# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 00:46:17 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: (2S,3R)-3-(4-hydroxyphenyl)-2-[4-(2-piperidin-1-ylethoxy)phenyl]-2,3-dihydro-1,4-benzoxathiin-6-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1)[C@H]2Sc3cc(O)ccc3O[C@H]2c4ccc(OCCN5CCCCC5)cc4
#
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
 E4D  E4D  (2S,3R)-3-(4-hydroxyphenyl)-2-[4-(2-piperidin-1-ylethoxy)phenyl]-2,3-dihydro-1,4-benzoxathiin-6-ol  ligand  62  33  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E4D
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
 E4D  C1    C  CH1   0  -0.555  -0.2003   1.4317  -2.2028
 E4D  C2    C  CH1   0   0.023  -1.3268   0.4188  -1.9244
 E4D  O3    O  O2    0  -0.491  -1.0990  -0.7940  -2.6044
 E4D  C4    C  CR6   0   0.406  -1.0834  -0.7631  -3.9624
 E4D  C5    C  CR16  0  -0.333  -1.4334  -1.9301  -4.6289
 E4D  C6    C  CR16  0  -0.386  -1.4204  -1.9974  -6.0108
 E4D  C7    C  CR6   0   0.352  -1.0621  -0.8752  -6.7543
 E4D  O8    O  OH1   0  -0.636  -1.0413  -0.8696  -8.1041
 E4D  C9    C  CR16  0  -0.365  -0.7047   0.2935  -6.0965
 E4D  C10   C  CR6   0  -0.196  -0.7083   0.3566  -4.7044
 E4D  S11   S  S2    0   0.104  -0.2339   1.8812  -3.9660
 E4D  C12   C  CR6   0   0.195   1.1462   0.9809  -1.7106
 E4D  C13   C  CR16  0  -0.279   1.9524   0.0974  -2.4193
 E4D  C14   C  CR16  0  -0.376   3.1631  -0.3401  -1.9044
 E4D  C15   C  CR6   0   0.343   3.5954   0.1051  -0.6578
 E4D  O16   O  OH1   0  -0.633   4.7649  -0.2831  -0.1107
 E4D  C17   C  CR16  0  -0.325   2.8022   0.9951   0.0608
 E4D  C18   C  CR16  0  -0.265   1.5954   1.4197  -0.4672
 E4D  C19   C  CR6   0   0.043  -1.4281   0.1272  -0.4543
 E4D  C20   C  CR16  0  -0.286  -2.1649   0.9804   0.3533
 E4D  C21   C  CR16  0  -0.371  -2.2254   0.8101   1.7307
 E4D  C22   C  CR6   0   0.380  -1.5404  -0.2482   2.3230
 E4D  C23   C  CR16  0  -0.335  -0.8052  -1.1185   1.5156
 E4D  C24   C  CR16  0  -0.256  -0.7449  -0.9274   0.1487
 E4D  O25   O  O2    0  -0.465  -1.5333  -0.5065   3.6434
 E4D  C26   C  CH2   0  -0.228  -2.1095   0.4409   4.5232
 E4D  C27   C  CH2   0  -0.287  -1.8795  -0.0093   5.9494
 E4D  N28   N  NT    0  -0.408  -0.4993  -0.2793   6.2904
 E4D  C29   C  CH2   0  -0.280   0.3665   0.8765   6.1357
 E4D  C30   C  CH2   0  -0.436   1.8159   0.5235   6.4347
 E4D  C31   C  CH2   0  -0.439   1.9623  -0.0725   7.8280
 E4D  C32   C  CH2   0  -0.439   1.0013  -1.2432   7.9868
 E4D  C33   C  CH2   0  -0.275  -0.4171  -0.8258   7.6346
 E4D  H1    H  HCH1  0   0.322  -0.4786   2.3563  -1.6918
 E4D  H2    H  HCH1  0   0.266  -2.2680   0.8680  -2.2674
 E4D  H5    H  HCR6  0   0.272  -1.7205  -2.7996  -4.0507
 E4D  H6    H  HCR6  0   0.275  -1.7009  -2.9201  -6.5044
 E4D  HO8   H  HOH1  0   0.474  -1.3280  -1.7237  -8.4453
 E4D  H9    H  HCR6  0   0.273  -0.4145   1.1631  -6.6751
 E4D  H13   H  HCR6  0   0.253   1.6582  -0.2544  -3.4001
 E4D  H14   H  HCR6  0   0.269   3.7733  -1.0259  -2.4813
 E4D  H16   H  HOH1  0   0.473   5.2244  -0.8946  -0.6966
 E4D  H17   H  HCR6  0   0.260   3.1307   1.3527   1.0287
