# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 14:10:25 2021
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-[(2~{S},3~{S},4~{R},4~{a}~{S},10~{a}~{S})-2-methyl-3,4-bis(oxidanyl)-3,4,4~{a},10~{a}-tetrahydro-2~{H}-pyrano[2,3-b][1,4]benzoxathiin-7-yl]-~{N}-(3-oxidanylpropyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1O[C@H]2Oc3ccc(CC(=O)NCCCO)cc3S[C@H]2[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
 QJB  QJB  2-[(2~{S},3~{S},4~{R},4~{a}~{S},10~{a}~{S})-2-methyl-3,4-bis(oxidanyl)-3,4,4~{a},10~{a}-tetrahydro-2~{H}-pyrano[2,3-b][1,4]benzoxathiin-7-yl]-~{N}-(3-oxidanylpropyl)ethanamide  ligand  48  25  .  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_QJB
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
 QJB  C10  C  CH2   0  -0.309  24.5664  24.0114  45.0487
 QJB  C11  C  CH2   0  -0.458  25.7263  24.9899  44.9032
 QJB  C12  C  CH2   0  -0.138  25.3363  26.2809  44.2084
 QJB  C14  C  CR6   0  -0.214  18.0741  23.7359  45.4449
 QJB  C15  C  CH1   0  -0.561  16.2632  22.2598  44.1140
 QJB  C17  C  CH1   0  -0.002  16.7004  19.9428  43.3525
 QJB  C6   C  CR16  0  -0.295  20.0820  23.4303  47.3318
 QJB  C5   C  CR16  0  -0.333  19.0285  22.5347  47.2921
 QJB  C4   C  CR6   0   0.421  18.0084  22.6826  46.3561
 QJB  C3   C  CH1   0   0.305  15.9235  21.7166  45.4963
 QJB  C2   C  CH1   0   0.004  16.4119  19.4936  44.7871
 QJB  C1   C  CH3   0  -0.707  15.7739  18.1221  44.8594
 QJB  O1   O  O2    0  -0.481  15.5206  20.3998  45.4418
 QJB  O2   O  O2    0  -0.498  17.0146  21.7700  46.4060
 QJB  C7   C  CR6   0   0.119  20.1531  24.4929  46.4342
 QJB  C8   C  CH2   0  -0.655  21.3257  25.4360  46.4440
 QJB  C9   C  C     0   0.546  22.3384  25.0113  45.3924
 QJB  O3   O  O     0  -0.495  22.0865  25.1059  44.1995
 QJB  N1   N  NH1   0  -0.616  23.4836  24.5050  45.8731
 QJB  O4   O  OH1   0  -0.676  26.4976  27.0672  44.0373
 QJB  C13  C  CR16  0  -0.311  19.1464  24.6219  45.4885
 QJB  S1   S  S2    0   0.096  16.8109  23.9756  44.2466
 QJB  C16  C  CH1   0   0.094  17.2597  21.3602  43.3833
 QJB  O5   O  OH1   0  -0.661  17.4977  21.7909  42.0740
 QJB  O6   O  OH1   0  -0.670  15.5521  19.9453  42.5429
 QJB  H1   H  HCH2  0   0.246  24.1623  23.7563  44.0697
 QJB  H2   H  HCH2  0   0.260  24.9301  23.0842  45.4930
 QJB  H3   H  HCH2  0   0.234  26.5089  24.4905  44.3252
 QJB  H4   H  HCH2  0   0.229  26.1495  25.2103  45.8878
 QJB  H5   H  HCH2  0   0.192  24.5865  26.8122  44.8077
 QJB  H6   H  HCH2  0   0.189  24.8657  26.0461  43.2445
 QJB  H7   H  HCH1  0   0.331  15.3306  22.3071  43.5474
 QJB  H8   H  HCH1  0   0.244  17.4744  19.2735  42.9498
 QJB  H10  H  HCR6  0   0.271  18.9826  21.7113  47.9937
 QJB  H11  H  HCH1  0   0.270  15.0882  22.2822  45.9170
