# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:48:19 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[(4-methoxyphenyl)-diphenyl-methyl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C(SC[C@H](N)C(O)=O)(c2ccccc2)c3ccccc3
#
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
 4C5  4C5  '(2~{R})-2-azanyl-3-[(4-methoxyphenyl)-diphenyl-methyl]sulfanyl-propanoic acid'  ligand  51  28  .  2022-07-23  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4C5
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
 4C5  O1   O  OH1   0  -0.589   4.3289   1.3743  -1.4826
 4C5  C1   C  C     0   0.527   4.4206   0.1888  -0.8949
 4C5  O2   O  O     0  -0.432   5.3031  -0.1133  -0.1331
 4C5  C2   C  CH1   0  -0.213   3.2717  -0.7372  -1.2905
 4C5  N    N  NH2   0  -0.764   3.4864  -2.1139  -0.9320
 4C5  C3   C  CH2   0  -0.551   1.9882  -0.1958  -0.6516
 4C5  S    S  S2    0   0.045   0.5636  -1.1307  -1.2739
 4C5  C4   C  CT    0  -0.437  -0.7613  -0.5992  -0.0939
 4C5  C12  C  CR6   0   0.183  -2.0636  -1.1488  -0.6828
 4C5  C17  C  CR16  0  -0.280  -2.1228  -2.4821  -1.0929
 4C5  C16  C  CR16  0  -0.242  -3.3044  -3.0310  -1.5664
 4C5  C15  C  CR16  0  -0.267  -4.4604  -2.2627  -1.6227
 4C5  C14  C  CR16  0  -0.242  -4.4184  -0.9447  -1.1956
 4C5  C13  C  CR16  0  -0.312  -3.2308  -0.3926  -0.7297
 4C5  C18  C  CR6   0   0.187  -0.6151  -1.2496   1.2842
 4C5  C23  C  CR16  0  -0.274  -1.5742  -0.9558   2.2573
 4C5  C22  C  CR16  0  -0.240  -1.5203  -1.5381   3.5125
 4C5  C21  C  CR16  0  -0.269  -0.5067  -2.4377   3.8238
 4C5  C20  C  CR16  0  -0.238   0.4432  -2.7442   2.8638
 4C5  C19  C  CR16  0  -0.333   0.3870  -2.1565   1.6036
 4C5  C5   C  CR6   0   0.116  -0.7109   0.9200  -0.0417
 4C5  C11  C  CR16  0  -0.244  -0.9827   1.6595  -1.1993
 4C5  C10  C  CR16  0  -0.333  -0.8809   3.0331  -1.2202
 4C5  C8   C  CR6   0   0.371  -0.4821   3.7296  -0.0739
 4C5  O3   O  O2    0  -0.470  -0.4114   5.0689  -0.1833
 4C5  C9   C  CH3   0  -0.436  -0.0470   5.8189   0.9585
 4C5  C7   C  CR16  0  -0.374  -0.1835   3.0124   1.0762
 4C5  C6   C  CR16  0  -0.282  -0.2971   1.6232   1.0782
 4C5  H1   H  HOH1  0   0.484   5.0482   1.9528  -1.1872
 4C5  H2   H  HCH1  0   0.285   3.1694  -0.6743  -2.3789
 4C5  H3   H  HNH2  0   0.361   4.2778  -2.4909  -1.4367
 4C5  H4   H  HNH2  0   0.348   3.7100  -2.1935   0.0523
 4C5  H6   H  HCH2  0   0.276   2.0488  -0.2925   0.4353
 4C5  H7   H  HCH2  0   0.292   1.8552   0.8596  -0.8844
 4C5  H8   H  HCR6  0   0.255  -1.2425  -3.1106  -1.0331
 4C5  H9   H  HCR6  0   0.258  -3.3220  -4.0655  -1.8842
 4C5  H10  H  HCR6  0   0.257  -5.3846  -2.6909  -1.9879
 4C5  H11  H  HCR6  0   0.257  -5.3125  -0.3351  -1.2197
 4C5  H12  H  HCR6  0   0.261  -3.2300   0.6369  -0.3980
 4C5  H13  H  HCR6  0   0.258  -2.3762  -0.2621   2.0353
 4C5  H14  H  HCR6  0   0.256  -2.2741  -1.2920   4.2493
 4C5  H15  H  HCR6  0   0.256  -0.4645  -2.8959   4.8033
 4C5  H16  H  HCR6  0   0.255   1.2363  -3.4466   3.0862
 4C5  H17  H  HCR6  0   0.262   1.1285  -2.4251   0.8623
 4C5  H18  H  HCR6  0   0.259  -1.2727   1.1487  -2.1089
 4C5  H19  H  HCR6  0   0.262  -1.1052   3.5807  -2.1272
