# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:03:26 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-azanyl-3-[[3,4-bis(fluoranyl)phenyl]sulfanylmethyl]-4-oxidanyl-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@]1([C@H](CSc2ccc(F)c(F)c2)[C@@H](O)[C@H]3[C@@H]([C@@H]13)C(O)=O)C(O)=O
#
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
 6YS  6YS  '(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2-azanyl-3-[[3,4-bis(fluoranyl)phenyl]sulfanylmethyl]-4-oxidanyl-bicyclo[3.1.0]hexane-2,6-dicarboxylic acid'  ligand  37  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6YS
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
 6YS  C7   C  C      0   0.427  -5.4257  -1.0888   0.1777
 6YS  C6   C  CR6    0  -0.099   2.8912  -0.4533   0.2765
 6YS  C1   C  CR16   0  -0.387   4.5671   1.2621   0.0173
 6YS  C5   C  CR6    0   0.412   5.1903  -1.0449  -0.0463
 6YS  C4   C  CR6    0   0.380   5.5383   0.2948  -0.1098
 6YS  C3   C  CR16   0  -0.411   3.8822  -1.4284   0.1407
 6YS  C2   C  CR16   0  -0.254   3.2424   0.8915   0.2150
 6YS  C8   C  C      0   0.415  -1.7443   2.4091  -0.3249
 6YS  C9   C  CH1    0  -0.418  -3.9572  -0.7439   0.2983
 6YS  C10  C  CR15   0  -0.266  -3.1737  -0.5355  -0.9735
 6YS  C11  C  CR15   0  -0.218  -3.5104   0.6309  -0.1243
 6YS  C12  C  CR15   0  -0.305  -1.2414   0.0147   0.3493
 6YS  C13  C  CR15   0   0.117  -1.6857  -0.7521  -0.9098
 6YS  C14  C  CR5    0   0.001  -2.2476   1.1894   0.5053
 6YS  C15  C  CH2    0  -0.595   0.2196   0.4453   0.3516
 6YS  N16  N  NH2    0  -0.805  -2.4457   1.4949   1.9168
 6YS  O17  O  OC    -1  -0.624  -5.8814  -1.8798   1.0306
 6YS  O19  O  O      0  -0.613  -6.0664  -0.5624  -0.7567
 6YS  O21  O  OH1    0  -0.676  -1.3842  -2.1326  -0.8916
 6YS  F22  F  F      0  -0.307   6.8206   0.6287  -0.2953
 6YS  F23  F  F      0  -0.305   6.1454  -1.9707  -0.1755
 6YS  S24  S  S2     0   0.045   1.2548  -1.0340   0.5575
 6YS  H1   H  HCR6   0   0.296   4.8399   2.3080  -0.0332
 6YS  H2   H  HCR6   0   0.298   3.6418  -2.4840   0.1775
 6YS  H3   H  HCR6   0   0.280   2.5019   1.6700   0.3227
 6YS  H4   H  HCH1   0   0.223  -3.4462  -1.2095   1.1346
 6YS  H5   H  HCR5   0   0.234  -3.6801  -0.7068  -1.9159
 6YS  H6   H  HCR5   0   0.234  -4.2839   1.3282  -0.4263
 6YS  H7   H  HCR5   0   0.248  -1.4044  -0.6354   1.2158
 6YS  H8   H  HCR5   0   0.200  -1.2349  -0.2739  -1.7889
 6YS  H9   H  HCH2   0   0.278   0.4821   0.9323  -0.5890
 6YS  H10  H  HCH2   0   0.283   0.4184   1.1377   1.1710
 6YS  H11  H  HNH2   0   0.329  -1.7445   2.1797   2.1793
 6YS  H12  H  HNH2   0   0.333  -3.3227   1.9949   2.0124
 6YS  H16  H  HOH1   0   0.440  -0.4328  -2.2336  -1.0051
 6YS  O18  O  O      0  -0.592  -1.8161   2.3128  -1.5659
 6YS  O20  O  OC    -1  -0.599  -1.2743   3.3717   0.3143

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
 6YS  O19  C7   deloc     1.249  0.020  1.249
 6YS  C7   O17  deloc     1.249  0.020  1.249
 6YS  C7   C9   single    1.513  0.020  1.513
