# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:53:45 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: 5,5'-[(2R,3S)-2,3-dimethylbutane-1,4-diyl]bis(2H-1,3-benzodioxole)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](Cc1ccc2OCOc2c1)[C@@H](C)Cc3ccc4OCOc4c3
#
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
 9G9  9G9  5,5'-[(2R,3S)-2,3-dimethylbutane-1,4-diyl]bis(2H-1,3-benzodioxole)  ligand  46  24  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_9G9
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
 9G9  O1   O  O     0  -0.489   5.8495   1.4838  -0.9946
 9G9  O2   O  O     0  -0.489  -6.2397   1.6816  -0.3205
 9G9  O3   O  O     0  -0.489   7.1175  -0.3048  -0.3533
 9G9  O4   O  O     0  -0.489  -7.1193  -0.3784   0.1236
 9G9  C5   C  CH1   0  -0.215   0.7667  -0.3675  -0.0408
 9G9  C6   C  CH1   0  -0.206  -0.7174  -0.2942   0.3797
 9G9  C7   C  CH2   0  -0.509   1.7189  -0.2391   1.1595
 9G9  C8   C  CH2   0  -0.509  -1.6067  -0.0603  -0.8557
 9G9  C9   C  CH3   0  -0.661   1.0630  -1.6547  -0.8079
 9G9  C10  C  CH3   0  -0.675  -0.9999   0.7811   1.4253
 9G9  C11  C  CR6   0   0.130   3.1761  -0.3107   0.7912
 9G9  C12  C  CR6   0   0.126  -3.0813  -0.1927  -0.5856
 9G9  C13  C  CR16  0  -0.394   3.7527   0.7323   0.0444
 9G9  C14  C  CR16  0  -0.404  -3.9098   0.9401  -0.5971
 9G9  C15  C  CR16  0  -0.332   3.9587  -1.3906   1.1761
 9G9  C16  C  CR16  0  -0.323  -3.6309  -1.4419  -0.3166
 9G9  C17  C  CR56  0   0.313   5.0823   0.6269  -0.2740
 9G9  C18  C  CR56  0   0.310  -5.2458   0.7566  -0.3363
 9G9  C19  C  CR56  0   0.278   5.8519  -0.4574   0.1172
 9G9  C20  C  CR56  0   0.277  -5.7781  -0.4916  -0.0665
 9G9  C21  C  CR16  0  -0.331   5.3181  -1.4869   0.8480
 9G9  C22  C  CR16  0  -0.329  -4.9929  -1.6176  -0.0492
 9G9  C23  C  CH2   0   0.070   7.1846   1.0151  -0.8713
 9G9  C24  C  CH2   0   0.068  -7.3825   1.0146   0.1958
 9G9  H1   H  HCH1  0   0.214   0.9550   0.4836  -0.7088
 9G9  H2   H  HCH1  0   0.217  -0.9859  -1.2668   0.8127
 9G9  H3   H  HCH2  0   0.251   1.5375   0.7102   1.6670
 9G9  H4   H  HCH2  0   0.234   1.4924  -1.0276   1.8841
 9G9  H5   H  HCH2  0   0.236  -1.3943   0.9375  -1.2512
 9G9  H6   H  HCH2  0   0.249  -1.3360  -0.7634  -1.6455
 9G9  H7   H  HCH3  0   0.232   0.3859  -1.8014  -1.6488
 9G9  H8   H  HCH3  0   0.235   2.0766  -1.6553  -1.2086
 9G9  H9   H  HCH3  0   0.214   0.9689  -2.5240  -0.1519
 9G9  H10  H  HCH3  0   0.215  -0.6618   1.7631   1.0838
 9G9  H11  H  HCH3  0   0.238  -2.0686   0.8544   1.6284
 9G9  H12  H  HCH3  0   0.235  -0.5105   0.5690   2.3754
 9G9  H13  H  HCR6  0   0.261   3.1688   1.5889  -0.2700
 9G9  H14  H  HCR6  0   0.264  -3.5087   1.9229  -0.8109