 4C5  H20  H  HCH3  0   0.229  -0.7486   5.6700   1.7834
 4C5  H21  H  HCH3  0   0.228   0.9601   5.5736   1.3058
 4C5  H22  H  HCH3  0   0.260  -0.0698   6.8646   0.6624
 4C5  H23  H  HCR6  0   0.277   0.1453   3.5024   1.9822
 4C5  H24  H  HCR6  0   0.260  -0.0380   1.1008   1.9890

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
 4C5  C15  C16  aromatic  1.389  0.020  1.389
 4C5  C15  C14  aromatic  1.386  0.020  1.386
 4C5  C16  C17  aromatic  1.386  0.020  1.386
 4C5  C14  C13  aromatic  1.390  0.020  1.390
 4C5  C17  C12  aromatic  1.396  0.020  1.396
 4C5  C13  C12  aromatic  1.392  0.020  1.392
 4C5  C12  C4   single    1.531  0.020  1.531
 4C5  C6   C7   aromatic  1.394  0.020  1.394
 4C5  C6   C5   aromatic  1.386  0.020  1.386
 4C5  C7   C8   aromatic  1.388  0.020  1.388
 4C5  C19  C20  aromatic  1.392  0.020  1.392
 4C5  C19  C18  aromatic  1.389  0.020  1.389
 4C5  C4   C5   single    1.521  0.020  1.521
 4C5  C4   C18  single    1.531  0.020  1.531
 4C5  C4   S    single    1.852  0.020  1.852
 4C5  C5   C11  aromatic  1.400  0.020  1.400
 4C5  C20  C21  aromatic  1.385  0.020  1.385
 4C5  C18  C23  aromatic  1.398  0.020  1.398
 4C5  C8   O3   single    1.346  0.020  1.346
 4C5  C8   C10  aromatic  1.399  0.020  1.399
 4C5  O3   C9   single    1.414  0.020  1.414
 4C5  C11  C10  aromatic  1.377  0.020  1.377
 4C5  C21  C22  aromatic  1.391  0.020  1.391
 4C5  S    C3   single    1.814  0.020  1.814
 4C5  C23  C22  aromatic  1.385  0.020  1.385
 4C5  C3   C2   single    1.533  0.020  1.533
 4C5  N    C2   single    1.439  0.020  1.439
 4C5  C2   C1   single    1.528  0.020  1.528
 4C5  C1   O2   double    1.204  0.020  1.204
 4C5  C1   O1   single    1.326  0.020  1.326
 4C5  O1   H1   single    0.850  0.020  0.980
 4C5  C2   H2   single    0.970  0.020  1.090
 4C5  N    H3   single    0.890  0.020  1.040
 4C5  N    H4   single    0.890  0.020  1.040
 4C5  C3   H6   single    0.970  0.020  1.090
 4C5  C3   H7   single    0.970  0.020  1.090
 4C5  C17  H8   single    0.930  0.020  1.080
 4C5  C16  H9   single    0.930  0.020  1.080
 4C5  C15  H10  single    0.930  0.020  1.080
 4C5  C14  H11  single    0.930  0.020  1.080
 4C5  C13  H12  single    0.930  0.020  1.080
 4C5  C23  H13  single    0.930  0.020  1.080
 4C5  C22  H14  single    0.930  0.020  1.080
 4C5  C21  H15  single    0.930  0.020  1.080
 4C5  C20  H16  single    0.930  0.020  1.080
 4C5  C19  H17  single    0.930  0.020  1.080
 4C5  C11  H18  single    0.930  0.020  1.080
 4C5  C10  H19  single    0.930  0.020  1.080
 4C5  C9   H20  single    0.970  0.020  1.090
 4C5  C9   H21  single    0.970  0.020  1.090
 4C5  C9   H22  single    0.970  0.020  1.090
 4C5  C7   H23  single    0.930  0.020  1.080
 4C5  C6   H24  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
 4C5  H1   O1   C1   110.31  3.000
 4C5  C2   C1   O2   124.25  3.000
 4C5  O2   C1   O1   123.73  3.000
 4C5  C2   C1   O1   112.02  3.000
 4C5  H2   C2   C3   108.41  3.000
 4C5  H2   C2   N    108.46  3.000
 4C5  C3   C2   N    111.05  3.000
 4C5  H2   C2   C1   107.03  3.000
 4C5  N    C2   C1   113.78  3.000
 4C5  C3   C2   C1   107.92  3.000
 4C5  H4   N    H3   106.44  3.000
