# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:06:40 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: (2S,3R)-3-(4-hydroxyphenyl)-2-(4-{[(2R)-2-pyrrolidin-1-ylpropyl]oxy}phenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](COc1ccc(cc1)[C@@H]2Oc3ccc(O)cc3S[C@@H]2c4ccc(O)cc4)N5CCCC5
#
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
 AIT  AIT  (2S,3R)-3-(4-hydroxyphenyl)-2-(4-{[(2R)-2-pyrrolidin-1-ylpropyl]oxy}phenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol  ligand  62  33  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AIT
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
 AIT  C1    C  CH1   0  -0.549   2.4779  -0.0710   1.5316
 AIT  C2    C  CH1   0   0.009   1.7091   1.0077   0.7452
 AIT  O3    O  O2    0  -0.488   2.2088   1.1283  -0.5696
 AIT  C4    C  CR6   0   0.405   3.4902   1.5540  -0.7178
 AIT  C5    C  CR16  0  -0.334   3.8068   2.2266  -1.8932
 AIT  C6    C  CR16  0  -0.342   5.0920   2.6693  -2.1418
 AIT  C7    C  CR6   0   0.357   6.0919   2.4515  -1.1949
 AIT  O8    O  OH1   0  -0.637   7.3319   2.9074  -1.4719
 AIT  C9    C  CR16  0  -0.410   5.7860   1.7799  -0.0206
 AIT  C10   C  CR6   0  -0.197   4.4897   1.3233   0.2230
 AIT  S11   S  S2    0   0.103   4.2075   0.4662   1.7322
 AIT  C12   C  CR6   0   0.185   2.3307  -1.4527   0.9616
 AIT  C13   C  CR16  0  -0.277   3.0493  -1.8961  -0.1435
 AIT  C14   C  CR16  0  -0.375   2.8254  -3.1506  -0.6891
 AIT  C15   C  CR6   0   0.344   1.8702  -3.9965  -0.1306
 AIT  O16   O  OH1   0  -0.633   1.6095  -5.2251  -0.6206
 AIT  C17   C  CR16  0  -0.325   1.1546  -3.5729   0.9856
 AIT  C18   C  CR16  0  -0.265   1.3884  -2.3156   1.5153
 AIT  C19   C  CR6   0   0.055   0.2429   0.6951   0.6531
 AIT  C20   C  CR16  0  -0.287  -0.6316   1.2265   1.5974
 AIT  C21   C  CR16  0  -0.341  -1.9839   0.9419   1.5633
 AIT  C22   C  CR6   0   0.384  -2.5001   0.1114   0.5668
 AIT  C23   C  CR16  0  -0.370  -1.6326  -0.4345  -0.3774
 AIT  C24   C  CR16  0  -0.254  -0.2765  -0.1419  -0.3257
 AIT  O25   O  O2    0  -0.467  -3.8286  -0.0955   0.5900
 AIT  C26   C  CH2   0  -0.214  -4.4065  -0.9599  -0.3698
 AIT  C27   C  CH1   0  -0.078  -5.9140  -0.9785  -0.1734
 AIT  C28   C  CH3   0  -0.682  -6.2792  -1.5443   1.1958
 AIT  N29   N  NT    0  -0.423  -6.4934   0.3369  -0.3747
 AIT  C30   C  CH2   0  -0.282  -6.2126   0.9245  -1.6794
 AIT  C31   C  CH2   0  -0.474  -7.2639   2.0306  -1.8586
 AIT  C32   C  CH2   0  -0.456  -8.2935   1.7726  -0.7462
 AIT  C33   C  CH2   0  -0.276  -7.9409   0.3799  -0.2449
 AIT  H1    H  HCH1  0   0.323   2.0826  -0.0610   2.5503
 AIT  H2    H  HCH1  0   0.266   1.8348   1.9575   1.2816
 AIT  H5    H  HCR6  0   0.270   3.0257   2.4006  -2.6229
 AIT  H6    H  HCR6  0   0.267   5.3205   3.1919  -3.0617
 AIT  HO8   H  HOH1  0   0.474   7.9396   2.6922  -0.7559
 AIT  H9    H  HCR6  0   0.280   6.5610   1.5961   0.7165
 AIT  H13   H  HCR6  0   0.253   3.8120  -1.2728  -0.5921
 AIT  H14   H  HCR6  0   0.269   3.3995  -3.4694  -1.5519
 AIT  H16   H  HOH1  0   0.474   2.1708  -5.4088  -1.3820