 9G9  H15  H  HCR6  0   0.247   3.5063  -2.1898   1.7499
 9G9  H16  H  HCR6  0   0.247  -2.9864  -2.3126  -0.3144
 9G9  H17  H  HCR6  0   0.268   5.9112  -2.3365   1.1586
 9G9  H18  H  HCR6  0   0.269  -5.4037  -2.5974   0.1531
 9G9  H19  H  HCH2  0   0.243   7.6639   1.0042  -1.8505
 9G9  H20  H  HCH2  0   0.229  -7.5452   1.3096   1.2390
 9G9  H21  H  HCH2  0   0.229   7.7419   1.6587  -0.1810
 9G9  H22  H  HCH2  0   0.244  -8.2563   1.2576  -0.4088

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
 9G9  O3   C23  single    1.419  0.020  1.419
 9G9  O3   C19  single    1.359  0.020  1.359
 9G9  C21  C19  aromatic  1.371  0.020  1.371
 9G9  C21  C15  aromatic  1.402  0.020  1.402
 9G9  C23  O1   single    1.420  0.020  1.420
 9G9  C19  C17  aromatic  1.386  0.020  1.386
 9G9  C15  C11  aromatic  1.388  0.020  1.388
 9G9  C17  O1   single    1.357  0.020  1.357
 9G9  C17  C13  aromatic  1.371  0.020  1.371
 9G9  C10  C6   single    1.526  0.020  1.526
 9G9  C11  C13  aromatic  1.406  0.020  1.406
 9G9  C11  C7   single    1.505  0.020  1.505
 9G9  C5   C9   single    1.527  0.020  1.527
 9G9  C5   C6   single    1.544  0.020  1.544
 9G9  C5   C7   single    1.537  0.020  1.537
 9G9  C6   C8   single    1.540  0.020  1.540
 9G9  C8   C12  single    1.505  0.020  1.505
 9G9  C12  C14  aromatic  1.404  0.020  1.404
 9G9  C12  C16  aromatic  1.391  0.020  1.391
 9G9  C14  C18  aromatic  1.373  0.020  1.373
 9G9  C16  C22  aromatic  1.399  0.020  1.399
 9G9  C18  O2   single    1.358  0.020  1.358
 9G9  C18  C20  aromatic  1.384  0.020  1.384
 9G9  O2   C24  single    1.420  0.020  1.420
 9G9  C20  C22  aromatic  1.373  0.020  1.373
 9G9  C20  O4   single    1.359  0.020  1.359
 9G9  C24  O4   single    1.419  0.020  1.419
 9G9  C5   H1   single    0.970  0.020  1.090
 9G9  C6   H2   single    0.970  0.020  1.090
 9G9  C7   H3   single    0.970  0.020  1.090
 9G9  C7   H4   single    0.970  0.020  1.090
 9G9  C8   H5   single    0.970  0.020  1.090
 9G9  C8   H6   single    0.970  0.020  1.090
 9G9  C9   H7   single    0.970  0.020  1.090
 9G9  C9   H8   single    0.970  0.020  1.090
 9G9  C9   H9   single    0.970  0.020  1.090
 9G9  C10  H10  single    0.970  0.020  1.090
 9G9  C10  H11  single    0.970  0.020  1.090
 9G9  C10  H12  single    0.970  0.020  1.090
 9G9  C13  H13  single    0.930  0.020  1.080
 9G9  C14  H14  single    0.930  0.020  1.080
 9G9  C15  H15  single    0.930  0.020  1.080
 9G9  C16  H16  single    0.930  0.020  1.080
 9G9  C21  H17  single    0.930  0.020  1.080
 9G9  C22  H18  single    0.930  0.020  1.080
 9G9  C23  H19  single    0.970  0.020  1.090
 9G9  C24  H20  single    0.970  0.020  1.090
