# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 23:17:06 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: (2~{S},3~{R},4~{R},5~{S},6~{R})-2-[4-chloranyl-3-[[4-[(3~{S})-oxolan-3-yl]oxyphenyl]methyl]phenyl]-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2ccc(Cl)c(Cc3ccc(O[C@H]4CCOC4)cc3)c2
#
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
 7R3  7R3  "(2S,3R,4R,5S,6R)-2-[4-chloranyl-3-[[4-[(3S)-oxolan-3-yl]oxyphenyl]methyl]phenyl]-6-(hydroxymethyl)oxane-3,4,5-triol"
  ligand  58  31  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7R3
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
 7R3  C10  C   CH1   0   0.002  37.7316  46.7857  43.3107
 7R3  C13  C   CH1   0  -0.014  40.2097  48.1595  42.9067
 7R3  C15  C   CH2   0  -0.162  40.9687  49.4510  42.6904
 7R3  C17  C   CR16  0  -0.345  38.0825  46.5159  46.7735
 7R3  C21  C   CR16  0  -0.178  37.4296  46.7647  47.9713
 7R3  C22  C   CR6   0  -0.138  36.7079  47.9363  48.1249
 7R3  C24  C   CH2   0  -0.155  40.3260  55.8857  50.4298
 7R3  C26  C   CR6   0   0.127  36.6221  51.2283  47.9674
 7R3  C28  C   CR16  0  -0.277  37.7934  51.7421  47.4230
 7R3  C09  C   CH1   0   0.022  38.5052  46.5622  42.0160
 7R3  C11  C   CH1   0   0.017  39.3404  47.7929  41.6938
 7R3  C12  C   CH1   0  -0.041  38.7110  47.1655  44.4277
 7R3  C14  C   CR6   0   0.132  38.0099  47.4281  45.7300
 7R3  C16  C   CR16  0  -0.383  37.2592  48.5860  45.9053
 7R3  C18  C   CR6   0   0.267  36.6002  48.8715  47.0963
 7R3  C19  C   CR15  0  -0.068  39.7807  54.9378  49.3786
 7R3  C23  C   CH2   0  -0.541  39.3199  55.9291  48.3168
 7R3  C25  C   CH2   0  -0.141  38.7902  57.0819  49.1650
 7R3  C27  C   CR6   0   0.373  38.0603  53.2731  49.2608
 7R3  C29  C   CR16  0  -0.303  36.1888  51.7548  49.1811
 7R3  C30  C   CR16  0  -0.354  38.5114  52.7521  48.0493
 7R3  C31  C   CR16  0  -0.338  36.8900  52.7633  49.8212
 7R3  O2   O   O2    0  -0.491  39.4114  48.3294  44.0590
 7R3  O3   O   OH1   0  -0.663  37.6508  46.3117  40.9309
 7R3  O4   O   OH1   0  -0.665  37.0415  45.5969  43.6063
 7R3  O5   O   OH1   0  -0.665  40.1353  47.5017  40.5692
 7R3  O6   O   OH1   0  -0.664  41.7992  49.6827  43.8019
 7R3  O7   O   O     0  -0.495  39.4986  57.0326  50.3977
 7R3  O8   O   O2    0  -0.484  38.6869  54.2430  49.9610
 7R3  CL1  CL  CL    0  -0.127  35.9196  48.2237  49.6444
 7R3  H1   H   HCH1  0   0.223  37.0348  47.6241  43.1598
 7R3  H2   H   HCH1  0   0.215  40.9311  47.3412  43.0690
 7R3  H3   H   HCH2  0   0.202  41.5514  49.3633  41.7661
 7R3  H4   H   HCH2  0   0.197  40.2460  50.2662  42.5415
 7R3  H5   H   HCR6  0   0.262  38.6579  45.6049  46.6638
 7R3  H6   H   HCH2  0   0.275  35.5766  50.5183  46.2449
 7R3  H7   H   HCH2  0   0.270  34.8921  49.9845  47.7612
 7R3  H8   H   HCR6  0   0.277  37.4911  46.0521  48.7827
 7R3  H10  H   HCH2  0   0.214  41.3630  56.1375  50.1767
 7R3  H11  H   HCR6  0   0.252  38.1635  51.3585  46.4788
 7R3  H12  H   HCH1  0   0.205  39.1953  45.7163  42.1800
