# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Aug  2 10:37:16 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: (2~{R})-~{N},3-diphenyl-2-sulfanyl-propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S[C@H](Cc1ccccc1)C(=O)Nc2ccccc2
#
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
 V85  V85  "(2R)-N,3-diphenyl-2-sulfanyl-propanamide"
  ligand  33  18  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_V85
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
 V85  C10  C  CR16  0  -0.315  -21.2910  -10.8580  -3.1808
 V85  C13  C  CR6   0   0.108  -17.3471  -11.5755  -6.3568
 V85  C15  C  CR16  0  -0.237  -18.4484  -12.1361  -8.4353
 V85  C17  C  CR16  0  -0.238  -18.7031   -9.9373  -7.5056
 V85  C02  C  CH1   0  -0.524  -17.3336  -12.8396  -4.1980
 V85  C03  C  C     0   0.586  -18.5302  -12.0340  -3.7076
 V85  C05  C  CR6   0   0.368  -21.0104  -12.0189  -3.9032
 V85  C06  C  CR16  0  -0.343  -22.0652  -12.7294  -4.4833
 V85  C07  C  CR16  0  -0.242  -23.3713  -12.2937  -4.3451
 V85  C08  C  CR16  0  -0.269  -23.6535  -11.1389  -3.6263
 V85  C09  C  CR16  0  -0.242  -22.6073  -10.4332  -3.0522
 V85  C12  C  CH2   0  -0.489  -16.5112  -11.9907  -5.1764
 V85  C14  C  CR16  0  -0.301  -17.6353  -12.4903  -7.3684
 V85  C16  C  CR16  0  -0.266  -18.9876  -10.8572  -8.5054
 V85  C18  C  CR16  0  -0.296  -17.8885  -10.2956  -6.4389
 V85  N04  N  NH1   0  -0.733  -19.7244  -12.5375  -4.0975
 V85  O11  O  O     0  -0.449  -18.3854  -11.0183  -3.0552
 V85  S01  S  S2    0  -0.200  -16.2552  -13.3031  -2.8050
 V85  H1   H  HCR6  0   0.281  -20.5021  -10.2861  -2.7221
 V85  H2   H  HCR6  0   0.254  -18.6602  -12.8580  -9.2137
 V85  H3   H  HCR6  0   0.254  -19.1137   -8.9370  -7.5555
 V85  H4   H  HCH1  0   0.310  -17.6467  -13.7545  -4.7044
 V85  H5   H  HCR6  0   0.269  -21.8582  -13.6299  -5.0502
 V85  H6   H  HCR6  0   0.258  -24.1704  -12.8611  -4.8040
 V85  H7   H  HCR6  0   0.254  -24.6737  -10.7964  -3.5157
 V85  H8   H  HCR6  0   0.256  -22.8094   -9.5309  -2.4893
 V85  H9   H  HCH2  0   0.276  -15.6545  -12.5822  -5.5056
 V85  H10  H  HCH2  0   0.267  -16.1208  -11.1129  -4.6581
 V85  H11  H  HCR6  0   0.250  -17.2159  -13.4891  -7.3206
 V85  H12  H  HCR6  0   0.254  -19.6220  -10.5791  -9.3372
 V85  H13  H  HCR6  0   0.250  -17.6703   -9.5709  -5.6637
 V85  H14  H  HNH1  0   0.418  -19.6939  -13.3912  -4.6353
 V85  H15  H  HSH1  0   0.234  -17.0699  -14.2092  -2.2511

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
 V85  C16  C15  aromatic  1.390  0.020  1.390
 V85  C16  C17  aromatic  1.388  0.020  1.388
 V85  C15  C14  aromatic  1.387  0.020  1.387
 V85  C17  C18  aromatic  1.389  0.020  1.389
 V85  C14  C13  aromatic  1.394  0.020  1.394
 V85  C18  C13  aromatic  1.392  0.020  1.392
 V85  C13  C12  single    1.505  0.020  1.505
 V85  C12  C02  single    1.534  0.020  1.534
 V85  C06  C07  aromatic  1.384  0.020  1.384
 V85  C06  C05  aromatic  1.398  0.020  1.398
 V85  C07  C08  aromatic  1.389  0.020  1.389
 V85  C02  C03  single    1.524  0.020  1.524
 V85  C02  S01  single    1.822  0.020  1.822
 V85  C03  O11  double    1.216  0.020  1.216
 V85  C03  N04  single    1.353  0.020  1.353