 AIT  H17   H  HCR6  0   0.260   0.4176  -4.2265   1.4350
 AIT  H18   H  HCR6  0   0.251   0.8182  -1.9994   2.3807
 AIT  H20   H  HCR6  0   0.252  -0.2526   1.8811   2.3739
 AIT  H21   H  HCR6  0   0.260  -2.6509   1.3712   2.3004
 AIT  H23   H  HCR6  0   0.276  -1.9900  -1.0884  -1.1609
 AIT  H24   H  HCR6  0   0.256   0.3715  -0.5848  -1.0705
 AIT  H261  H  HCH2  0   0.239  -4.0227  -1.9800  -0.2519
 AIT  H262  H  HCH2  0   0.240  -4.1531  -0.6368  -1.3845
 AIT  H27   H  HCH1  0   0.202  -6.2851  -1.6835  -0.9430
 AIT  H281  H  HCH3  0   0.229  -6.0653  -0.8266   1.9881
 AIT  H282  H  HCH3  0   0.238  -7.3356  -1.8034   1.2538
 AIT  H283  H  HCH3  0   0.234  -5.7141  -2.4549   1.3978
 AIT  H301  H  HCH2  0   0.231  -5.1947   1.3156  -1.7260
 AIT  H302  H  HCH2  0   0.195  -6.3094   0.1781  -2.4850
 AIT  H311  H  HCH2  0   0.237  -6.8233   3.0236  -1.7704
 AIT  H312  H  HCH2  0   0.234  -7.7157   1.9709  -2.8487
 AIT  H321  H  HCH2  0   0.230  -8.1766   2.4978   0.0602
 AIT  H322  H  HCH2  0   0.233  -9.3239   1.8356  -1.0946
 AIT  H331  H  HCH2  0   0.187  -8.4304  -0.3903  -0.8672
 AIT  H332  H  HCH2  0   0.235  -8.2579   0.2167   0.7859

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
 AIT  C1   C2    single    1.541  0.020  1.541
 AIT  C1   S11   single    1.822  0.020  1.822
 AIT  C1   C12   single    1.502  0.020  1.502
 AIT  C1   H1    single    0.970  0.020  1.090
 AIT  C2   O3    single    1.412  0.020  1.412
 AIT  C2   C19   single    1.502  0.020  1.502
 AIT  C2   H2    single    0.970  0.020  1.090
 AIT  O3   C4    single    1.358  0.020  1.358
 AIT  C4   C5    aromatic  1.391  0.020  1.391
 AIT  C4   C10   aromatic  1.392  0.020  1.392
 AIT  C5   C6    aromatic  1.382  0.020  1.382
 AIT  C5   H5    single    0.930  0.020  1.080
 AIT  C6   C7    aromatic  1.394  0.020  1.394
 AIT  C6   H6    single    0.930  0.020  1.080
 AIT  C7   O8    single    1.350  0.020  1.350
 AIT  C7   C9    aromatic  1.387  0.020  1.387
 AIT  O8   HO8   single    0.850  0.020  0.980
 AIT  C9   C10   aromatic  1.396  0.020  1.396
 AIT  C9   H9    single    0.930  0.020  1.080
 AIT  C10  S11   single    1.758  0.020  1.758
 AIT  C12  C13   aromatic  1.391  0.020  1.391
 AIT  C12  C18   aromatic  1.393  0.020  1.393
 AIT  C13  C14   aromatic  1.386  0.020  1.386
 AIT  C13  H13   single    0.930  0.020  1.080
 AIT  C14  C15   aromatic  1.393  0.020  1.393
 AIT  C14  H14   single    0.930  0.020  1.080
 AIT  C15  O16   single    1.348  0.020  1.348
 AIT  C15  C17   aromatic  1.392  0.020  1.392
 AIT  O16  H16   single    0.850  0.020  0.980
 AIT  C17  C18   aromatic  1.384  0.020  1.384
 AIT  C17  H17   single    0.930  0.020  1.080
 AIT  C18  H18   single    0.930  0.020  1.080
 AIT  C19  C20   aromatic  1.392  0.020  1.392
 AIT  C19  C24   aromatic  1.389  0.020  1.389
 AIT  C20  C21   aromatic  1.382  0.020  1.382
 AIT  C20  H20   single    0.930  0.020  1.080
 AIT  C21  C22   aromatic  1.396  0.020  1.396
 AIT  C21  H21   single    0.930  0.020  1.080
 AIT  C22  C23   aromatic  1.394  0.020  1.394
 AIT  C22  O25   single    1.345  0.020  1.345