 7R3  H13  H   HCH1  0   0.222  38.6540  48.6292  41.4934
 7R3  H14  H   HCH1  0   0.236  39.4117  46.3257  44.5643
 7R3  H15  H   HCR6  0   0.255  37.1764  49.3018  45.0952
 7R3  H16  H   HCR5  0   0.266  40.5486  54.2412  49.0302
 7R3  H17  H   HCH2  0   0.270  38.5744  55.5291  47.6301
 7R3  H18  H   HCH2  0   0.258  40.1823  56.2396  47.7239
 7R3  H19  H   HCH2  0   0.222  38.9469  58.0497  48.6829
 7R3  H20  H   HCH2  0   0.212  37.7174  56.9745  49.3545
 7R3  H21  H   HCR6  0   0.248  35.2797  51.3799  49.6357
 7R3  H22  H   HCR6  0   0.276  39.4112  53.1176  47.5733
 7R3  H23  H   HCR6  0   0.256  36.5319  53.1641  50.7616
 7R3  H24  H   HOH1  0   0.447  37.1044  45.5508  41.1541
 7R3  H25  H   HOH1  0   0.459  36.3181  45.7960  44.2089
 7R3  H26  H   HOH1  0   0.456  40.2812  48.3099  40.0702
 7R3  H27  H   HOH1  0   0.454  42.3036  50.4837  43.6348
 7R3  C20  C   CH2   0  -0.616  35.8364  50.1596  47.2433
 7R3  H9   H   HCH2  0   0.238  40.3211  55.4526  51.4327

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
 7R3  O5   C11  single    1.408  0.020  1.408
 7R3  O3   C09  single    1.404  0.020  1.404
 7R3  C11  C09  single    1.522  0.020  1.522
 7R3  C11  C13  single    1.537  0.020  1.537
 7R3  C09  C10  single    1.525  0.020  1.525
 7R3  C13  C15  single    1.514  0.020  1.514
 7R3  C13  O2   single    1.412  0.020  1.412
 7R3  C10  O4   single    1.406  0.020  1.406
 7R3  C10  C12  single    1.533  0.020  1.533
 7R3  C15  O6   single    1.407  0.020  1.407
 7R3  O2   C12  single    1.408  0.020  1.408
 7R3  C12  C14  single    1.502  0.020  1.502
 7R3  C14  C16  aromatic  1.391  0.020  1.391
 7R3  C14  C17  aromatic  1.388  0.020  1.388
 7R3  C16  C18  aromatic  1.391  0.020  1.391
 7R3  C17  C21  aromatic  1.387  0.020  1.387
 7R3  C28  C30  aromatic  1.389  0.020  1.389
 7R3  C28  C26  aromatic  1.390  0.020  1.390
 7R3  C18  C20  single    1.505  0.020  1.505
 7R3  C18  C22  aromatic  1.394  0.020  1.394
 7R3  C20  C26  single    1.511  0.020  1.511
 7R3  C30  C27  aromatic  1.394  0.020  1.394
 7R3  C26  C29  aromatic  1.392  0.020  1.392
 7R3  C23  C25  single    1.526  0.020  1.526
 7R3  C23  C19  single    1.524  0.020  1.524
 7R3  C21  C22  aromatic  1.385  0.020  1.385
 7R3  C22  CL1  single    1.736  0.020  1.736
 7R3  C25  O7   single    1.423  0.020  1.423
 7R3  C19  O8   single    1.421  0.020  1.421
 7R3  C19  C24  single    1.517  0.020  1.517
 7R3  C27  O8   single    1.350  0.020  1.350
 7R3  C27  C31  aromatic  1.394  0.020  1.394
 7R3  C29  C31  aromatic  1.385  0.020  1.385
 7R3  O7   C24  single    1.415  0.020  1.415
 7R3  C10  H1   single    0.970  0.020  1.090
 7R3  C13  H2   single    0.970  0.020  1.090
 7R3  C15  H3   single    0.970  0.020  1.090
 7R3  C15  H4   single    0.970  0.020  1.090
 7R3  C17  H5   single    0.930  0.020  1.080
 7R3  C20  H6   single    0.970  0.020  1.090
 7R3  C20  H7   single    0.970  0.020  1.090
 7R3  C21  H8   single    0.930  0.020  1.080
 7R3  C24  H9   single    0.970  0.020  1.090
