# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 00:31:24 2021
#   Inital geometry file: a 127 line input string
#   Ligand name: 4-{[3-chloro-4-(alpha-D-mannopyranosyloxy)phenyl]carbamoyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(NC(=O)c3ccc(cc3)C(O)=O)cc2Cl)[C@@H](O)[C@@H](O)[C@@H]1O
#
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
 3XJ  3XJ  '4-{[3-chloro-4-(alpha-D-mannopyranosyloxy)phenyl]carbamoyl}benzoic acid'  ligand  51  31  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XJ
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
 3XJ  O3   O   OH1   0  -0.591  -14.7108  50.8341  -13.6526
 3XJ  C4   C   CR16  0  -0.273   -6.7901  46.7562  -10.8929
 3XJ  C5   C   CR6   0  -0.145   -5.4754  46.5837  -10.4931
 3XJ  O4   O   O2    0  -0.483   -2.8800  49.0848   -8.9861
 3XJ  C7   C   CR6   0  -0.037  -10.7697  48.0027  -12.5814
 3XJ  C8   C   CR16  0  -0.251  -11.6424  47.2185  -13.3321
 3XJ  C9   C   CR16  0  -0.243  -12.8359  47.7454  -13.7881
 3XJ  O5   O   OH1   0  -0.676   -2.0482  47.1250   -6.0086
 3XJ  C10  C   CR6   0  -0.080  -13.1886  49.0581  -13.4817
 3XJ  O6   O   OH1   0  -0.675   -0.0053  46.3597   -7.8393
 3XJ  C11  C   CR16  0  -0.243  -12.3278  49.8373  -12.7136
 3XJ  C12  C   CR16  0  -0.276  -11.1244  49.3126  -12.2704
 3XJ  C13  C   C     0   0.539  -14.4862  49.5742  -13.9912
 3XJ  O7   O   OH1   0  -0.669   -0.0797  48.5914   -9.4823
 3XJ  C14  C   CH1   0   0.213   -2.3501  48.2828   -9.9792
 3XJ  C15  C   CH1   0  -0.017   -3.1261  48.4395   -7.7400
 3XJ  O2   O   O     0  -0.432  -15.2541  48.9132  -14.6471
 3XJ  O1   O   O     0  -0.456   -9.4433  46.1770  -11.8758
 3XJ  N    N   NH1   0  -0.758   -8.4594  48.2257  -11.9559
 3XJ  C3   C   CR6   0   0.367   -7.1578  47.9391  -11.5297
 3XJ  C2   C   CR16  0  -0.338   -6.1878  48.9181  -11.7405
 3XJ  C1   C   CR16  0  -0.345   -4.8788  48.7279  -11.3397
 3XJ  C    C   CR6   0   0.451   -4.4947  47.5445  -10.7195
 3XJ  O    O   O2    0  -0.495   -3.2358  47.2413  -10.3406
 3XJ  C18  C   CH1   0  -0.009   -1.0569  47.5860   -9.5640
 3XJ  C17  C   CH1   0   0.003   -1.2561  46.8740   -8.2282
 3XJ  C16  C   CH1   0   0.009   -1.8215  47.8462   -7.1999
 3XJ  C19  C   CH2   0  -0.193   -3.7769  49.4471   -6.8193
 3XJ  H19  H   HOH1  0   0.490  -15.5613  51.1294  -14.0110
 3XJ  H6   H   HCR6  0   0.301   -7.5073  45.9773  -10.6937
 3XJ  H8   H   HCR6  0   0.271  -11.3837  46.1961  -13.5714
 3XJ  H9   H   HCR6  0   0.274  -13.4961  47.1318  -14.3853
 3XJ  H14  H   HOH1  0   0.454   -0.0824  46.0369   -6.9347
 3XJ  H10  H   HCR6  0   0.277  -12.5823  50.8530  -12.4470
 3XJ  H11  H   HCR6  0   0.275  -10.4852  49.9343  -11.6565
 3XJ  H15  H   HOH1  0   0.456    0.7057  48.2113   -9.0736
 3XJ  H    H   HCH1  0   0.267   -2.1567  48.9419  -10.8331
 3XJ  H18  H   HOH1  0   0.460   -3.2888  51.0713   -5.8878
 3XJ  H12  H   HCH1  0   0.230   -3.8547  47.6256   -7.8663
 3XJ  H7   H   HNH1  0   0.427   -8.5898  49.1668  -12.2951
 3XJ  H5   H   HCR6  0   0.283   -6.4572  49.8477  -12.2267
 3XJ  H4   H   HCR6  0   0.289   -4.1601  49.5125  -11.5319