 AIT  C23  C24   aromatic  1.388  0.020  1.388
 AIT  C23  H23   single    0.930  0.020  1.080
 AIT  C24  H24   single    0.930  0.020  1.080
 AIT  O25  C26   single    1.415  0.020  1.415
 AIT  C26  C27   single    1.520  0.020  1.520
 AIT  C26  H261  single    0.970  0.020  1.090
 AIT  C26  H262  single    0.970  0.020  1.090
 AIT  C27  C28   single    1.526  0.020  1.526
 AIT  C27  N29   single    1.451  0.020  1.451
 AIT  C27  H27   single    0.970  0.020  1.090
 AIT  C28  H281  single    0.970  0.020  1.090
 AIT  C28  H282  single    0.970  0.020  1.090
 AIT  C28  H283  single    0.970  0.020  1.090
 AIT  N29  C30   single    1.458  0.020  1.458
 AIT  N29  C33   single    1.454  0.020  1.454
 AIT  C30  C31   single    1.536  0.020  1.536
 AIT  C30  H301  single    0.970  0.020  1.090
 AIT  C30  H302  single    0.970  0.020  1.090
 AIT  C31  C32   single    1.538  0.020  1.538
 AIT  C31  H311  single    0.970  0.020  1.090
 AIT  C31  H312  single    0.970  0.020  1.090
 AIT  C32  C33   single    1.522  0.020  1.522
 AIT  C32  H321  single    0.970  0.020  1.090
 AIT  C32  H322  single    0.970  0.020  1.090
 AIT  C33  H331  single    0.970  0.020  1.090
 AIT  C33  H332  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
 AIT  H1    C1   C12   109.08  3.000
 AIT  H1    C1   S11   103.77  3.000
 AIT  C12   C1   S11   113.96  3.000
 AIT  H1    C1   C2    106.79  3.000
 AIT  C12   C1   C2    113.67  3.000
 AIT  S11   C1   C2    108.87  3.000
 AIT  H2    C2   C19   108.77  3.000
 AIT  H2    C2   O3    109.91  3.000
 AIT  C19   C2   O3    107.82  3.000
 AIT  H2    C2   C1    107.42  3.000
 AIT  C19   C2   C1    111.88  3.000
 AIT  O3    C2   C1    111.02  3.000
 AIT  C4    O3   C2    117.53  3.000
 AIT  C10   C4   C5    119.20  3.000
 AIT  C10   C4   O3    123.49  3.000
 AIT  C5    C4   O3    117.29  3.000
 AIT  H5    C5   C6    119.88  3.000
 AIT  H5    C5   C4    118.87  3.000
 AIT  C6    C5   C4    121.25  3.000
 AIT  H6    C6   C7    120.08  3.000
 AIT  H6    C6   C5    120.26  3.000
 AIT  C7    C6   C5    119.66  3.000
 AIT  C9    C7   O8    122.68  3.000
 AIT  C9    C7   C6    119.50  3.000
 AIT  O8    C7   C6    117.82  3.000
 AIT  HO8   O8   C7    110.58  3.000
 AIT  H9    C9   C10   119.30  3.000
 AIT  H9    C9   C7    119.97  3.000
 AIT  C10   C9   C7    120.73  3.000
 AIT  S11   C10  C9    117.28  3.000
 AIT  S11   C10  C4    123.07  3.000
 AIT  C9    C10  C4    119.65  3.000
 AIT  C10   S11  C1    101.63  3.000
 AIT  C18   C12  C13   117.91  3.000
 AIT  C18   C12  C1    119.04  3.000
 AIT  C13   C12  C1    122.97  3.000
 AIT  H13   C13  C14   118.15  3.000
 AIT  H13   C13  C12   120.66  3.000
 AIT  C14   C13  C12   121.18  3.000
 AIT  H14   C14  C15   120.24  3.000
 AIT  H14   C14  C13   119.59  3.000
 AIT  C15   C14  C13   120.17  3.000
 AIT  C17   C15  O16   117.99  3.000
 AIT  C17   C15  C14   119.30  3.000
 AIT  O16   C15  C14   122.71  3.000
 AIT  H16   O16  C15   110.38  3.000
 AIT  H17   C17  C18   120.29  3.000
 AIT  H17   C17  C15   119.95  3.000
 AIT  C18   C17  C15   119.76  3.000