 6YS  F22  C4   single    1.338  0.020  1.338
 6YS  C1   C4   aromatic  1.377  0.020  1.377
 6YS  C1   C2   aromatic  1.390  0.020  1.390
 6YS  C9   C11  single    1.506  0.020  1.506
 6YS  C9   C10  single    1.508  0.020  1.508
 6YS  C4   C5   aromatic  1.386  0.020  1.386
 6YS  C2   C6   aromatic  1.391  0.020  1.391
 6YS  N16  C14  single    1.458  0.020  1.458
 6YS  C11  C10  single    1.482  0.020  1.482
 6YS  C11  C14  single    1.518  0.020  1.518
 6YS  O21  C13  single    1.413  0.020  1.413
 6YS  C10  C13  single    1.505  0.020  1.505
 6YS  C14  C12  single    1.555  0.020  1.555
 6YS  C14  C8   single    1.559  0.020  1.559
 6YS  C5   F23  single    1.336  0.020  1.336
 6YS  C5   C3   aromatic  1.376  0.020  1.376
 6YS  C6   C3   aromatic  1.397  0.020  1.397
 6YS  C6   S24  single    1.759  0.020  1.759
 6YS  C12  C13  single    1.540  0.020  1.540
 6YS  C12  C15  single    1.523  0.020  1.523
 6YS  S24  C15  single    1.817  0.020  1.817
 6YS  C8   O18  deloc     1.247  0.020  1.247
 6YS  C8   O20  deloc     1.247  0.020  1.247
 6YS  C1   H1   single    0.930  0.020  1.080
 6YS  C3   H2   single    0.930  0.020  1.080
 6YS  C2   H3   single    0.930  0.020  1.080
 6YS  C9   H4   single    0.970  0.020  1.090
 6YS  C10  H5   single    0.970  0.020  1.090
 6YS  C11  H6   single    0.970  0.020  1.090
 6YS  C12  H7   single    0.970  0.020  1.090
 6YS  C13  H8   single    0.970  0.020  1.090
 6YS  C15  H9   single    0.970  0.020  1.090
 6YS  C15  H10  single    0.970  0.020  1.090
 6YS  N16  H11  single    0.890  0.020  1.040
 6YS  N16  H12  single    0.890  0.020  1.040
 6YS  O21  H16  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
 6YS  O19  C7   O17  126.18  3.000
 6YS  O17  C7   C9   116.35  3.000
 6YS  O19  C7   C9   117.47  3.000
 6YS  S24  C6   C2   124.12  3.000
 6YS  S24  C6   C3   116.43  3.000
 6YS  C2   C6   C3   119.43  3.000
 6YS  H1   C1   C2   120.31  3.000
 6YS  H1   C1   C4   119.80  3.000
 6YS  C2   C1   C4   119.88  3.000
 6YS  F23  C5   C3   119.97  3.000
 6YS  C3   C5   C4   120.96  3.000
 6YS  F23  C5   C4   119.07  3.000
 6YS  F22  C4   C5   119.23  3.000
 6YS  C5   C4   C1   119.87  3.000
 6YS  F22  C4   C1   120.90  3.000
 6YS  H2   C3   C5   119.16  3.000
 6YS  H2   C3   C6   121.29  3.000
 6YS  C5   C3   C6   119.55  3.000
 6YS  H3   C2   C1   118.40  3.000
 6YS  H3   C2   C6   121.29  3.000
 6YS  C1   C2   C6   120.31  3.000
 6YS  O20  C8   O18  126.25  3.000
 6YS  O20  C8   C14  116.90  3.000
 6YS  O18  C8   C14  116.81  3.000
 6YS  H4   C9   C11  117.92  3.000
 6YS  H4   C9   C10  117.69  3.000
 6YS  C11  C9   C10   58.88  3.000
 6YS  H4   C9   C7   114.88  3.000
 6YS  C10  C9   C7   117.93  3.000
 6YS  C11  C9   C7   118.26  3.000
 6YS  H5   C10  C13  118.44  3.000
 6YS  H5   C10  C11  121.12  3.000
 6YS  C13  C10  C11  108.28  3.000
 6YS  H5   C10  C9   117.96  3.000
 6YS  C13  C10  C9   117.26  3.000
 6YS  C11  C10  C9    60.49  3.000
 6YS  H6   C11  C14  118.20  3.000
 6YS  H6   C11  C10  120.58  3.000
