C08  C07   121.50  3.000
 RNW  C09   C08  C13   118.98  3.000
 RNW  C07   C08  C13   119.51  3.000
 RNW  H091  C09  C08   120.65  3.000
 RNW  H091  C09  C10   118.97  3.000
 RNW  C08   C09  C10   120.38  3.000
 RNW  H111  C11  C12   120.20  3.000
 RNW  H111  C11  C10   120.14  3.000
 RNW  C12   C11  C10   119.66  3.000
 RNW  H121  C12  C11   120.22  3.000
 RNW  H121  C12  C13   119.73  3.000
 RNW  C11   C12  C13   120.05  3.000
 RNW  H162  C16  H161  109.32  3.000
 RNW  H162  C16  S14   108.91  3.000
 RNW  H161  C16  S14   109.09  3.000
 RNW  H162  C16  C17   109.23  3.000
 RNW  H161  C16  C17   113.82  3.000
 RNW  S14   C16  C17   106.34  3.000
 RNW  H191  N19  O20   115.32  3.000
 RNW  H191  N19  C17   122.90  3.000
 RNW  O20   N19  C17   120.07  3.000
 RNW  H201  O20  N19   106.24  3.000
 RNW  O15   S14  C16   105.35  3.000
 RNW  C16   S14  C07    96.53  3.000
 RNW  O15   S14  C07   106.79  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
 RNW  CONST_01  C13   C08  C09  C10     0.00   0.0  0
 RNW  CONST_02  C13   C12  C11  C10     0.00   0.0  0
 RNW  CONST_03  C04   C05  C06  C01     0.00   0.0  0
 RNW  CONST_04  C04   C03  C02  C01     0.00   0.0  0
 RNW  CONST_05  C05   C06  C01  C02     0.00   0.0  0
 RNW  CONST_06  C05   C04  C03  C02     0.00   0.0  0
 RNW  CONST_07  C06   C05  C04  C03     0.00   0.0  0
 RNW  CONST_08  C06   C01  C02  C03     0.00   0.0  0
 RNW  CONST_09  C11   C10  C09  C08     0.00   0.0  0
 RNW  CONST_10  C11   C12  C13  C08     0.00   0.0  0
 RNW  CONST_11  C12   C13  C08  C09     0.00   0.0  0
 RNW  CONST_12  C12   C11  C10  C09     0.00   0.0  0
 RNW  CONST_13  C07   C08  C09  C10   180.00   0.0  0
 RNW  CONST_14  C07   C04  C03  C02   180.00   0.0  0
 RNW  CONST_15  C07   C04  C05  C06   180.00   0.0  0
 RNW  CONST_16  C12   C13  C08  C07   180.00   0.0  0
 RNW  CONST_17  H121  C12  C11  C10   180.00   0.0  0
 RNW  CONST_18  H091  C09  C08  C13   180.00   0.0  0
 RNW  CONST_19  H111  C11  C12  C13   180.00   0.0  0
 RNW  CONST_20  H051  C05  C06  C01   180.00   0.0  0
 RNW  CONST_21  H031  C03  C02  C01   180.00   0.0  0
 RNW  CONST_22  H061  C06  C01  C02   180.00   0.0  0
 RNW  CONST_23  H011  C01  C02  C03   180.00   0.0  0
 RNW  CONST_24  H021  C02  C03  C04   180.00   0.0  0
 RNW  CONST_25  H101  C10  C09  C08   180.00   0.0  0
 RNW  CONST_26  H131  C13  C08  C09   180.00   0.0  0
 RNW  CONST_27  O20   N19  C17  C16   180.00   0.0  0
 RNW  CONST_28  O20   N19  C17  O18     0.00   0.0  0
 RNW  CONST_29  H191  N19  C17  C16     0.00   0.0  0
 RNW  Var_01    C04   C07  C08  C13   119.58  30.0  2
 RNW  Var_02    C08   C07  C04  C03  -101.00  30.0  2
 RNW  Var_03    O15   S14  C07  C04   -60.09  30.0  2
 RNW  Var_04    S14   C16  C17  N19  -130.23  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
 RNW  plan-1  C01   0.020
 RNW  plan-1  C02   0.020
 RNW  plan-1  C03   0.020
 RNW  plan-1  C04   0.020
 RNW  plan-1  C05   0.020
 RNW  plan-1  C06   0.020
 RNW  plan-1  C07   0.020
 RNW  plan-1  H011  0.020
 RNW  plan-1  H021  0.020
 RNW  plan-1  H031  0.020
 RNW  plan-1  H051  0.020
 RNW  plan-1  H061  0.020
 RNW  plan-2  C10   0.020
 RNW  plan-2  C13   0.020
 RNW  plan-2  C07   0.020
 RNW  plan-2  C08   0.020
 RNW  plan-2  C09   0.020
 RNW  plan-2  C11   0.020
 RNW  plan-2  C12   0.020
 RNW  plan-2  H101  0.020
 RNW  plan-2  H131  0.020
 RNW  plan-2  H091  0.020
 RNW  plan-2  H111  0.020
 RNW  plan-2  H121  0.020
 RNW  plan-3  C17   0.020
 RNW  plan-3  C16   0.020
 RNW  plan-3  N19   0.020
 RNW  plan-3  O18   0.020
 RNW  plan-3  O20   0.020
 RNW  plan-3  H191  0.020
 RNW  plan-4  C07   0.020
 RNW  plan-4  C16   0.020
 RNW  plan-4  O15   0.020
 RNW  plan-4  S14   0.020