 QJB  H12  H  HCH1  0   0.234  17.3689  19.4602  45.3215
 QJB  H13  H  HCH3  0   0.254  15.6614  17.8013  45.8945
 QJB  H14  H  HCH3  0   0.231  14.7868  18.1082  44.3953
 QJB  H15  H  HCH3  0   0.241  16.4028  17.3896  44.3527
 QJB  H16  H  HCH2  0   0.273  21.7723  25.4710  47.4391
 QJB  H17  H  HCH2  0   0.287  21.0013  26.4496  46.2009
 QJB  H18  H  HNH1  0   0.401  23.6154  24.4794  46.8708
 QJB  H19  H  HOH1  0   0.452  26.2358  27.9016  43.6384
 QJB  H20  H  HCR6  0   0.262  19.1906  25.4273  44.7655
 QJB  H21  H  HCH1  0   0.231  18.1980  21.3181  43.9558
 QJB  H22  H  HOH1  0   0.449  17.8988  22.6665  42.1160
 QJB  H23  H  HOH1  0   0.459  15.2924  19.0362  42.3672
 QJB  H9   H  HCR6  0   0.256  20.8582  23.2966  48.0755

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
 QJB  O5   C16  single    1.399  0.020  1.399
 QJB  O6   C17  single    1.405  0.020  1.405
 QJB  C17  C16  single    1.524  0.020  1.524
 QJB  C17  C2   single    1.531  0.020  1.531
 QJB  C16  C15  single    1.528  0.020  1.528
 QJB  O3   C9   double    1.223  0.020  1.223
 QJB  C15  S1   single    1.806  0.020  1.806
 QJB  C15  C3   single    1.524  0.020  1.524
 QJB  S1   C14  single    1.758  0.020  1.758
 QJB  O4   C12  single    1.413  0.020  1.413
 QJB  C2   C1   single    1.514  0.020  1.514
 QJB  C2   O1   single    1.430  0.020  1.430
 QJB  C12  C11  single    1.517  0.020  1.517
 QJB  C9   N1   single    1.341  0.020  1.341
 QJB  C9   C8   single    1.520  0.020  1.520
 QJB  C11  C10  single    1.524  0.020  1.524
 QJB  C13  C14  aromatic  1.392  0.020  1.392
 QJB  C13  C7   aromatic  1.387  0.020  1.387
 QJB  C14  C4   aromatic  1.394  0.020  1.394
 QJB  O1   C3   single    1.378  0.020  1.378
 QJB  C3   O2   single    1.422  0.020  1.422
 QJB  C10  N1   single    1.448  0.020  1.448
 QJB  C8   C7   single    1.505  0.020  1.505
 QJB  C7   C6   aromatic  1.393  0.020  1.393
 QJB  C4   O2   single    1.350  0.020  1.350
 QJB  C4   C5   aromatic  1.392  0.020  1.392
 QJB  C6   C5   aromatic  1.383  0.020  1.383
 QJB  C10  H1   single    0.970  0.020  1.090
 QJB  C10  H2   single    0.970  0.020  1.090
 QJB  C11  H3   single    0.970  0.020  1.090
 QJB  C11  H4   single    0.970  0.020  1.090
 QJB  C12  H5   single    0.970  0.020  1.090
 QJB  C12  H6   single    0.970  0.020  1.090
 QJB  C15  H7   single    0.970  0.020  1.090
 QJB  C17  H8   single    0.970  0.020  1.090
 QJB  C6   H9   single    0.930  0.020  1.080
 QJB  C5   H10  single    0.930  0.020  1.080
 QJB  C3   H11  single    0.970  0.020  1.090
 QJB  C2   H12  single    0.970  0.020  1.090
 QJB  C1   H13  single    0.970  0.020  1.090
 QJB  C1   H14  single    0.970  0.020  1.090
