# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:16:48 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 4-(beta-D-glucopyranosyloxy)-2,2-dihydroxybutyl propanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)OCC(O)(O)CCO[C@@H]1O[C@H](CO)[C@@H](O)[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
 IN1  IN1  '4-(beta-D-glucopyranosyloxy)-2,2-dihydroxybutyl propanoate'  D-saccharide  47  23  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IN1
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
 IN1  C1A   C  CH2   0  -0.164  24.9137  39.8129   3.4392
 IN1  C2A   C  CH2   0  -0.516  24.4923  39.2567   4.7827
 IN1  C3A   C  CH2   0  -0.215  25.2349  41.0798   6.3776
 IN1  C7    C  CH3   0  -0.661  25.7225  44.6001   9.7493
 IN1  C1    C  CH1   0   0.323  26.4822  41.3013   2.4921
 IN1  C2    C  CH1   0  -0.001  27.5689  42.2832   2.9127
 IN1  C3    C  CH1   0  -0.005  28.0300  43.0531   1.6808
 IN1  C4    C  CH1   0   0.002  28.4574  42.0990   0.5715
 IN1  C5    C  CH1   0  -0.022  27.3121  41.1190   0.2885
 IN1  C6    C  CH2   0  -0.157  27.6883  40.0709  -0.7358
 IN1  O5    O  O2    0  -0.498  26.9725  40.4520   1.4871
 IN1  O2    O  OH1   0  -0.661  27.0350  43.1390   3.8891
 IN1  O3    O  OH1   0  -0.668  29.0747  43.9031   2.0828
 IN1  O4    O  OH1   0  -0.669  28.7723  42.8848  -0.5560
 IN1  O6    O  OH1   0  -0.664  26.5571  39.2843  -1.0206
 IN1  O1    O  O2    0  -0.493  26.1303  40.5287   3.5732
 IN1  C6A   C  CT    0   0.426  24.0516  40.2623   5.8498
 IN1  O1R   O  OH1   0  -0.666  23.0872  41.0934   5.2674
 IN1  O2A   O  O2    0  -0.487  24.7392  41.8560   7.4758
 IN1  C4A   C  C     0   0.604  25.5481  42.7665   8.0195
 IN1  C5A   C  CH2   0  -0.572  24.8720  43.4952   9.1488
 IN1  O3A   O  O     0  -0.438  26.6743  42.9545   7.6396
 IN1  O4S   O  OH1   0  -0.670  23.5054  39.4840   6.8819
 IN1  H11   H  HCH2  0   0.226  25.0370  38.9759   2.7444
 IN1  H12   H  HCH2  0   0.216  24.1344  40.4624   3.0255
 IN1  H21   H  HCH2  0   0.261  23.6487  38.5851   4.5980
 IN1  H22   H  HCH2  0   0.250  25.2924  38.6339   5.1906
 IN1  H31   H  HCH2  0   0.239  26.0318  40.4164   6.7220
 IN1  H32   H  HCH2  0   0.261  25.6356  41.7321   5.6051
 IN1  H71   H  HCH3  0   0.239  25.1773  45.0901  10.5547
 IN1  H72   H  HCH3  0   0.231  26.6517  44.2135  10.1658
 IN1  H73   H  HCH3  0   0.231  25.9741  45.3598   9.0102
 IN1  H1    H  HCH1  0   0.185  25.6096  41.8648   2.1084
 IN1  H2    H  HCH1  0   0.217  28.4193  41.7036   3.3055
 IN1  H3    H  HCH1  0   0.211  27.1729  43.6382   1.3071
 IN1  H4    H  HCH1  0   0.224  29.3319  41.5278   0.9150
 IN1  H5    H  HCH1  0   0.220  26.4485  41.6922  -0.0880
 IN1  H61   H  HCH2  0   0.202  28.0586  40.5820  -1.6322
 IN1  H62   H  HCH2  0   0.198  28.5189  39.4704  -0.3393
 IN1  HO2   H  HOH1  0   0.453  27.7124  43.7794   4.1306
 IN1  HO3   H  HOH1  0   0.452  29.2927  44.4832   1.3463
 IN1  HO4   H  HOH1  0   0.460  29.4631  42.4499  -1.0637
 IN1  HO6   H  HOH1  0   0.454  26.8040  38.6345  -1.6847
 IN1  HO1   H  HOH1  0   0.449  22.8971  41.8391   5.8488