 AIT  H18   C18  C17   118.80  3.000
 AIT  H18   C18  C12   119.53  3.000
 AIT  C17   C18  C12   121.67  3.000
 AIT  C24   C19  C20   118.24  3.000
 AIT  C24   C19  C2    122.26  3.000
 AIT  C20   C19  C2    119.47  3.000
 AIT  H20   C20  C21   118.95  3.000
 AIT  H20   C20  C19   119.78  3.000
 AIT  C21   C20  C19   121.27  3.000
 AIT  H21   C21  C22   119.60  3.000
 AIT  H21   C21  C20   120.28  3.000
 AIT  C22   C21  C20   120.12  3.000
 AIT  O25   C22  C23   124.50  3.000
 AIT  O25   C22  C21   116.39  3.000
 AIT  C23   C22  C21   119.11  3.000
 AIT  H23   C23  C24   118.51  3.000
 AIT  H23   C23  C22   121.48  3.000
 AIT  C24   C23  C22   120.02  3.000
 AIT  H24   C24  C23   118.23  3.000
 AIT  H24   C24  C19   120.52  3.000
 AIT  C23   C24  C19   121.24  3.000
 AIT  C26   O25  C22   119.06  3.000
 AIT  H262  C26  H261  107.06  3.000
 AIT  H262  C26  C27   110.66  3.000
 AIT  H261  C26  C27   108.77  3.000
 AIT  H262  C26  O25   110.73  3.000
 AIT  H261  C26  O25   110.64  3.000
 AIT  C27   C26  O25   108.95  3.000
 AIT  H27   C27  N29   110.29  3.000
 AIT  H27   C27  C28   107.90  3.000
 AIT  N29   C27  C28   111.41  3.000
 AIT  H27   C27  C26   104.49  3.000
 AIT  N29   C27  C26   111.52  3.000
 AIT  C28   C27  C26   110.96  3.000
 AIT  H283  C28  H282  107.10  3.000
 AIT  H283  C28  H281  108.26  3.000
 AIT  H282  C28  H281  107.95  3.000
 AIT  H283  C28  C27   110.60  3.000
 AIT  H282  C28  C27   111.60  3.000
 AIT  H281  C28  C27   111.16  3.000
 AIT  C33   N29  C30   105.05  3.000
 AIT  C33   N29  C27   114.32  3.000
 AIT  C30   N29  C27   114.36  3.000
 AIT  H302  C30  H301  107.06  3.000
 AIT  H302  C30  C31   110.01  3.000
 AIT  H301  C30  C31   112.04  3.000
 AIT  H302  C30  N29   111.34  3.000
 AIT  H301  C30  N29   111.23  3.000
 AIT  C31   C30  N29   105.23  3.000
 AIT  H312  C31  H311  106.91  3.000
 AIT  H312  C31  C32   111.74  3.000
 AIT  H311  C31  C32   111.41  3.000
 AIT  H312  C31  C30   110.50  3.000
 AIT  H311  C31  C30   111.71  3.000
 AIT  C32   C31  C30   104.66  3.000
 AIT  H322  C32  H321  107.42  3.000
 AIT  H322  C32  C33   112.17  3.000
 AIT  H321  C32  C33   109.89  3.000
 AIT  H322  C32  C31   113.10  3.000
 AIT  H321  C32  C31   110.58  3.000
 AIT  C33   C32  C31   103.69  3.000
 AIT  H332  C33  H331  107.42  3.000
 AIT  H332  C33  C32   112.39  3.000
 AIT  H331  C33  C32   110.48  3.000
 AIT  H332  C33  N29   111.67  3.000
 AIT  H331  C33  N29   111.73  3.000
 AIT  C32   C33  N29   103.20  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
 AIT  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 AIT  CONST_02  C7   C9   C10  C4      0.00   0.0  0
 AIT  CONST_03  C9   C10  C4   C5      0.00   0.0  0
 AIT  CONST_04  C9   C7   C6   C5      0.00   0.0  0
 AIT  CONST_05  C10  C4   C5   C6      0.00   0.0  0
 AIT  CONST_06  C10  C9   C7   C6      0.00   0.0  0
 AIT  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 AIT  CONST_08  C15  C17  C18  C12     0.00   0.0  0
 AIT  CONST_09  C17  C18  C12  C13     0.00   0.0  0
 AIT  CONST_10  C17  C15  C14  C13     0.00   0.0  0