 E4D  H18   H  HCR6  0   0.250   0.9876   2.1073   0.1084
 E4D  H20   H  HCR6  0   0.254  -2.7099   1.8068  -0.0897
 E4D  H21   H  HCR6  0   0.279  -2.8137   1.5034   2.3161
 E4D  H23   H  HCR6  0   0.258  -0.2709  -1.9416   1.9736
 E4D  H24   H  HCR6  0   0.252  -0.1496  -1.6080  -0.4450
 E4D  H261  H  HCH2  0   0.243  -3.1905   0.5201   4.3614
 E4D  H262  H  HCH2  0   0.228  -1.6864   1.4346   4.3413
 E4D  H271  H  HCH2  0   0.240  -2.4557  -0.9221   6.1267
 E4D  H272  H  HCH2  0   0.200  -2.3280   0.7662   6.5954
 E4D  H291  H  HCH2  0   0.237   0.3002   1.2453   5.1107
 E4D  H292  H  HCH2  0   0.181   0.0468   1.7084   6.7906
 E4D  H301  H  HCH2  0   0.229   2.4344   1.4170   6.3249
 E4D  H302  H  HCH2  0   0.214   2.1647  -0.1997   5.6913
 E4D  H311  H  HCH2  0   0.210   1.7377   0.6912   8.5804
 E4D  H312  H  HCH2  0   0.230   2.9923  -0.3902   8.0053
 E4D  H321  H  HCH2  0   0.229   1.0199  -1.6293   9.0084
 E4D  H322  H  HCH2  0   0.214   1.3090  -2.0626   7.3298
 E4D  H331  H  HCH2  0   0.180  -0.7773  -0.0969   8.3843
 E4D  H332  H  HCH2  0   0.232  -1.0857  -1.6884   7.6968

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
 E4D  C1   C2    single    1.540  0.020  1.540
 E4D  C1   S11   single    1.820  0.020  1.820
 E4D  C1   C12   single    1.503  0.020  1.503
 E4D  C1   H1    single    0.970  0.020  1.090
 E4D  C2   O3    single    1.409  0.020  1.409
 E4D  C2   C19   single    1.502  0.020  1.502
 E4D  C2   H2    single    0.970  0.020  1.090
 E4D  O3   C4    single    1.358  0.020  1.358
 E4D  C4   C5    aromatic  1.389  0.020  1.389
 E4D  C4   C10   aromatic  1.395  0.020  1.395
 E4D  C5   C6    aromatic  1.384  0.020  1.384
 E4D  C5   H5    single    0.930  0.020  1.080
 E4D  C6   C7    aromatic  1.393  0.020  1.393
 E4D  C6   H6    single    0.930  0.020  1.080
 E4D  C7   O8    single    1.350  0.020  1.350
 E4D  C7   C9    aromatic  1.388  0.020  1.388
 E4D  O8   HO8   single    0.850  0.020  0.980
 E4D  C9   C10   aromatic  1.394  0.020  1.394
 E4D  C9   H9    single    0.930  0.020  1.080
 E4D  C10  S11   single    1.759  0.020  1.759
 E4D  C12  C13   aromatic  1.390  0.020  1.390
 E4D  C12  C18   aromatic  1.393  0.020  1.393
 E4D  C13  C14   aromatic  1.386  0.020  1.386
 E4D  C13  H13   single    0.930  0.020  1.080
 E4D  C14  C15   aromatic  1.392  0.020  1.392
 E4D  C14  H14   single    0.930  0.020  1.080
 E4D  C15  O16   single    1.348  0.020  1.348
 E4D  C15  C17   aromatic  1.392  0.020  1.392
 E4D  O16  H16   single    0.850  0.020  0.980
 E4D  C17  C18   aromatic  1.384  0.020  1.384
 E4D  C17  H17   single    0.930  0.020  1.080
 E4D  C18  H18   single    0.930  0.020  1.080
 E4D  C19  C20   aromatic  1.387  0.020  1.387
 E4D  C19  C24   aromatic  1.394  0.020  1.394
 E4D  C20  C21   aromatic  1.389  0.020  1.389
 E4D  C20  H20   single    0.930  0.020  1.080
 E4D  C21  C22   aromatic  1.393  0.020  1.393
 E4D  C21  H21   single    0.930  0.020  1.080
 E4D  C22  C23   aromatic  1.396  0.020  1.396
 E4D  C22  O25   single    1.346  0.020  1.346
 E4D  C23  C24   aromatic  1.381  0.020  1.381