 4C5  H4   N    C2   110.51  3.000
 4C5  H3   N    C2   110.43  3.000
 4C5  H7   C3   H6   107.77  3.000
 4C5  H7   C3   S    109.29  3.000
 4C5  H6   C3   S    109.82  3.000
 4C5  H7   C3   C2   110.82  3.000
 4C5  H6   C3   C2   109.69  3.000
 4C5  S    C3   C2   109.42  3.000
 4C5  C4   S    C3   101.26  3.000
 4C5  C5   C4   C18  112.97  3.000
 4C5  C18  C4   C12  105.96  3.000
 4C5  C5   C4   C12  113.57  3.000
 4C5  C18  C4   S    112.54  3.000
 4C5  C5   C4   S    106.55  3.000
 4C5  C12  C4   S    105.09  3.000
 4C5  C13  C12  C17  118.26  3.000
 4C5  C13  C12  C4   122.09  3.000
 4C5  C17  C12  C4   119.46  3.000
 4C5  H8   C17  C16  118.80  3.000
 4C5  H8   C17  C12  120.22  3.000
 4C5  C16  C17  C12  120.97  3.000
 4C5  H9   C16  C15  120.21  3.000
 4C5  H9   C16  C17  119.51  3.000
 4C5  C15  C16  C17  120.28  3.000
 4C5  H10  C15  C14  120.40  3.000
 4C5  H10  C15  C16  120.37  3.000
 4C5  C14  C15  C16  119.22  3.000
 4C5  H11  C14  C13  119.31  3.000
 4C5  H11  C14  C15  120.24  3.000
 4C5  C13  C14  C15  120.45  3.000
 4C5  H12  C13  C14  118.78  3.000
 4C5  H12  C13  C12  120.41  3.000
 4C5  C14  C13  C12  120.80  3.000
 4C5  C19  C18  C23  118.19  3.000
 4C5  C23  C18  C4   118.16  3.000
 4C5  C19  C18  C4   123.60  3.000
 4C5  H13  C23  C22  118.93  3.000
 4C5  H13  C23  C18  120.00  3.000
 4C5  C22  C23  C18  121.06  3.000
 4C5  H14  C22  C21  120.15  3.000
 4C5  H14  C22  C23  119.63  3.000
 4C5  C21  C22  C23  120.22  3.000
 4C5  H15  C21  C20  120.46  3.000
 4C5  H15  C21  C22  120.33  3.000
 4C5  C20  C21  C22  119.21  3.000
 4C5  H16  C20  C19  119.31  3.000
 4C5  H16  C20  C21  120.25  3.000
 4C5  C19  C20  C21  120.44  3.000
 4C5  H17  C19  C20  119.19  3.000
 4C5  H17  C19  C18  119.93  3.000
 4C5  C20  C19  C18  120.87  3.000
 4C5  C6   C5   C11  117.26  3.000
 4C5  C11  C5   C4   119.52  3.000
 4C5  C6   C5   C4   123.00  3.000
 4C5  H18  C11  C10  118.52  3.000
 4C5  H18  C11  C5   119.82  3.000
 4C5  C10  C11  C5   121.66  3.000
 4C5  H19  C10  C8   119.56  3.000
 4C5  H19  C10  C11  120.11  3.000
 4C5  C8   C10  C11  120.33  3.000
 4C5  C7   C8   O3   124.78  3.000
 4C5  O3   C8   C10  116.35  3.000
 4C5  C7   C8   C10  118.87  3.000
 4C5  C9   O3   C8   118.41  3.000
 4C5  H22  C9   H21  108.76  3.000
 4C5  H22  C9   H20  108.85  3.000
 4C5  H21  C9   H20  108.73  3.000
 4C5  H22  C9   O3   106.55  3.000
 4C5  H21  C9   O3   112.02  3.000
 4C5  H20  C9   O3   111.82  3.000
 4C5  H23  C7   C6   118.38  3.000
 4C5  H23  C7   C8   121.70  3.000
 4C5  C6   C7   C8   119.91  3.000
 4C5  H24  C6   C7   117.59  3.000
 4C5  H24  C6   C5   120.46  3.000
 4C5  C7   C6   C5   121.94  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
 4C5  CONST_01  C15  C16  C17  C12    0.00   0.0  0
 4C5  CONST_02  C15  C14  C13  C12    0.00   0.0  0
 4C5  CONST_03  C14  C15  C16  C17    0.00   0.0  0
 4C5  CONST_04  C14  C13  C12  C17    0.00   0.0  0
 4C5  CONST_05  C13  C14  C15  C16    0.00   0.0  0
 4C5  CONST_06  C13  C12  C17  C16    0.00   0.0  0
 4C5  CONST_07  C21  C20  C19  C18    0.00   0.0  0
 4C5  CONST_08  C21  C22  C23  C18    0.00   0.0  0
 4C5  CONST_09  C20  C19  C18  C23    0.00   0.0  0