 V85  N04  C05  single    1.400  0.020  1.400
 V85  C05  C10  aromatic  1.396  0.020  1.396
 V85  C08  C09  aromatic  1.386  0.020  1.386
 V85  C10  C09  aromatic  1.389  0.020  1.389
 V85  C10  H1   single    0.930  0.020  1.080
 V85  C15  H2   single    0.930  0.020  1.080
 V85  C17  H3   single    0.930  0.020  1.080
 V85  C02  H4   single    0.970  0.020  1.090
 V85  C06  H5   single    0.930  0.020  1.080
 V85  C07  H6   single    0.930  0.020  1.080
 V85  C08  H7   single    0.930  0.020  1.080
 V85  C09  H8   single    0.930  0.020  1.080
 V85  C12  H9   single    0.970  0.020  1.090
 V85  C12  H10  single    0.970  0.020  1.090
 V85  C14  H11  single    0.930  0.020  1.080
 V85  C16  H12  single    0.930  0.020  1.080
 V85  C18  H13  single    0.930  0.020  1.080
 V85  N04  H14  single    0.860  0.020  1.020
 V85  S01  H15  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
 V85  H1   C10  C09  119.49  3.000
 V85  H1   C10  C05  120.99  3.000
 V85  C09  C10  C05  119.52  3.000
 V85  C18  C13  C14  118.69  3.000
 V85  C18  C13  C12  121.06  3.000
 V85  C14  C13  C12  120.20  3.000
 V85  H2   C15  C16  120.11  3.000
 V85  H2   C15  C14  119.82  3.000
 V85  C16  C15  C14  120.07  3.000
 V85  H3   C17  C18  119.75  3.000
 V85  H3   C17  C16  120.09  3.000
 V85  C18  C17  C16  120.15  3.000
 V85  H4   C02  S01  108.14  3.000
 V85  H4   C02  C12  108.77  3.000
 V85  S01  C02  C12  108.13  3.000
 V85  H4   C02  C03  111.54  3.000
 V85  S01  C02  C03  110.69  3.000
 V85  C12  C02  C03  109.49  3.000
 V85  O11  C03  N04  124.78  3.000
 V85  N04  C03  C02  113.80  3.000
 V85  O11  C03  C02  121.40  3.000
 V85  N04  C05  C06  116.57  3.000
 V85  N04  C05  C10  124.37  3.000
 V85  C06  C05  C10  119.07  3.000
 V85  H5   C06  C07  119.61  3.000
 V85  H5   C06  C05  119.68  3.000
 V85  C07  C06  C05  120.71  3.000
 V85  H6   C07  C08  120.35  3.000
 V85  H6   C07  C06  119.31  3.000
 V85  C08  C07  C06  120.34  3.000
 V85  H7   C08  C09  120.54  3.000
 V85  H7   C08  C07  120.51  3.000
 V85  C09  C08  C07  118.95  3.000
 V85  H8   C09  C08  119.92  3.000
 V85  H8   C09  C10  118.68  3.000
 V85  C08  C09  C10  121.40  3.000
 V85  H10  C12  H9   107.35  3.000
 V85  H10  C12  C02  109.50  3.000
 V85  H9   C12  C02  108.24  3.000
 V85  H10  C12  C13  110.45  3.000
 V85  H9   C12  C13  110.42  3.000
 V85  C02  C12  C13  110.80  3.000
 V85  H11  C14  C15  119.72  3.000
 V85  H11  C14  C13  119.50  3.000
 V85  C15  C14  C13  120.78  3.000
 V85  H12  C16  C17  120.23  3.000
 V85  H12  C16  C15  120.17  3.000
 V85  C17  C16  C15  119.61  3.000
 V85  H13  C18  C17  119.67  3.000
 V85  H13  C18  C13  119.63  3.000
 V85  C17  C18  C13  120.70  3.000
 V85  H14  N04  C05  114.52  3.000
 V85  H14  N04  C03  116.20  3.000
 V85  C05  N04  C03  129.25  3.000
 V85  H15  S01  C02   97.38  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
 V85  CONST_01  C07  C06  C05  C10     0.00   0.0  0
 V85  CONST_02  C07  C08  C09  C10     0.00   0.0  0
 V85  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 V85  CONST_04  C16  C17  C18  C13     0.00   0.0  0
 V85  CONST_05  C18  C17  C16  C15     0.00   0.0  0
 V85  CONST_06  C18  C13  C14  C15     0.00   0.0  0