 9G9  C23  H21  single    0.970  0.020  1.090
 9G9  C24  H22  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
 9G9  C23  O1   C17  106.08  3.000
 9G9  C24  O2   C18  105.86  3.000
 9G9  C23  O3   C19  105.95  3.000
 9G9  C24  O4   C20  105.77  3.000
 9G9  H1   C5   C9   108.32  3.000
 9G9  H1   C5   C7   107.69  3.000
 9G9  C9   C5   C7   110.02  3.000
 9G9  H1   C5   C6   107.07  3.000
 9G9  C7   C5   C6   112.25  3.000
 9G9  C9   C5   C6   111.30  3.000
 9G9  H2   C6   C10  107.98  3.000
 9G9  H2   C6   C8   108.04  3.000
 9G9  C10  C6   C8   109.61  3.000
 9G9  H2   C6   C5   107.48  3.000
 9G9  C8   C6   C5   110.10  3.000
 9G9  C10  C6   C5   113.44  3.000
 9G9  H4   C7   H3   106.51  3.000
 9G9  H4   C7   C11  109.15  3.000
 9G9  H3   C7   C11  108.43  3.000
 9G9  H4   C7   C5   109.18  3.000
 9G9  H3   C7   C5   109.43  3.000
 9G9  C11  C7   C5   113.87  3.000
 9G9  H6   C8   H5   106.13  3.000
 9G9  H6   C8   C12  108.43  3.000
 9G9  H5   C8   C12  109.59  3.000
 9G9  H6   C8   C6   109.84  3.000
 9G9  H5   C8   C6   108.45  3.000
 9G9  C12  C8   C6   114.11  3.000
 9G9  H9   C9   H8   107.48  3.000
 9G9  H9   C9   H7   107.61  3.000
 9G9  H8   C9   H7   107.10  3.000
 9G9  H9   C9   C5   110.62  3.000
 9G9  H8   C9   C5   111.44  3.000
 9G9  H7   C9   C5   112.36  3.000
 9G9  H12  C10  H11  106.92  3.000
 9G9  H12  C10  H10  107.96  3.000
 9G9  H11  C10  H10  107.51  3.000
 9G9  H12  C10  C6   112.15  3.000
 9G9  H11  C10  C6   110.87  3.000
 9G9  H10  C10  C6   111.20  3.000
 9G9  C15  C11  C13  119.54  3.000
 9G9  C13  C11  C7   119.45  3.000
 9G9  C15  C11  C7   121.01  3.000
 9G9  C16  C12  C14  119.55  3.000
 9G9  C16  C12  C8   120.06  3.000
 9G9  C14  C12  C8   120.40  3.000
 9G9  H13  C13  C17  121.07  3.000
 9G9  H13  C13  C11  121.30  3.000
 9G9  C17  C13  C11  117.63  3.000
 9G9  H14  C14  C18  121.27  3.000
 9G9  H14  C14  C12  121.03  3.000
 9G9  C18  C14  C12  117.70  3.000
 9G9  H15  C15  C21  118.59  3.000
 9G9  H15  C15  C11  119.05  3.000
 9G9  C21  C15  C11  122.36  3.000
 9G9  H16  C16  C22  118.54  3.000
 9G9  H16  C16  C12  119.15  3.000
 9G9  C22  C16  C12  122.31  3.000
 9G9  C19  C17  C13  122.21  3.000
 9G9  C13  C17  O1   128.53  3.000
 9G9  C19  C17  O1   109.26  3.000
 9G9  C20  C18  C14  122.13  3.000
 9G9  C20  C18  O2   109.31  3.000
 9G9  C14  C18  O2   128.55  3.000
 9G9  C21  C19  C17  121.45  3.000
 9G9  C17  C19  O3   109.37  3.000
 9G9  C21  C19  O3   129.17  3.000
 9G9  C22  C20  C18  121.49  3.000
 9G9  C22  C20  O4   129.12  3.000
 9G9  C18  C20  O4   109.38  3.000
 9G9  H17  C21  C19  121.97  3.000
 9G9  H17  C21  C15  121.23  3.000
 9G9  C19  C21  C15  116.80  3.000
 9G9  H18  C22  C20  121.88  3.000