 3XJ  H3   H   HCH1  0   0.245   -0.8005  46.8454  -10.3346
 3XJ  H2   H   HCH1  0   0.218   -1.9835  46.0617   -8.3727
 3XJ  H1   H   HCH1  0   0.232   -1.0942  48.6497   -7.0401
 3XJ  H16  H   HCH2  0   0.221   -4.6800  49.8297   -7.3127
 3XJ  H17  H   HCH2  0   0.210   -4.1140  48.9125   -5.9235
 3XJ  C6   C   C     0   0.530   -9.5016  47.3732  -12.1003
 3XJ  CL   CL  CL    0  -0.100   -5.0335  45.1207   -9.6841
 3XJ  H13  H   HOH1  0   0.462   -1.9261  47.7144   -5.2591
 3XJ  O8   O   OH1   0  -0.670   -2.8671  50.4747   -6.5122

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
 3XJ  O2   C13  double    1.207  0.020  1.207
 3XJ  C9   C8   aromatic  1.382  0.020  1.382
 3XJ  C9   C10  aromatic  1.393  0.020  1.393
 3XJ  C13  C10  single    1.486  0.020  1.486
 3XJ  C13  O3   single    1.324  0.020  1.324
 3XJ  C8   C7   aromatic  1.393  0.020  1.393
 3XJ  C10  C11  aromatic  1.392  0.020  1.392
 3XJ  C7   C6   single    1.495  0.020  1.495
 3XJ  C7   C12  aromatic  1.392  0.020  1.392
 3XJ  C11  C12  aromatic  1.386  0.020  1.386
 3XJ  C6   N    single    1.354  0.020  1.354
 3XJ  C6   O1   double    1.218  0.020  1.218
 3XJ  N    C3   single    1.399  0.020  1.399
 3XJ  C2   C3   aromatic  1.394  0.020  1.394
 3XJ  C2   C1   aromatic  1.382  0.020  1.382
 3XJ  C3   C4   aromatic  1.393  0.020  1.393
 3XJ  C1   C    aromatic  1.390  0.020  1.390
 3XJ  C4   C5   aromatic  1.385  0.020  1.385
 3XJ  C    C5   aromatic  1.391  0.020  1.391
 3XJ  C    O    single    1.349  0.020  1.349
 3XJ  C5   CL   single    1.729  0.020  1.729
 3XJ  O    C14  single    1.414  0.020  1.414
 3XJ  C14  C18  single    1.527  0.020  1.527
 3XJ  C14  O4   single    1.382  0.020  1.382
 3XJ  C18  O7   single    1.404  0.020  1.404
 3XJ  C18  C17  single    1.527  0.020  1.527
 3XJ  O4   C15  single    1.425  0.020  1.425
 3XJ  C17  O6   single    1.407  0.020  1.407
 3XJ  C17  C16  single    1.524  0.020  1.524
 3XJ  C15  C16  single    1.532  0.020  1.532
 3XJ  C15  C19  single    1.512  0.020  1.512
 3XJ  C16  O5   single    1.411  0.020  1.411
 3XJ  C19  O8   single    1.406  0.020  1.406
 3XJ  O3   H19  single    0.850  0.020  0.980
 3XJ  C4   H6   single    0.930  0.020  1.080
 3XJ  C8   H8   single    0.930  0.020  1.080
 3XJ  C9   H9   single    0.930  0.020  1.080
 3XJ  O5   H13  single    0.850  0.020  0.980
 3XJ  O6   H14  single    0.850  0.020  0.980
 3XJ  C11  H10  single    0.930  0.020  1.080
 3XJ  C12  H11  single    0.930  0.020  1.080
 3XJ  O7   H15  single    0.850  0.020  0.980
 3XJ  C14  H    single    0.970  0.020  1.090
 3XJ  O8   H18  single    0.850  0.020  0.980
 3XJ  C15  H12  single    0.970  0.020  1.090
 3XJ  N    H7   single    0.860  0.020  1.020
 3XJ  C2   H5   single    0.930  0.020  1.080
 3XJ  C1   H4   single    0.930  0.020  1.080
 3XJ  C18  H3   single    0.970  0.020  1.090
 3XJ  C17  H2   single    0.970  0.020  1.090
 3XJ  C16  H1   single    0.970  0.020  1.090
 3XJ  C19  H16  single    0.970  0.020  1.090
 3XJ  C19  H17  single    0.970  0.020  1.090

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
 3XJ  H19  O3   C13  110.14  3.000
 3XJ  H6   C4   C3   121.52  3.000