 IN1  H51   H  HCH2  0   0.276  24.6038  42.7573   9.9104
 IN1  H52   H  HCH2  0   0.273  23.9219  43.8929   8.7818
 IN1  HOS4  H  HOH1  0   0.446  23.3742  40.0280   7.6675

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
 IN1  C1A  C2A   single  1.514  0.020  1.514
 IN1  C1A  O1    single  1.418  0.020  1.418
 IN1  C1A  H11   single  0.970  0.020  1.090
 IN1  C1A  H12   single  0.970  0.020  1.090
 IN1  C2A  C6A   single  1.531  0.020  1.531
 IN1  C2A  H21   single  0.970  0.020  1.090
 IN1  C2A  H22   single  0.970  0.020  1.090
 IN1  C3A  C6A   single  1.532  0.020  1.532
 IN1  C3A  O2A   single  1.433  0.020  1.433
 IN1  C3A  H31   single  0.970  0.020  1.090
 IN1  C3A  H32   single  0.970  0.020  1.090
 IN1  C7   C5A   single  1.518  0.020  1.518
 IN1  C7   H71   single  0.970  0.020  1.090
 IN1  C7   H72   single  0.970  0.020  1.090
 IN1  C7   H73   single  0.970  0.020  1.090
 IN1  C1   C2    single  1.524  0.020  1.524
 IN1  C1   O5    single  1.404  0.020  1.404
 IN1  C1   O1    single  1.375  0.020  1.375
 IN1  C1   H1    single  0.970  0.020  1.090
 IN1  C2   C3    single  1.524  0.020  1.524
 IN1  C2   O2    single  1.404  0.020  1.404
 IN1  C2   H2    single  0.970  0.020  1.090
 IN1  C3   C4    single  1.524  0.020  1.524
 IN1  C3   O3    single  1.406  0.020  1.406
 IN1  C3   H3    single  0.970  0.020  1.090
 IN1  C4   C5    single  1.534  0.020  1.534
 IN1  C4   O4    single  1.410  0.020  1.410
 IN1  C4   H4    single  0.970  0.020  1.090
 IN1  C5   C6    single  1.513  0.020  1.513
 IN1  C5   O5    single  1.413  0.020  1.413
 IN1  C5   H5    single  0.970  0.020  1.090
 IN1  C6   O6    single  1.407  0.020  1.407
 IN1  C6   H61   single  0.970  0.020  1.090
 IN1  C6   H62   single  0.970  0.020  1.090
 IN1  O2   HO2   single  0.850  0.020  0.980
 IN1  O3   HO3   single  0.850  0.020  0.980
 IN1  O4   HO4   single  0.850  0.020  0.980
 IN1  O6   HO6   single  0.850  0.020  0.980
 IN1  C6A  O1R   single  1.400  0.020  1.400
 IN1  C6A  O4S   single  1.403  0.020  1.403
 IN1  O1R  HO1   single  0.850  0.020  0.980
 IN1  O2A  C4A   single  1.334  0.020  1.334
 IN1  C4A  C5A   single  1.504  0.020  1.504
 IN1  C4A  O3A   double  1.203  0.020  1.203
 IN1  C5A  H51   single  0.970  0.020  1.090
 IN1  C5A  H52   single  0.970  0.020  1.090
 IN1  O4S  HOS4  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
 IN1  H12   C1A  H11  107.09  3.000
 IN1  H12   C1A  O1   110.29  3.000
 IN1  H11   C1A  O1   110.44  3.000
 IN1  H12   C1A  C2A  110.79  3.000
 IN1  H11   C1A  C2A  108.28  3.000
 IN1  O1    C1A  C2A  109.90  3.000
 IN1  H22   C2A  H21  106.12  3.000
 IN1  H22   C2A  C6A  108.95  3.000
 IN1  H21   C2A  C6A  107.39  3.000
 IN1  H22   C2A  C1A  109.68  3.000
 IN1  H21   C2A  C1A  106.88  3.000
 IN1  C6A   C2A  C1A  117.22  3.000
 IN1  H32   C3A  H31  108.62  3.000
 IN1  H32   C3A  O2A  110.30  3.000
 IN1  H31   C3A  O2A  109.84  3.000
 IN1  H32   C3A  C6A  111.10  3.000
 IN1  H31   C3A  C6A  110.36  3.000
 IN1  O2A   C3A  C6A  106.61  3.000
 IN1  H73   C7   H72  108.05  3.000
 IN1  H73   C7   H71  107.67  3.000