 6YS  C14  C11  C10  109.78  3.000
 6YS  H6   C11  C9   116.97  3.000
 6YS  C14  C11  C9   117.80  3.000
 6YS  C10  C11  C9    60.63  3.000
 6YS  H7   C12  C15  108.02  3.000
 6YS  H7   C12  C14  105.82  3.000
 6YS  C15  C12  C14  114.02  3.000
 6YS  H7   C12  C13  107.96  3.000
 6YS  C15  C12  C13  114.76  3.000
 6YS  C14  C12  C13  105.76  3.000
 6YS  H8   C13  O21  110.38  3.000
 6YS  H8   C13  C12  108.63  3.000
 6YS  O21  C13  C12  114.49  3.000
 6YS  H8   C13  C10  108.02  3.000
 6YS  C12  C13  C10  104.37  3.000
 6YS  O21  C13  C10  110.61  3.000
 6YS  N16  C14  C12  110.09  3.000
 6YS  C12  C14  C11  102.64  3.000
 6YS  N16  C14  C11  111.46  3.000
 6YS  C12  C14  C8   109.19  3.000
 6YS  C11  C14  C8   109.61  3.000
 6YS  N16  C14  C8   113.30  3.000
 6YS  H10  C15  H9   108.68  3.000
 6YS  H10  C15  S24  109.13  3.000
 6YS  H9   C15  S24  108.90  3.000
 6YS  H10  C15  C12  110.82  3.000
 6YS  H9   C15  C12  110.83  3.000
 6YS  S24  C15  C12  108.45  3.000
 6YS  H12  N16  H11  103.91  3.000
 6YS  H12  N16  C14  108.19  3.000
 6YS  H11  N16  C14  107.34  3.000
 6YS  H16  O21  C13  108.15  3.000
 6YS  C15  S24  C6   104.07  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
 6YS  CONST_01  C4   C1   C2   C6      0.00   0.0  0
 6YS  CONST_02  C4   C5   C3   C6      0.00   0.0  0
 6YS  CONST_03  C3   C5   C4   C1      0.00   0.0  0
 6YS  CONST_04  C3   C6   C2   C1      0.00   0.0  0
 6YS  CONST_05  C2   C1   C4   C5      0.00   0.0  0
 6YS  CONST_06  C2   C6   C3   C5      0.00   0.0  0
 6YS  CONST_07  F23  C5   C3   C6    180.00   0.0  0
 6YS  CONST_08  F23  C5   C4   C1    180.00   0.0  0
 6YS  CONST_09  S24  C6   C2   C1    180.00   0.0  0
 6YS  CONST_10  S24  C6   C3   C5    180.00   0.0  0
 6YS  CONST_11  F22  C4   C5   C3    180.00   0.0  0
 6YS  CONST_12  F22  C4   C1   C2    180.00   0.0  0
 6YS  CONST_13  H1   C1   C2   C6    180.00   0.0  0
 6YS  CONST_14  H3   C2   C1   C4    180.00   0.0  0
 6YS  CONST_15  H2   C3   C5   C4    180.00   0.0  0
 6YS  Var_01    C13  C10  C11  C9   -111.54  30.0  1
 6YS  Var_02    C12  C15  S24  C6    170.88  30.0  3
 6YS  Var_03    O19  C7   C9   C10   -35.45  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
 6YS  chir_04  C12  C14  C13  C15  negativ
 6YS  chir_05  C13  O21  C12  C10  positiv
 6YS  chir_06  C14  C8   C12  C11  positiv
 6YS  chir_07  C9   C7   C11  C10  both
 6YS  chir_08  C10  C9   C11  C13  both
 6YS  chir_09  C11  C14  C10  C9   both

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
 6YS  plan-1  C6   0.020
 6YS  plan-1  C1   0.020
 6YS  plan-1  C5   0.020
 6YS  plan-1  C4   0.020
 6YS  plan-1  C3   0.020
 6YS  plan-1  C2   0.020
 6YS  plan-1  F22  0.020
 6YS  plan-1  F23  0.020
 6YS  plan-1  S24  0.020
 6YS  plan-1  H1   0.020
 6YS  plan-1  H2   0.020
 6YS  plan-1  H3   0.020
 6YS  plan-2  C7   0.020
 6YS  plan-2  C9   0.020
 6YS  plan-2  O17  0.020
 6YS  plan-2  O19  0.020
 6YS  plan-3  C8   0.020
 6YS  plan-3  C14  0.020
 6YS  plan-3  O18  0.020
 6YS  plan-3  O20  0.020