 7R3  C24  H10  single    0.970  0.020  1.090
 7R3  C28  H11  single    0.930  0.020  1.080
 7R3  C09  H12  single    0.970  0.020  1.090
 7R3  C11  H13  single    0.970  0.020  1.090
 7R3  C12  H14  single    0.970  0.020  1.090
 7R3  C16  H15  single    0.930  0.020  1.080
 7R3  C19  H16  single    0.970  0.020  1.090
 7R3  C23  H17  single    0.970  0.020  1.090
 7R3  C23  H18  single    0.970  0.020  1.090
 7R3  C25  H19  single    0.970  0.020  1.090
 7R3  C25  H20  single    0.970  0.020  1.090
 7R3  C29  H21  single    0.930  0.020  1.080
 7R3  C30  H22  single    0.930  0.020  1.080
 7R3  C31  H23  single    0.930  0.020  1.080
 7R3  O3   H24  single    0.850  0.020  0.980
 7R3  O4   H25  single    0.850  0.020  0.980
 7R3  O5   H26  single    0.850  0.020  0.980
 7R3  O6   H27  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
 7R3  H1   C10  O4   111.24  3.000
 7R3  H1   C10  C12  108.40  3.000
 7R3  O4   C10  C12  111.70  3.000
 7R3  H1   C10  C09  108.45  3.000
 7R3  C12  C10  C09  109.32  3.000
 7R3  O4   C10  C09  107.67  3.000
 7R3  H2   C13  O2   109.81  3.000
 7R3  H2   C13  C11  108.01  3.000
 7R3  O2   C13  C11  110.67  3.000
 7R3  H2   C13  C15  109.03  3.000
 7R3  O2   C13  C15  107.30  3.000
 7R3  C11  C13  C15  111.99  3.000
 7R3  H4   C15  H3   107.13  3.000
 7R3  H4   C15  O6   111.90  3.000
 7R3  H3   C15  O6   111.44  3.000
 7R3  H4   C15  C13  108.81  3.000
 7R3  H3   C15  C13  108.59  3.000
 7R3  O6   C15  C13  108.88  3.000
 7R3  H5   C17  C14  120.30  3.000
 7R3  H5   C17  C21  119.25  3.000
 7R3  C14  C17  C21  120.45  3.000
 7R3  H8   C21  C22  120.26  3.000
 7R3  H8   C21  C17  120.19  3.000
 7R3  C22  C21  C17  119.54  3.000
 7R3  CL1  C22  C18  119.98  3.000
 7R3  CL1  C22  C21  118.29  3.000
 7R3  C18  C22  C21  121.73  3.000
 7R3  H10  C24  H9   107.89  3.000
 7R3  H10  C24  O7   111.21  3.000
 7R3  H9   C24  O7   109.86  3.000
 7R3  H10  C24  C19  108.87  3.000
 7R3  H9   C24  C19  112.76  3.000
 7R3  O7   C24  C19  106.30  3.000
 7R3  C29  C26  C28  117.64  3.000
 7R3  C29  C26  C20  121.56  3.000
 7R3  C28  C26  C20  120.78  3.000
 7R3  H11  C28  C30  118.27  3.000
 7R3  H11  C28  C26  119.86  3.000
 7R3  C30  C28  C26  121.86  3.000
 7R3  H12  C09  O3   111.02  3.000
 7R3  H12  C09  C11  107.94  3.000
 7R3  O3   C09  C11  108.35  3.000
 7R3  H12  C09  C10  107.66  3.000
 7R3  C11  C09  C10  109.85  3.000
 7R3  O3   C09  C10  111.95  3.000
 7R3  H13  C11  O5   111.35  3.000
 7R3  H13  C11  C09  108.11  3.000
 7R3  O5   C11  C09  108.16  3.000
 7R3  H13  C11  C13  108.39  3.000
 7R3  C09  C11  C13  109.65  3.000
 7R3  O5   C11  C13  111.13  3.000
 7R3  H14  C12  O2   110.25  3.000
 7R3  H14  C12  C14  108.81  3.000
 7R3  O2   C12  C14  108.35  3.000
 7R3  H14  C12  C10  107.92  3.000
 7R3  C14  C12  C10  112.13  3.000
 7R3  O2   C12  C10  109.38  3.000
 7R3  C16  C14  C12  120.44  3.000
 7R3  C16  C14  C17  118.72  3.000
 7R3  C12  C14  C17  120.83  3.000
 7R3  H15  C16  C18  117.91  3.000