 IN1  H72   C7   H71  107.70  3.000
 IN1  H73   C7   C5A  111.62  3.000
 IN1  H72   C7   C5A  111.77  3.000
 IN1  H71   C7   C5A  109.85  3.000
 IN1  H1    C1   O1   110.91  3.000
 IN1  H1    C1   O5   109.57  3.000
 IN1  O1    C1   O5   108.20  3.000
 IN1  H1    C1   C2   109.25  3.000
 IN1  O1    C1   C2   109.13  3.000
 IN1  O5    C1   C2   109.77  3.000
 IN1  H2    C2   O2   111.49  3.000
 IN1  H2    C2   C3   108.68  3.000
 IN1  O2    C2   C3   111.67  3.000
 IN1  H2    C2   C1   108.06  3.000
 IN1  O2    C2   C1   108.28  3.000
 IN1  C3    C2   C1   108.55  3.000
 IN1  H3    C3   O3   110.72  3.000
 IN1  H3    C3   C4   107.65  3.000
 IN1  O3    C3   C4   112.23  3.000
 IN1  H3    C3   C2   107.86  3.000
 IN1  O3    C3   C2   107.41  3.000
 IN1  C4    C3   C2   110.91  3.000
 IN1  H4    C4   O4   111.20  3.000
 IN1  H4    C4   C5   108.64  3.000
 IN1  O4    C4   C5   112.05  3.000
 IN1  H4    C4   C3   108.71  3.000
 IN1  O4    C4   C3   107.20  3.000
 IN1  C5    C4   C3   108.96  3.000
 IN1  H5    C5   O5   110.29  3.000
 IN1  H5    C5   C6   108.88  3.000
 IN1  O5    C5   C6   107.88  3.000
 IN1  H5    C5   C4   108.40  3.000
 IN1  O5    C5   C4   108.94  3.000
 IN1  C6    C5   C4   112.45  3.000
 IN1  H62   C6   H61  107.12  3.000
 IN1  H62   C6   O6   112.04  3.000
 IN1  H61   C6   O6   111.51  3.000
 IN1  H62   C6   C5   108.80  3.000
 IN1  H61   C6   C5   108.33  3.000
 IN1  O6    C6   C5   108.93  3.000
 IN1  C5    O5   C1   113.92  3.000
 IN1  HO2   O2   C2   108.20  3.000
 IN1  HO3   O3   C3   108.29  3.000
 IN1  HO4   O4   C4   109.31  3.000
 IN1  HO6   O6   C6   108.14  3.000
 IN1  C1    O1   C1A  115.41  3.000
 IN1  O4S   C6A  O1R  111.53  3.000
 IN1  O4S   C6A  C3A  110.08  3.000
 IN1  O1R   C6A  C3A  111.02  3.000
 IN1  O4S   C6A  C2A  105.09  3.000
 IN1  O1R   C6A  C2A  107.35  3.000
 IN1  C3A   C6A  C2A  111.61  3.000
 IN1  HO1   O1R  C6A  110.12  3.000
 IN1  C4A   O2A  C3A  118.18  3.000
 IN1  O3A   C4A  C5A  125.59  3.000
 IN1  O3A   C4A  O2A  123.06  3.000
 IN1  C5A   C4A  O2A  111.35  3.000
 IN1  H52   C5A  H51  105.43  3.000
 IN1  H52   C5A  C4A  108.35  3.000
 IN1  H51   C5A  C4A  107.82  3.000
 IN1  H52   C5A  C7   110.79  3.000
 IN1  H51   C5A  C7   110.66  3.000
 IN1  C4A   C5A  C7   113.43  3.000
 IN1  HOS4  O4S  C6A  109.82  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
 IN1  Var_01  H11  C1A  O1   C1     72.96  30.0  1
 IN1  Var_02  C3A  C6A  C2A  C1A   -70.66  30.0  3
 IN1  Var_03  O2A  C3A  C6A  C2A  -172.85  30.0  1
 IN1  Var_04  C5A  C4A  O2A  C3A   179.61  30.0  3
 IN1  Var_05  O2A  C4A  C5A  C7   -176.61  30.0  1
 IN1  Var_06  C6A  C2A  C1A  O1     68.52  30.0  3
 IN1  Var_07  H71  C7   C5A  C4A   179.72  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
 IN1  chir_01  C1  C2  O5  O1  negativ
 IN1  chir_02  C2  O2  C1  C3  negativ
 IN1  chir_03  C3  O3  C2  C4  positiv
 IN1  chir_04  C4  O4  C5  C3  positiv
 IN1  chir_05  C5  O5  C4  C6  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
 IN1  plan-1  O2A  0.020
 IN1  plan-1  C4A  0.020
 IN1  plan-1  C5A  0.020
 IN1  plan-1  O3A  0.020