 9G9  H18  C22  C16  121.29  3.000
 9G9  C20  C22  C16  116.83  3.000
 9G9  H21  C23  H19  110.36  3.000
 9G9  H21  C23  O3   109.89  3.000
 9G9  H19  C23  O3   109.83  3.000
 9G9  H21  C23  O1   109.80  3.000
 9G9  H19  C23  O1   109.79  3.000
 9G9  O3   C23  O1   107.10  3.000
 9G9  H22  C24  H20  110.42  3.000
 9G9  H22  C24  O4   109.83  3.000
 9G9  H20  C24  O4   109.88  3.000
 9G9  H22  C24  O2   109.79  3.000
 9G9  H20  C24  O2   109.81  3.000
 9G9  O4   C24  O2   107.05  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
 9G9  CONST_01  C19  C21  C15  C11     0.00   0.0  0
 9G9  CONST_02  C19  C17  C13  C11     0.00   0.0  0
 9G9  CONST_03  C20  C18  C14  C12     0.00   0.0  0
 9G9  CONST_04  C20  C22  C16  C12     0.00   0.0  0
 9G9  CONST_05  C21  C19  C17  C13     0.00   0.0  0
 9G9  CONST_06  C21  C15  C11  C13     0.00   0.0  0
 9G9  CONST_07  C22  C16  C12  C14     0.00   0.0  0
 9G9  CONST_08  C22  C20  C18  C14     0.00   0.0  0
 9G9  CONST_09  C17  C19  C21  C15     0.00   0.0  0
 9G9  CONST_10  C17  C13  C11  C15     0.00   0.0  0
 9G9  CONST_11  C18  C14  C12  C16     0.00   0.0  0
 9G9  CONST_12  C18  C20  C22  C16     0.00   0.0  0
 9G9  CONST_13  C21  C15  C11  C7    180.00   0.0  0
 9G9  CONST_14  C17  C13  C11  C7    180.00   0.0  0
 9G9  CONST_15  C18  C14  C12  C8    180.00   0.0  0
 9G9  CONST_16  C22  C16  C12  C8    180.00   0.0  0
 9G9  CONST_17  H13  C13  C17  O1      0.00   0.0  0
 9G9  CONST_18  H14  C14  C18  O2      0.00   0.0  0
 9G9  CONST_19  H17  C21  C19  O3      0.00   0.0  0
 9G9  CONST_20  H18  C22  C20  O4      0.00   0.0  0
 9G9  CONST_21  H15  C15  C11  C13   180.00   0.0  0
 9G9  CONST_22  H16  C16  C12  C14   180.00   0.0  0
 9G9  Var_01    H19  C23  O1   C17   133.76  30.0  1
 9G9  Var_02    H20  C24  O2   C18   103.45  30.0  1
 9G9  Var_03    C15  C11  C7   C5   -111.89  30.0  2
 9G9  Var_04    C14  C12  C8   C6    109.55  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
 9G9  chir_01  C5  C9  C6  C7   negativ
 9G9  chir_02  C6  C8  C5  C10  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
 9G9  plan-1  O1   0.020
 9G9  plan-1  O3   0.020
 9G9  plan-1  C7   0.020
 9G9  plan-1  C11  0.020
 9G9  plan-1  C13  0.020
 9G9  plan-1  C15  0.020
 9G9  plan-1  C17  0.020
 9G9  plan-1  C19  0.020
 9G9  plan-1  C21  0.020
 9G9  plan-1  H13  0.020
 9G9  plan-1  H15  0.020
 9G9  plan-1  H17  0.020
 9G9  plan-2  O2   0.020
 9G9  plan-2  O4   0.020
 9G9  plan-2  C8   0.020
 9G9  plan-2  C12  0.020
 9G9  plan-2  C14  0.020
 9G9  plan-2  C16  0.020
 9G9  plan-2  C18  0.020
 9G9  plan-2  C20  0.020
 9G9  plan-2  C22  0.020
 9G9  plan-2  H14  0.020
 9G9  plan-2  H16  0.020
 9G9  plan-2  H18  0.020