 7R3  H15  C16  C14  119.77  3.000
 7R3  C18  C16  C14  122.31  3.000
 7R3  C16  C18  C22  117.22  3.000
 7R3  C22  C18  C20  122.77  3.000
 7R3  C16  C18  C20  120.00  3.000
 7R3  H16  C19  O8   111.08  3.000
 7R3  H16  C19  C23  113.87  3.000
 7R3  O8   C19  C23  111.77  3.000
 7R3  H16  C19  C24  111.49  3.000
 7R3  O8   C19  C24  107.36  3.000
 7R3  C23  C19  C24  100.67  3.000
 7R3  H18  C23  H17  107.61  3.000
 7R3  H18  C23  C25  111.18  3.000
 7R3  H17  C23  C25  112.96  3.000
 7R3  H18  C23  C19  108.94  3.000
 7R3  H17  C23  C19  114.03  3.000
 7R3  C25  C23  C19  102.07  3.000
 7R3  H20  C25  H19  107.69  3.000
 7R3  H20  C25  O7   109.55  3.000
 7R3  H19  C25  O7   109.97  3.000
 7R3  H20  C25  C23  111.24  3.000
 7R3  H19  C25  C23  111.97  3.000
 7R3  O7   C25  C23  106.41  3.000
 7R3  O8   C27  C31  116.34  3.000
 7R3  C31  C27  C30  118.98  3.000
 7R3  O8   C27  C30  124.68  3.000
 7R3  H21  C29  C31  118.87  3.000
 7R3  H21  C29  C26  119.75  3.000
 7R3  C31  C29  C26  121.38  3.000
 7R3  H22  C30  C27  121.70  3.000
 7R3  H22  C30  C28  118.52  3.000
 7R3  C27  C30  C28  119.78  3.000
 7R3  H23  C31  C29  120.21  3.000
 7R3  H23  C31  C27  119.42  3.000
 7R3  C29  C31  C27  120.36  3.000
 7R3  C12  O2   C13  113.30  3.000
 7R3  H24  O3   C09  107.89  3.000
 7R3  H25  O4   C10  109.01  3.000
 7R3  H26  O5   C11  109.06  3.000
 7R3  H27  O6   C15  108.04  3.000
 7R3  C25  O7   C24  109.82  3.000
 7R3  C27  O8   C19  119.73  3.000
 7R3  H7   C20  H6   106.30  3.000
 7R3  H7   C20  C18  110.38  3.000
 7R3  H6   C20  C18  108.21  3.000
 7R3  H7   C20  C26  109.64  3.000
 7R3  H6   C20  C26  109.23  3.000
 7R3  C18  C20  C26  112.85  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
 7R3  CONST_01  C18  C16  C14  C17     0.00   0.0  0
 7R3  CONST_02  C18  C22  C21  C17     0.00   0.0  0
 7R3  CONST_03  C16  C14  C17  C21     0.00   0.0  0
 7R3  CONST_04  C16  C18  C22  C21     0.00   0.0  0
 7R3  CONST_05  C14  C16  C18  C22     0.00   0.0  0
 7R3  CONST_06  C14  C17  C21  C22     0.00   0.0  0
 7R3  CONST_07  C27  C30  C28  C26     0.00   0.0  0
 7R3  CONST_08  C27  C31  C29  C26     0.00   0.0  0
 7R3  CONST_09  C31  C27  C30  C28     0.00   0.0  0
 7R3  CONST_10  C31  C29  C26  C28     0.00   0.0  0
 7R3  CONST_11  C30  C28  C26  C29     0.00   0.0  0
 7R3  CONST_12  C30  C27  C31  C29     0.00   0.0  0
 7R3  CONST_13  C12  C14  C17  C21   180.00   0.0  0
 7R3  CONST_14  C18  C16  C14  C12   180.00   0.0  0
 7R3  CONST_15  CL1  C22  C21  C17   180.00   0.0  0
 7R3  CONST_16  C14  C16  C18  C20   180.00   0.0  0
 7R3  CONST_17  C21  C22  C18  C20   180.00   0.0  0
 7R3  CONST_18  C30  C28  C26  C20   180.00   0.0  0
 7R3  CONST_19  C31  C29  C26  C20   180.00   0.0  0
 7R3  CONST_20  O8   C27  C30  C28   180.00   0.0  0
 7R3  CONST_21  CL1  C22  C18  C16   180.00   0.0  0
 7R3  CONST_22  O8   C27  C31  C29   180.00   0.0  0
 7R3  CONST_23  H15  C16  C14  C17   180.00   0.0  0
 7R3  CONST_24  H15  C16  C18  C22   180.00   0.0  0