 4C5  CONST_10  C20  C21  C22  C23    0.00   0.0  0
 4C5  CONST_11  C19  C20  C21  C22    0.00   0.0  0
 4C5  CONST_12  C19  C18  C23  C22    0.00   0.0  0
 4C5  CONST_13  C8   C7   C6   C5     0.00   0.0  0
 4C5  CONST_14  C8   C10  C11  C5     0.00   0.0  0
 4C5  CONST_15  C7   C6   C5   C11    0.00   0.0  0
 4C5  CONST_16  C7   C8   C10  C11    0.00   0.0  0
 4C5  CONST_17  C6   C7   C8   C10    0.00   0.0  0
 4C5  CONST_18  C6   C5   C11  C10    0.00   0.0  0
 4C5  CONST_19  C16  C17  C12  C4   180.00   0.0  0
 4C5  CONST_20  C14  C13  C12  C4   180.00   0.0  0
 4C5  CONST_21  C7   C6   C5   C4   180.00   0.0  0
 4C5  CONST_22  C10  C11  C5   C4   180.00   0.0  0
 4C5  CONST_23  C20  C19  C18  C4   180.00   0.0  0
 4C5  CONST_24  C22  C23  C18  C4   180.00   0.0  0
 4C5  CONST_25  O3   C8   C10  C11  180.00   0.0  0
 4C5  CONST_26  C6   C7   C8   O3   180.00   0.0  0
 4C5  CONST_27  H9   C16  C17  C12  180.00   0.0  0
 4C5  CONST_28  H11  C14  C13  C12  180.00   0.0  0
 4C5  CONST_29  H10  C15  C16  C17  180.00   0.0  0
 4C5  CONST_30  H12  C13  C12  C17  180.00   0.0  0
 4C5  CONST_31  H8   C17  C16  C15  180.00   0.0  0
 4C5  CONST_32  H16  C20  C19  C18  180.00   0.0  0
 4C5  CONST_33  H14  C22  C23  C18  180.00   0.0  0
 4C5  CONST_34  H17  C19  C18  C23  180.00   0.0  0
 4C5  CONST_35  H15  C21  C22  C23  180.00   0.0  0
 4C5  CONST_36  H13  C23  C22  C21  180.00   0.0  0
 4C5  CONST_37  H23  C7   C6   C5   180.00   0.0  0
 4C5  CONST_38  H19  C10  C11  C5   180.00   0.0  0
 4C5  CONST_39  H24  C6   C5   C11  180.00   0.0  0
 4C5  CONST_40  H18  C11  C10  C8   180.00   0.0  0
 4C5  CONST_41  H1   O1   C1   O2     0.00   0.0  0
 4C5  Var_01    C6   C5   C4   C12  133.51  30.0  2
 4C5  Var_02    C19  C18  C4   C12  113.21  30.0  2
 4C5  Var_03    C5   C4   C12  C17  164.41  30.0  2
 4C5  Var_04    C7   C8   O3   C9    -2.03  30.0  2
 4C5  Var_05    C12  C4   S    C3   170.50  30.0  3
 4C5  Var_06    H20  C9   O3   C8   -60.06  30.0  3
 4C5  Var_07    H6   C3   S    C4    46.53  30.0  3

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
 4C5  chir_01  C2  C3  N  C1  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
 4C5  plan-1  C4   0.020
 4C5  plan-1  C12  0.020
 4C5  plan-1  C17  0.020
 4C5  plan-1  C16  0.020
 4C5  plan-1  C15  0.020
 4C5  plan-1  C14  0.020
 4C5  plan-1  C13  0.020
 4C5  plan-1  H8   0.020
 4C5  plan-1  H9   0.020
 4C5  plan-1  H10  0.020
 4C5  plan-1  H11  0.020
 4C5  plan-1  H12  0.020
 4C5  plan-2  C4   0.020
 4C5  plan-2  C18  0.020
 4C5  plan-2  C23  0.020
 4C5  plan-2  C22  0.020
 4C5  plan-2  C21  0.020
 4C5  plan-2  C20  0.020
 4C5  plan-2  C19  0.020
 4C5  plan-2  H13  0.020
 4C5  plan-2  H14  0.020
 4C5  plan-2  H15  0.020
 4C5  plan-2  H16  0.020
 4C5  plan-2  H17  0.020
 4C5  plan-3  C4   0.020
 4C5  plan-3  C5   0.020
 4C5  plan-3  C11  0.020
 4C5  plan-3  C10  0.020
 4C5  plan-3  C8   0.020
 4C5  plan-3  O3   0.020
 4C5  plan-3  C7   0.020
 4C5  plan-3  C6   0.020
 4C5  plan-3  H18  0.020
 4C5  plan-3  H19  0.020
 4C5  plan-3  H23  0.020
 4C5  plan-3  H24  0.020
 4C5  plan-4  O1   0.020
 4C5  plan-4  C1   0.020
 4C5  plan-4  O2   0.020
 4C5  plan-4  C2   0.020
 4C5  plan-4  H1   0.020