 AIT  CONST_11  C18  C12  C13  C14     0.00   0.0  0
 AIT  CONST_12  C18  C17  C15  C14     0.00   0.0  0
 AIT  CONST_13  C22  C21  C20  C19     0.00   0.0  0
 AIT  CONST_14  C22  C23  C24  C19     0.00   0.0  0
 AIT  CONST_15  C23  C24  C19  C20     0.00   0.0  0
 AIT  CONST_16  C23  C22  C21  C20     0.00   0.0  0
 AIT  CONST_17  C24  C19  C20  C21     0.00   0.0  0
 AIT  CONST_18  C24  C23  C22  C21     0.00   0.0  0
 AIT  CONST_19  C14  C13  C12  C1    180.00   0.0  0
 AIT  CONST_20  C17  C18  C12  C1    180.00   0.0  0
 AIT  CONST_21  C21  C20  C19  C2    180.00   0.0  0
 AIT  CONST_22  C23  C24  C19  C2    180.00   0.0  0
 AIT  CONST_23  O8   C7   C6   C5    180.00   0.0  0
 AIT  CONST_24  C10  C9   C7   O8    180.00   0.0  0
 AIT  CONST_25  O16  C15  C14  C13   180.00   0.0  0
 AIT  CONST_26  C18  C17  C15  O16   180.00   0.0  0
 AIT  CONST_27  O25  C22  C21  C20   180.00   0.0  0
 AIT  CONST_28  O25  C22  C23  C24   180.00   0.0  0
 AIT  CONST_29  H13  C13  C12  C1      0.00   0.0  0
 AIT  CONST_30  H18  C18  C12  C1      0.00   0.0  0
 AIT  CONST_31  H20  C20  C19  C2      0.00   0.0  0
 AIT  CONST_32  H24  C24  C19  C2      0.00   0.0  0
 AIT  CONST_33  H5   C5   C4   O3      0.00   0.0  0
 AIT  CONST_34  H6   C6   C5   C4    180.00   0.0  0
 AIT  CONST_35  H9   C9   C10  C4    180.00   0.0  0
 AIT  CONST_36  H14  C14  C13  C12   180.00   0.0  0
 AIT  CONST_37  H17  C17  C18  C12   180.00   0.0  0
 AIT  CONST_38  H21  C21  C20  C19   180.00   0.0  0
 AIT  CONST_39  H23  C23  C24  C19   180.00   0.0  0
 AIT  Var_01    C4   C10  S11  C1      5.41  30.0  1
 AIT  Var_02    C5   C4   O3   C2   -152.19  30.0  1
 AIT  Var_03    C32  C31  C30  N29   -12.78  30.0  1
 AIT  Var_04    C31  C32  C33  N29    34.41  30.0  1
 AIT  Var_05    C32  C33  N29  C30   -43.83  30.0  1
 AIT  Var_06    C33  C32  C31  C30   -13.02  30.0  1
 AIT  Var_07    C33  N29  C30  C31    35.32  30.0  1
 AIT  Var_08    C27  C26  O25  C22  -177.52  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
 AIT  chir_01  C1   C2   S11  C12  positiv
 AIT  chir_02  C2   O3   C19  C1   negativ
 AIT  chir_03  C27  C26  C28  N29  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
 AIT  plan-1  C1   0.020
 AIT  plan-1  C12  0.020
 AIT  plan-1  C13  0.020
 AIT  plan-1  C14  0.020
 AIT  plan-1  C15  0.020
 AIT  plan-1  O16  0.020
 AIT  plan-1  C17  0.020
 AIT  plan-1  C18  0.020
 AIT  plan-1  H13  0.020
 AIT  plan-1  H14  0.020
 AIT  plan-1  H17  0.020
 AIT  plan-1  H18  0.020
 AIT  plan-2  O3   0.020
 AIT  plan-2  C4   0.020
 AIT  plan-2  C5   0.020
 AIT  plan-2  C6   0.020
 AIT  plan-2  C7   0.020
 AIT  plan-2  O8   0.020
 AIT  plan-2  C9   0.020
 AIT  plan-2  C10  0.020
 AIT  plan-2  S11  0.020
 AIT  plan-2  H5   0.020
 AIT  plan-2  H6   0.020
 AIT  plan-2  H9   0.020
 AIT  plan-3  C2   0.020
 AIT  plan-3  C19  0.020
 AIT  plan-3  C20  0.020
 AIT  plan-3  C21  0.020
 AIT  plan-3  C22  0.020
 AIT  plan-3  C23  0.020
 AIT  plan-3  C24  0.020
 AIT  plan-3  O25  0.020
 AIT  plan-3  H20  0.020
 AIT  plan-3  H21  0.020
 AIT  plan-3  H23  0.020
 AIT  plan-3  H24  0.020