 7R3  CONST_25  H5   C17  C21  C22   180.00   0.0  0
 7R3  CONST_26  H22  C30  C28  C26   180.00   0.0  0
 7R3  CONST_27  H23  C31  C29  C26   180.00   0.0  0
 7R3  CONST_28  H21  C29  C26  C28   180.00   0.0  0
 7R3  CONST_29  H15  C16  C14  C12     0.00   0.0  0
 7R3  CONST_30  H5   C17  C14  C12     0.00   0.0  0
 7R3  CONST_31  H8   C21  C17  C14   180.00   0.0  0
 7R3  CONST_32  H5   C17  C14  C16   180.00   0.0  0
 7R3  CONST_33  H8   C21  C22  C18   180.00   0.0  0
 7R3  CONST_34  H11  C28  C30  C27   180.00   0.0  0
 7R3  CONST_35  H21  C29  C31  C27   180.00   0.0  0
 7R3  CONST_36  H11  C28  C26  C29   180.00   0.0  0
 7R3  CONST_37  H23  C31  C27  C30   180.00   0.0  0
 7R3  CONST_38  H22  C30  C27  C31   180.00   0.0  0
 7R3  Var_01    C23  C25  O7   C24    -5.24  30.0  1
 7R3  Var_02    O7   C25  C23  C19    26.98  30.0  1
 7R3  Var_03    C25  O7   C24  C19   -19.15  30.0  1
 7R3  Var_04    C26  C20  C18  C22    80.39  30.0  2
 7R3  Var_05    C16  C18  C20  C26   -98.29  30.0  3
 7R3  Var_06    C18  C20  C26  C28    63.89  30.0  2
 7R3  Var_07    C29  C26  C20  C18  -117.59  30.0  2
 7R3  Var_08    C30  C27  O8   C19     9.21  30.0  2
 7R3  Var_09    C31  C27  O8   C19  -171.62  30.0  2
 7R3  Var_10    H19  C25  O7   C24  -126.71  30.0  1
 7R3  Var_11    H20  C25  O7   C24   115.12  30.0  1
 7R3  Var_12    H19  C25  C23  C19   147.17  30.0  1
 7R3  Var_13    H20  C25  C23  C19   -92.28  30.0  1
 7R3  Var_14    H9   C24  O7   C25  -141.43  30.0  1
 7R3  Var_15    H10  C24  O7   C25    99.20  30.0  1
 7R3  Var_16    H17  C23  C25  O7    149.86  30.0  1
 7R3  Var_17    H18  C23  C25  O7    -89.04  30.0  1
 7R3  Var_18    H6   C20  C18  C22  -158.62  30.0  2
 7R3  Var_19    H7   C20  C18  C22   -42.68  30.0  2
 7R3  Var_20    H6   C20  C26  C28   -56.51  30.0  2
 7R3  Var_21    H7   C20  C26  C28  -172.63  30.0  2
 7R3  Var_22    H6   C20  C18  C16    22.71  30.0  2
 7R3  Var_23    H7   C20  C18  C16   138.65  30.0  2
 7R3  Var_24    H6   C20  C26  C29   122.00  30.0  2
 7R3  Var_25    H7   C20  C26  C29     5.89  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
 7R3  chir_01  C10  C09  O4   C12  negativ
 7R3  chir_02  C13  O2   C11  C15  negativ
 7R3  chir_03  C09  O3   C11  C10  negativ
 7R3  chir_04  C11  O5   C13  C09  positiv
 7R3  chir_05  C12  O2   C10  C14  positiv
 7R3  chir_06  C19  C23  O8   C24  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
 7R3  plan-1  C26  0.020
 7R3  plan-1  C28  0.020
 7R3  plan-1  C27  0.020
 7R3  plan-1  C29  0.020
 7R3  plan-1  C30  0.020
 7R3  plan-1  C31  0.020
 7R3  plan-1  O8   0.020
 7R3  plan-1  H11  0.020
 7R3  plan-1  H21  0.020
 7R3  plan-1  H22  0.020
 7R3  plan-1  H23  0.020
 7R3  plan-1  C20  0.020
 7R3  plan-2  C17  0.020
 7R3  plan-2  C21  0.020
 7R3  plan-2  C22  0.020
 7R3  plan-2  C12  0.020
 7R3  plan-2  C14  0.020
 7R3  plan-2  C16  0.020
 7R3  plan-2  C18  0.020
 7R3  plan-2  CL1  0.020
 7R3  plan-2  H5   0.020
 7R3  plan-2  H8   0.020
 7R3  plan-2  H15  0.020
 7R3  plan-2  C20  0.020