 E4D  C23  H23   single    0.930  0.020  1.080
 E4D  C24  H24   single    0.930  0.020  1.080
 E4D  O25  C26   single    1.415  0.020  1.415
 E4D  C26  C27   single    1.513  0.020  1.513
 E4D  C26  H261  single    0.970  0.020  1.090
 E4D  C26  H262  single    0.970  0.020  1.090
 E4D  C27  N28   single    1.447  0.020  1.447
 E4D  C27  H271  single    0.970  0.020  1.090
 E4D  C27  H272  single    0.970  0.020  1.090
 E4D  N28  C29   single    1.452  0.020  1.452
 E4D  N28  C33   single    1.453  0.020  1.453
 E4D  C29  C30   single    1.521  0.020  1.521
 E4D  C29  H291  single    0.970  0.020  1.090
 E4D  C29  H292  single    0.970  0.020  1.090
 E4D  C30  C31   single    1.522  0.020  1.522
 E4D  C30  H301  single    0.970  0.020  1.090
 E4D  C30  H302  single    0.970  0.020  1.090
 E4D  C31  C32   single    1.523  0.020  1.523
 E4D  C31  H311  single    0.970  0.020  1.090
 E4D  C31  H312  single    0.970  0.020  1.090
 E4D  C32  C33   single    1.520  0.020  1.520
 E4D  C32  H321  single    0.970  0.020  1.090
 E4D  C32  H322  single    0.970  0.020  1.090
 E4D  C33  H331  single    0.970  0.020  1.090
 E4D  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
 E4D  H1    C1   C12   109.20  3.000
 E4D  H1    C1   S11   103.85  3.000
 E4D  C12   C1   S11   114.08  3.000
 E4D  H1    C1   C2    106.61  3.000
 E4D  C12   C1   C2    113.51  3.000
 E4D  S11   C1   C2    108.91  3.000
 E4D  H2    C2   C19   109.11  3.000
 E4D  H2    C2   O3    109.88  3.000
 E4D  C19   C2   O3    108.43  3.000
 E4D  H2    C2   C1    107.55  3.000
 E4D  C19   C2   C1    110.72  3.000
 E4D  O3    C2   C1    111.14  3.000
 E4D  C4    O3   C2    117.69  3.000
 E4D  C10   C4   C5    119.15  3.000
 E4D  C10   C4   O3    123.59  3.000
 E4D  C5    C4   O3    117.24  3.000
 E4D  H5    C5   C6    119.78  3.000
 E4D  H5    C5   C4    119.03  3.000
 E4D  C6    C5   C4    121.19  3.000
 E4D  H6    C6   C7    120.64  3.000
 E4D  H6    C6   C5    119.60  3.000
 E4D  C7    C6   C5    119.76  3.000
 E4D  C9    C7   O8    117.80  3.000
 E4D  C9    C7   C6    119.45  3.000
 E4D  O8    C7   C6    122.75  3.000
 E4D  HO8   O8   C7    110.23  3.000
 E4D  H9    C9   C10   119.83  3.000
 E4D  H9    C9   C7    119.44  3.000
 E4D  C10   C9   C7    120.73  3.000
 E4D  S11   C10  C9    117.25  3.000
 E4D  S11   C10  C4    123.03  3.000
 E4D  C9    C10  C4    119.72  3.000
 E4D  C10   S11  C1    101.39  3.000
 E4D  C18   C12  C13   117.92  3.000
 E4D  C18   C12  C1    119.13  3.000
 E4D  C13   C12  C1    122.90  3.000
 E4D  H13   C13  C14   118.11  3.000
 E4D  H13   C13  C12   120.71  3.000
 E4D  C14   C13  C12   121.17  3.000
 E4D  H14   C14  C15   120.26  3.000
 E4D  H14   C14  C13   119.56  3.000
 E4D  C15   C14  C13   120.18  3.000
 E4D  C17   C15  O16   117.97  3.000
 E4D  C17   C15  C14   119.32  3.000
 E4D  O16   C15  C14   122.72  3.000
 E4D  H16   O16  C15   110.47  3.000
 E4D  H17   C17  C18   120.28  3.000
 E4D  H17   C17  C15   119.97  3.000
 E4D  C18   C17  C15   119.74  3.000
 E4D  H18   C18  C17   118.76  3.000
 E4D  H18   C18  C12   119.56  3.000