 V85  CONST_07  C14  C15  C16  C17     0.00   0.0  0
 V85  CONST_08  C14  C13  C18  C17     0.00   0.0  0
 V85  CONST_09  C08  C07  C06  C05     0.00   0.0  0
 V85  CONST_10  C08  C09  C10  C05     0.00   0.0  0
 V85  CONST_11  C09  C08  C07  C06     0.00   0.0  0
 V85  CONST_12  C09  C10  C05  C06     0.00   0.0  0
 V85  CONST_13  C12  C13  C14  C15   180.00   0.0  0
 V85  CONST_14  C12  C13  C18  C17   180.00   0.0  0
 V85  CONST_15  N04  C05  C06  C07   180.00   0.0  0
 V85  CONST_16  N04  C05  C10  C09   180.00   0.0  0
 V85  CONST_17  H5   C06  C05  C10   180.00   0.0  0
 V85  CONST_18  H7   C08  C09  C10   180.00   0.0  0
 V85  CONST_19  H2   C15  C14  C13   180.00   0.0  0
 V85  CONST_20  H3   C17  C18  C13   180.00   0.0  0
 V85  CONST_21  H3   C17  C16  C15   180.00   0.0  0
 V85  CONST_22  H2   C15  C16  C17   180.00   0.0  0
 V85  CONST_23  H6   C07  C06  C05   180.00   0.0  0
 V85  CONST_24  H8   C09  C10  C05   180.00   0.0  0
 V85  CONST_25  H7   C08  C07  C06   180.00   0.0  0
 V85  CONST_26  H1   C10  C05  C06   180.00   0.0  0
 V85  CONST_27  H8   C09  C08  C07   180.00   0.0  0
 V85  CONST_28  H5   C06  C07  C08   180.00   0.0  0
 V85  CONST_29  H1   C10  C09  C08   180.00   0.0  0
 V85  CONST_30  H6   C07  C08  C09   180.00   0.0  0
 V85  CONST_31  H12  C16  C15  C14   180.00   0.0  0
 V85  CONST_32  H13  C18  C13  C14   180.00   0.0  0
 V85  CONST_33  H11  C14  C15  C16   180.00   0.0  0
 V85  CONST_34  H13  C18  C17  C16   180.00   0.0  0
 V85  CONST_35  H12  C16  C17  C18   180.00   0.0  0
 V85  CONST_36  H11  C14  C13  C18   180.00   0.0  0
 V85  CONST_37  C03  N04  C05  C10     0.00   0.0  0
 V85  CONST_38  C06  C05  N04  C03   180.00   0.0  0
 V85  CONST_39  H14  N04  C05  C10   180.00   0.0  0
 V85  CONST_40  H14  N04  C05  C06     0.00   0.0  0
 V85  CONST_41  C05  N04  C03  C02   180.00   0.0  0
 V85  CONST_42  O11  C03  N04  C05     0.00   0.0  0
 V85  CONST_43  H14  N04  C03  C02     0.00   0.0  0
 V85  CONST_44  H14  N04  C03  O11   180.00   0.0  0
 V85  Var_01    C14  C13  C12  C02   -76.42  30.0  2
 V85  Var_02    C18  C13  C12  C02   101.14  30.0  2
 V85  Var_03    H9   C12  C13  C14    43.50  30.0  2
 V85  Var_04    H10  C12  C13  C14   162.07  30.0  2
 V85  Var_05    H9   C12  C13  C18  -138.95  30.0  2
 V85  Var_06    H10  C12  C13  C18   -20.37  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 V85  chir_01  C02  C12  C03  S01  positiv

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
 V85  plan-1  C10  0.020
 V85  plan-1  C05  0.020
 V85  plan-1  C06  0.020
 V85  plan-1  C07  0.020
 V85  plan-1  C08  0.020
 V85  plan-1  C09  0.020
 V85  plan-1  N04  0.020
 V85  plan-1  H1   0.020
 V85  plan-1  H5   0.020
 V85  plan-1  H6   0.020
 V85  plan-1  H7   0.020
 V85  plan-1  H8   0.020
 V85  plan-2  C13  0.020
 V85  plan-2  C15  0.020
 V85  plan-2  C17  0.020
 V85  plan-2  C12  0.020
 V85  plan-2  C14  0.020
 V85  plan-2  C16  0.020
 V85  plan-2  C18  0.020
 V85  plan-2  H2   0.020
 V85  plan-2  H3   0.020
 V85  plan-2  H11  0.020
 V85  plan-2  H12  0.020
 V85  plan-2  H13  0.020
 V85  plan-3  C02  0.020
 V85  plan-3  C03  0.020
 V85  plan-3  C05  0.020
 V85  plan-3  N04  0.020
 V85  plan-3  O11  0.020
 V85  plan-3  H14  0.020