 3XJ  H6   C4   C5   119.24  3.000
 3XJ  C3   C4   C5   119.23  3.000
 3XJ  C    C5   CL   118.70  3.000
 3XJ  CL   C5   C4   118.88  3.000
 3XJ  C    C5   C4   122.42  3.000
 3XJ  C15  O4   C14  115.59  3.000
 3XJ  C12  C7   C8   119.38  3.000
 3XJ  C12  C7   C6   122.70  3.000
 3XJ  C8   C7   C6   117.88  3.000
 3XJ  H8   C8   C9   119.61  3.000
 3XJ  H8   C8   C7   120.11  3.000
 3XJ  C9   C8   C7   120.28  3.000
 3XJ  H9   C9   C10  120.10  3.000
 3XJ  H9   C9   C8   119.55  3.000
 3XJ  C10  C9   C8   120.35  3.000
 3XJ  H13  O5   C16  108.93  3.000
 3XJ  C13  C10  C11  122.31  3.000
 3XJ  C11  C10  C9   119.48  3.000
 3XJ  C13  C10  C9   118.21  3.000
 3XJ  H14  O6   C17  108.10  3.000
 3XJ  H10  C11  C12  118.78  3.000
 3XJ  H10  C11  C10  121.11  3.000
 3XJ  C12  C11  C10  120.10  3.000
 3XJ  H11  C12  C11  118.47  3.000
 3XJ  H11  C12  C7   121.11  3.000
 3XJ  C11  C12  C7   120.40  3.000
 3XJ  O2   C13  C10  123.47  3.000
 3XJ  C10  C13  O3   113.01  3.000
 3XJ  O2   C13  O3   123.52  3.000
 3XJ  H15  O7   C18  108.03  3.000
 3XJ  H    C14  C18  109.69  3.000
 3XJ  H    C14  O    110.75  3.000
 3XJ  C18  C14  O    105.30  3.000
 3XJ  H    C14  O4   106.17  3.000
 3XJ  C18  C14  O4   113.22  3.000
 3XJ  O    C14  O4   111.77  3.000
 3XJ  H12  C15  C19  106.14  3.000
 3XJ  H12  C15  C16  108.55  3.000
 3XJ  C19  C15  C16  114.21  3.000
 3XJ  H12  C15  O4   110.44  3.000
 3XJ  C19  C15  O4   107.76  3.000
 3XJ  C16  C15  O4   109.68  3.000
 3XJ  H7   N    C3   114.44  3.000
 3XJ  H7   N    C6   116.87  3.000
 3XJ  C3   N    C6   128.27  3.000
 3XJ  C2   C3   N    117.21  3.000
 3XJ  C2   C3   C4   118.80  3.000
 3XJ  N    C3   C4   123.97  3.000
 3XJ  H5   C2   C1   118.94  3.000
 3XJ  H5   C2   C3   119.83  3.000
 3XJ  C1   C2   C3   121.23  3.000
 3XJ  H4   C1   C    120.89  3.000
 3XJ  H4   C1   C2   118.56  3.000
 3XJ  C    C1   C2   120.54  3.000
 3XJ  O    C    C1   125.06  3.000
 3XJ  O    C    C5   117.18  3.000
 3XJ  C1   C    C5   117.76  3.000
 3XJ  C    O    C14  119.38  3.000
 3XJ  H3   C18  C17  109.25  3.000
 3XJ  H3   C18  C14  108.33  3.000
 3XJ  C17  C18  C14  109.89  3.000
 3XJ  H3   C18  O7   111.15  3.000
 3XJ  C17  C18  O7   111.94  3.000
 3XJ  C14  C18  O7   106.17  3.000
 3XJ  H2   C17  C16  108.33  3.000
 3XJ  H2   C17  C18  108.41  3.000
 3XJ  C16  C17  C18  109.95  3.000
 3XJ  H2   C17  O6   110.75  3.000
 3XJ  C16  C17  O6   112.12  3.000
 3XJ  C18  C17  O6   107.23  3.000
 3XJ  H1   C16  C17  108.67  3.000
 3XJ  H1   C16  C15  109.44  3.000
 3XJ  C17  C16  C15  108.98  3.000
 3XJ  H1   C16  O5   111.00  3.000
 3XJ  C15  C16  O5   111.04  3.000
 3XJ  C17  C16  O5   107.65  3.000
 3XJ  H17  C19  H16  106.51  3.000
 3XJ  H17  C19  C15  107.76  3.000
 3XJ  H16  C19  C15  108.22  3.000
 3XJ  H17  C19  O8   112.13  3.000
 3XJ  H16  C19  O8   112.06  3.000
 3XJ  C15  C19  O8   109.97  3.000
 3XJ  N    C6   O1   124.16  3.000
 3XJ  O1   C6   C7   120.88  3.000
 3XJ  N    C6   C7   114.96  3.000
 3XJ  H18  O8   C19  108.15  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