 E4D  C17   C18  C12   121.67  3.000
 E4D  C24   C19  C20   118.30  3.000
 E4D  C24   C19  C2    122.50  3.000
 E4D  C20   C19  C2    119.10  3.000
 E4D  H20   C20  C21   118.45  3.000
 E4D  H20   C20  C19   119.87  3.000
 E4D  C21   C20  C19   121.68  3.000
 E4D  H21   C21  C22   121.64  3.000
 E4D  H21   C21  C20   118.80  3.000
 E4D  C22   C21  C20   119.56  3.000
 E4D  O25   C22  C23   116.43  3.000
 E4D  O25   C22  C21   124.45  3.000
 E4D  C23   C22  C21   119.12  3.000
 E4D  H23   C23  C24   120.14  3.000
 E4D  H23   C23  C22   119.27  3.000
 E4D  C24   C23  C22   120.59  3.000
 E4D  H24   C24  C23   118.69  3.000
 E4D  H24   C24  C19   120.56  3.000
 E4D  C23   C24  C19   120.75  3.000
 E4D  C26   O25  C22   118.64  3.000
 E4D  H262  C26  H261  106.92  3.000
 E4D  H262  C26  C27   111.58  3.000
 E4D  H261  C26  C27   108.10  3.000
 E4D  H262  C26  O25   110.29  3.000
 E4D  H261  C26  O25   110.98  3.000
 E4D  C27   C26  O25   108.95  3.000
 E4D  H272  C27  H271  106.09  3.000
 E4D  H272  C27  N28   112.36  3.000
 E4D  H271  C27  N28   107.97  3.000
 E4D  H272  C27  C26   106.30  3.000
 E4D  H271  C27  C26   108.72  3.000
 E4D  N28   C27  C26   115.00  3.000
 E4D  C33   N28  C29   111.35  3.000
 E4D  C33   N28  C27   110.00  3.000
 E4D  C29   N28  C27   113.26  3.000
 E4D  H292  C29  H291  106.52  3.000
 E4D  H292  C29  C30   109.48  3.000
 E4D  H291  C29  C30   108.71  3.000
 E4D  H292  C29  N28   111.30  3.000
 E4D  H291  C29  N28   109.44  3.000
 E4D  C30   C29  N28   111.24  3.000
 E4D  H302  C30  H301  106.97  3.000
 E4D  H302  C30  C31   109.41  3.000
 E4D  H301  C30  C31   110.97  3.000
 E4D  H302  C30  C29   108.87  3.000
 E4D  H301  C30  C29   109.27  3.000
 E4D  C31   C30  C29   111.24  3.000
 E4D  H312  C31  H311  106.53  3.000
 E4D  H312  C31  C32   110.76  3.000
 E4D  H311  C31  C32   109.57  3.000
 E4D  H312  C31  C30   110.68  3.000
 E4D  H311  C31  C30   109.63  3.000
 E4D  C32   C31  C30   109.62  3.000
 E4D  H322  C32  H321  106.98  3.000
 E4D  H322  C32  C33   109.20  3.000
 E4D  H321  C32  C33   109.25  3.000
 E4D  H322  C32  C31   109.60  3.000
 E4D  H321  C32  C31   111.02  3.000
 E4D  C33   C32  C31   110.71  3.000
 E4D  H332  C33  H331  106.40  3.000
 E4D  H332  C33  C32   109.93  3.000
 E4D  H331  C33  C32   109.14  3.000
 E4D  H332  C33  N28   108.35  3.000
 E4D  H331  C33  N28   111.15  3.000
 E4D  C32   C33  N28   111.74  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
 E4D  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 E4D  CONST_02  C7   C9   C10  C4      0.00   0.0  0
 E4D  CONST_03  C9   C10  C4   C5      0.00   0.0  0
 E4D  CONST_04  C9   C7   C6   C5      0.00   0.0  0
 E4D  CONST_05  C10  C4   C5   C6      0.00   0.0  0
 E4D  CONST_06  C10  C9   C7   C6      0.00   0.0  0
 E4D  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 E4D  CONST_08  C15  C17  C18  C12     0.00   0.0  0
 E4D  CONST_09  C17  C18  C12  C13     0.00   0.0  0
 E4D  CONST_10  C17  C15  C14  C13     0.00   0.0  0
 E4D  CONST_11  C18  C12  C13  C14     0.00   0.0  0
 E4D  CONST_12  C18  C17  C15  C14     0.00   0.0  0