 QJB  C1   H15  single    0.970  0.020  1.090
 QJB  C8   H16  single    0.970  0.020  1.090
 QJB  C8   H17  single    0.970  0.020  1.090
 QJB  N1   H18  single    0.860  0.020  1.020
 QJB  O4   H19  single    0.850  0.020  0.980
 QJB  C13  H20  single    0.930  0.020  1.080
 QJB  C16  H21  single    0.970  0.020  1.090
 QJB  O5   H22  single    0.850  0.020  0.980
 QJB  O6   H23  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
 QJB  H2   C10  H1   106.90  3.000
 QJB  H2   C10  N1   107.90  3.000
 QJB  H1   C10  N1   108.31  3.000
 QJB  H2   C10  C11  109.32  3.000
 QJB  H1   C10  C11  110.29  3.000
 QJB  N1   C10  C11  113.87  3.000
 QJB  H4   C11  H3   106.90  3.000
 QJB  H4   C11  C12  109.89  3.000
 QJB  H3   C11  C12  109.30  3.000
 QJB  H4   C11  C10  109.74  3.000
 QJB  H3   C11  C10  107.57  3.000
 QJB  C12  C11  C10  113.23  3.000
 QJB  H6   C12  H5   106.87  3.000
 QJB  H6   C12  O4   111.41  3.000
 QJB  H5   C12  O4   111.00  3.000
 QJB  H6   C12  C11  109.28  3.000
 QJB  H5   C12  C11  109.73  3.000
 QJB  O4   C12  C11  108.53  3.000
 QJB  S1   C14  C13  119.23  3.000
 QJB  C13  C14  C4   119.79  3.000
 QJB  S1   C14  C4   120.98  3.000
 QJB  H7   C15  C16  109.52  3.000
 QJB  H7   C15  S1   104.82  3.000
 QJB  C16  C15  S1   113.36  3.000
 QJB  H7   C15  C3   107.20  3.000
 QJB  S1   C15  C3   109.86  3.000
 QJB  C16  C15  C3   111.67  3.000
 QJB  H8   C17  O6   111.42  3.000
 QJB  H8   C17  C16  108.37  3.000
 QJB  O6   C17  C16  108.06  3.000
 QJB  H8   C17  C2   107.29  3.000
 QJB  C16  C17  C2   108.86  3.000
 QJB  O6   C17  C2   112.74  3.000
 QJB  H9   C6   C7   120.00  3.000
 QJB  H9   C6   C5   119.05  3.000
 QJB  C7   C6   C5   120.95  3.000
 QJB  H10  C5   C4   119.04  3.000
 QJB  H10  C5   C6   120.40  3.000
 QJB  C4   C5   C6   120.56  3.000
 QJB  O2   C4   C5   116.27  3.000
 QJB  C5   C4   C14  119.02  3.000
 QJB  O2   C4   C14  124.71  3.000
 QJB  H11  C3   O2   108.71  3.000
 QJB  H11  C3   O1   106.63  3.000
 QJB  O2   C3   O1   106.59  3.000
 QJB  H11  C3   C15  109.58  3.000
 QJB  O2   C3   C15  113.33  3.000
 QJB  O1   C3   C15  111.71  3.000
 QJB  H12  C2   O1   109.89  3.000
 QJB  H12  C2   C1   108.47  3.000
 QJB  O1   C2   C1   106.83  3.000
 QJB  H12  C2   C17  107.53  3.000
 QJB  O1   C2   C17  111.14  3.000
 QJB  C1   C2   C17  112.95  3.000
 QJB  H15  C1   H14  108.40  3.000
 QJB  H15  C1   H13  107.65  3.000
 QJB  H14  C1   H13  107.88  3.000
 QJB  H15  C1   C2   110.08  3.000
 QJB  H14  C1   C2   111.87  3.000
 QJB  H13  C1   C2   110.83  3.000
 QJB  C2   O1   C3   116.20  3.000
 QJB  C3   O2   C4   124.52  3.000
 QJB  C13  C7   C8   120.77  3.000
 QJB  C8   C7   C6   120.91  3.000
 QJB  C13  C7   C6   118.24  3.000
 QJB  H17  C8   H16  107.15  3.000