 3XJ  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 3XJ  CONST_02  C1   C    C5   C4      0.00   0.0  0
 3XJ  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 3XJ  CONST_04  C2   C1   C    C5      0.00   0.0  0
 3XJ  CONST_05  C10  C9   C8   C7      0.00   0.0  0
 3XJ  CONST_06  C10  C11  C12  C7      0.00   0.0  0
 3XJ  CONST_07  C11  C10  C9   C8      0.00   0.0  0
 3XJ  CONST_08  C11  C12  C7   C8      0.00   0.0  0
 3XJ  CONST_09  C12  C7   C8   C9      0.00   0.0  0
 3XJ  CONST_10  C12  C11  C10  C9      0.00   0.0  0
 3XJ  CONST_11  C    C1   C2   C3      0.00   0.0  0
 3XJ  CONST_12  C    C5   C4   C3      0.00   0.0  0
 3XJ  CONST_13  O    C    C5   C4    180.00   0.0  0
 3XJ  CONST_14  N    C3   C4   C5    180.00   0.0  0
 3XJ  CONST_15  C9   C8   C7   C6    180.00   0.0  0
 3XJ  CONST_16  C11  C12  C7   C6    180.00   0.0  0
 3XJ  CONST_17  C13  C10  C9   C8    180.00   0.0  0
 3XJ  CONST_18  C13  C10  C11  C12   180.00   0.0  0
 3XJ  CONST_19  C1   C2   C3   N     180.00   0.0  0
 3XJ  CONST_20  CL   C5   C4   C3    180.00   0.0  0
 3XJ  CONST_21  O    C    C1   C2    180.00   0.0  0
 3XJ  CONST_22  CL   C5   C    C1    180.00   0.0  0
 3XJ  CONST_23  H5   C2   C3   C4    180.00   0.0  0
 3XJ  CONST_24  H4   C1   C    C5    180.00   0.0  0
 3XJ  CONST_25  H9   C9   C8   C7    180.00   0.0  0
 3XJ  CONST_26  H10  C11  C12  C7    180.00   0.0  0
 3XJ  CONST_27  H11  C12  C7   C8    180.00   0.0  0
 3XJ  CONST_28  H8   C8   C9   C10   180.00   0.0  0
 3XJ  CONST_29  H6   C4   C3   C2    180.00   0.0  0
 3XJ  CONST_30  C3   N    C6   C7    180.00   0.0  0
 3XJ  CONST_32  C2   C3   N    C6    180.00   0.0  0
 3XJ  CONST_33  H7   N    C3   C4    180.00   0.0  0
 3XJ  CONST_34  C3   N    C6   O1      0.00   0.0  0
 3XJ  CONST_35  H19  O3   C13  C10   180.00   0.0  0
 3XJ  Var_01    C1   C    O    C14    29.35  30.0  2
 3XJ  Var_02    C9   C10  C13  O3   -179.32  30.0  2
 3XJ  Var_03    N    C6   C7   C8    150.40  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
 3XJ  chir_01  C14  O   C18  O4   positiv
 3XJ  chir_02  C15  O4  C19  C16  positiv
 3XJ  chir_03  C18  O7  C14  C17  positiv
 3XJ  chir_04  C17  O6  C18  C16  positiv
 3XJ  chir_05  C16  O5  C17  C15  negativ

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
 3XJ  plan-1  C7   0.020
 3XJ  plan-1  C8   0.020
 3XJ  plan-1  C9   0.020
 3XJ  plan-1  C10  0.020
 3XJ  plan-1  C11  0.020
 3XJ  plan-1  C12  0.020
 3XJ  plan-1  C13  0.020
 3XJ  plan-1  H8   0.020
 3XJ  plan-1  H9   0.020
 3XJ  plan-1  H10  0.020
 3XJ  plan-1  H11  0.020
 3XJ  plan-1  C6   0.020
 3XJ  plan-2  C4   0.020
 3XJ  plan-2  C5   0.020
 3XJ  plan-2  N    0.020
 3XJ  plan-2  C3   0.020
 3XJ  plan-2  C2   0.020
 3XJ  plan-2  C1   0.020
 3XJ  plan-2  C    0.020
 3XJ  plan-2  O    0.020
 3XJ  plan-2  H6   0.020
 3XJ  plan-2  H5   0.020
 3XJ  plan-2  H4   0.020
 3XJ  plan-2  CL   0.020
 3XJ  plan-3  C7   0.020
 3XJ  plan-3  O1   0.020
 3XJ  plan-3  N    0.020
 3XJ  plan-3  C3   0.020
 3XJ  plan-3  H7   0.020
 3XJ  plan-3  C6   0.020
 3XJ  plan-4  O3   0.020
 3XJ  plan-4  C10  0.020
 3XJ  plan-4  C13  0.020
 3XJ  plan-4  O2   0.020
 3XJ  plan-4  H19  0.020