 E4D  CONST_13  C22  C21  C20  C19     0.00   0.0  0
 E4D  CONST_14  C22  C23  C24  C19     0.00   0.0  0
 E4D  CONST_15  C23  C24  C19  C20     0.00   0.0  0
 E4D  CONST_16  C23  C22  C21  C20     0.00   0.0  0
 E4D  CONST_17  C24  C19  C20  C21     0.00   0.0  0
 E4D  CONST_18  C24  C23  C22  C21     0.00   0.0  0
 E4D  CONST_19  C14  C13  C12  C1    180.00   0.0  0
 E4D  CONST_20  C17  C18  C12  C1    180.00   0.0  0
 E4D  CONST_21  C21  C20  C19  C2    180.00   0.0  0
 E4D  CONST_22  C23  C24  C19  C2    180.00   0.0  0
 E4D  CONST_23  O8   C7   C6   C5    180.00   0.0  0
 E4D  CONST_24  C10  C9   C7   O8    180.00   0.0  0
 E4D  CONST_25  O16  C15  C14  C13   180.00   0.0  0
 E4D  CONST_26  C18  C17  C15  O16   180.00   0.0  0
 E4D  CONST_27  O25  C22  C21  C20   180.00   0.0  0
 E4D  CONST_28  O25  C22  C23  C24   180.00   0.0  0
 E4D  CONST_29  H13  C13  C12  C1      0.00   0.0  0
 E4D  CONST_30  H18  C18  C12  C1      0.00   0.0  0
 E4D  CONST_31  H20  C20  C19  C2      0.00   0.0  0
 E4D  CONST_32  H24  C24  C19  C2      0.00   0.0  0
 E4D  CONST_33  H5   C5   C4   O3      0.00   0.0  0
 E4D  CONST_34  H6   C6   C5   C4    180.00   0.0  0
 E4D  CONST_35  H9   C9   C10  C4    180.00   0.0  0
 E4D  CONST_36  H14  C14  C13  C12   180.00   0.0  0
 E4D  CONST_37  H17  C17  C18  C12   180.00   0.0  0
 E4D  CONST_38  H21  C21  C20  C19   180.00   0.0  0
 E4D  CONST_39  H23  C23  C24  C19   180.00   0.0  0
 E4D  Var_01    C4   C10  S11  C1      6.58  30.0  1
 E4D  Var_02    C5   C4   O3   C2   -153.01  30.0  1
 E4D  Var_03    C31  C30  C29  N28   -56.22  30.0  1
 E4D  Var_04    C31  C32  C33  N28    56.40  30.0  1
 E4D  Var_05    C32  C33  N28  C29   -58.82  30.0  1
 E4D  Var_06    C32  C31  C30  C29    53.36  30.0  1
 E4D  Var_07    C33  N28  C29  C30    58.41  30.0  1
 E4D  Var_08    C33  C32  C31  C30   -53.18  30.0  1
 E4D  Var_09    C29  N28  C27  C26    60.22  30.0  3
 E4D  Var_10    C27  C26  O25  C22  -175.27  30.0  3
 E4D  Var_11    N28  C27  C26  O25    54.00  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
 E4D  chir_01  C1  C2  S11  C12  positiv
 E4D  chir_02  C2  O3  C19  C1   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
 E4D  plan-1  C1   0.020
 E4D  plan-1  C12  0.020
 E4D  plan-1  C13  0.020
 E4D  plan-1  C14  0.020
 E4D  plan-1  C15  0.020
 E4D  plan-1  O16  0.020
 E4D  plan-1  C17  0.020
 E4D  plan-1  C18  0.020
 E4D  plan-1  H13  0.020
 E4D  plan-1  H14  0.020
 E4D  plan-1  H17  0.020
 E4D  plan-1  H18  0.020
 E4D  plan-2  C2   0.020
 E4D  plan-2  C19  0.020
 E4D  plan-2  C20  0.020
 E4D  plan-2  C21  0.020
 E4D  plan-2  C22  0.020
 E4D  plan-2  C23  0.020
 E4D  plan-2  C24  0.020
 E4D  plan-2  O25  0.020
 E4D  plan-2  H20  0.020
 E4D  plan-2  H21  0.020
 E4D  plan-2  H23  0.020
 E4D  plan-2  H24  0.020
 E4D  plan-3  O3   0.020
 E4D  plan-3  C4   0.020
 E4D  plan-3  C5   0.020
 E4D  plan-3  C6   0.020
 E4D  plan-3  C7   0.020
 E4D  plan-3  O8   0.020
 E4D  plan-3  C9   0.020
 E4D  plan-3  C10  0.020
 E4D  plan-3  S11  0.020
 E4D  plan-3  H5   0.020
 E4D  plan-3  H6   0.020
 E4D  plan-3  H9   0.020