 QJB  H17  C8   C9   107.65  3.000
 QJB  H16  C8   C9   111.54  3.000
 QJB  H17  C8   C7   110.42  3.000
 QJB  H16  C8   C7   110.18  3.000
 QJB  C9   C8   C7   109.84  3.000
 QJB  N1   C9   O3   123.68  3.000
 QJB  N1   C9   C8   115.23  3.000
 QJB  O3   C9   C8   121.06  3.000
 QJB  H18  N1   C9   118.46  3.000
 QJB  H18  N1   C10  117.24  3.000
 QJB  C9   N1   C10  124.28  3.000
 QJB  H19  O4   C12  108.03  3.000
 QJB  H20  C13  C7   119.64  3.000
 QJB  H20  C13  C14  118.94  3.000
 QJB  C7   C13  C14  121.42  3.000
 QJB  C15  S1   C14   97.95  3.000
 QJB  H21  C16  O5   110.72  3.000
 QJB  H21  C16  C17  106.74  3.000
 QJB  O5   C16  C17  109.26  3.000
 QJB  H21  C16  C15  109.26  3.000
 QJB  C17  C16  C15  108.52  3.000
 QJB  O5   C16  C15  112.16  3.000
 QJB  H22  O5   C16  108.04  3.000
 QJB  H23  O6   C17  108.93  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
 QJB  CONST_01  C6   C7   C13  C14     0.00   0.0  0
 QJB  CONST_02  C6   C5   C4   C14     0.00   0.0  0
 QJB  CONST_03  C13  C14  C4   C5      0.00   0.0  0
 QJB  CONST_04  C13  C7   C6   C5      0.00   0.0  0
 QJB  CONST_05  C7   C13  C14  C4      0.00   0.0  0
 QJB  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 QJB  CONST_07  C8   C7   C13  C14   180.00   0.0  0
 QJB  CONST_08  C8   C7   C6   C5    180.00   0.0  0
 QJB  CONST_09  H10  C5   C4   C14   180.00   0.0  0
 QJB  CONST_10  H20  C13  C7   C6    180.00   0.0  0
 QJB  CONST_11  H9   C6   C5   C4    180.00   0.0  0
 QJB  CONST_12  O3   C9   N1   C10     0.00   0.0  0
 QJB  CONST_13  C8   C9   N1   C10   180.00   0.0  0
 QJB  CONST_14  H18  N1   C9   C8      0.00   0.0  0
 QJB  Var_01    C13  C14  S1   C15   153.47  30.0  1
 QJB  Var_02    C9   C8   C7   C6     96.56  30.0  2
 QJB  Var_03    O3   C9   C8   C7     68.64  30.0  1
 QJB  Var_04    O4   C12  C11  C10  -175.68  30.0  1
 QJB  Var_05    C9   N1   C10  C11   101.08  30.0  3
 QJB  Var_06    N1   C10  C11  C12   -63.03  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
 QJB  chir_01  C15  C16  S1   C3   positiv
 QJB  chir_02  C17  O6   C2   C16  positiv
 QJB  chir_03  C3   O1   O2   C15  negativ
 QJB  chir_04  C2   O1   C17  C1   positiv
 QJB  chir_05  C16  O5   C17  C15  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
 QJB  plan-1  C10  0.020
 QJB  plan-1  C8   0.020
 QJB  plan-1  C9   0.020
 QJB  plan-1  O3   0.020
 QJB  plan-1  N1   0.020
 QJB  plan-1  H18  0.020
 QJB  plan-2  C14  0.020
 QJB  plan-2  C6   0.020
 QJB  plan-2  C5   0.020
 QJB  plan-2  C4   0.020
 QJB  plan-2  O2   0.020
 QJB  plan-2  C7   0.020
 QJB  plan-2  C8   0.020
 QJB  plan-2  C13  0.020
 QJB  plan-2  S1   0.020
 QJB  plan-2  H10  0.020
 QJB  plan-2  H20  0.020
 QJB  plan-2  H9   0.020

