# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:58:54 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-methylethyl 1-thio-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)S[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
 IPT  IPT  '1-methylethyl 1-thio-beta-D-galactopyranoside'  D-saccharide  33  15  .  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_IPT
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
 IPT  C1    C  CH1   0  -0.125  41.7490  12.2081  35.5090
 IPT  C2    C  CH1   0   0.045  40.8517  11.2108  34.7723
 IPT  O2    O  OH1   0  -0.665  39.6607  11.8863  34.4594
 IPT  C3    C  CH1   0   0.009  40.5922  10.0157  35.6851
 IPT  O3    O  OH1   0  -0.667  39.7912   9.1101  34.9670
 IPT  C4    C  CH1   0  -0.015  41.9018   9.4080  36.1793
 IPT  O4    O  OH1   0  -0.666  42.5909   8.8503  35.0876
 IPT  C5    C  CH1   0  -0.004  42.6956  10.5187  36.8712
 IPT  O5    O  O2    0  -0.471  42.9126  11.6091  35.9948
 IPT  C6    C  CH2   0  -0.193  44.0790  10.0917  37.3365
 IPT  O6    O  OH1   0  -0.666  43.9364   8.9464  38.1419
 IPT  S1    S  S2    0  -0.012  42.1861  13.6713  34.5275
 IPT  C1'   C  CH1   0  -0.357  43.6178  13.2146  33.4714
 IPT  C2'   C  CH3   0  -0.652  43.4788  11.8955  32.7294
 IPT  C3'   C  CH3   0  -0.629  44.9457  13.3274  34.2070
 IPT  H1    H  HCH1  0   0.255  41.1511  12.6297  36.3347
 IPT  H2    H  HCH1  0   0.230  41.3553  10.8605  33.8650
 IPT  HO2   H  HOH1  0   0.449  39.0611  11.2508  34.0546
 IPT  H3    H  HCH1  0   0.218  40.0602  10.3856  36.5757
 IPT  HO3   H  HOH1  0   0.454  39.3998   8.4831  35.5835
 IPT  H4    H  HCH1  0   0.235  41.6636   8.6434  36.9308
 IPT  HO4   H  HOH1  0   0.456  43.2655   8.2522  35.4227
 IPT  H5    H  HCH1  0   0.222  42.1104  10.8502  37.7443
 IPT  H61   H  HCH2  0   0.204  44.7119   9.9010  36.4599
 IPT  H62   H  HCH2  0   0.222  44.5369  10.9234  37.8862
 IPT  HO6   H  HOH1  0   0.460  44.8124   8.6519  38.4063
 IPT  H1'   H  HCH1  0   0.271  43.5742  14.0202  32.7322
 IPT  H2'1  H  HCH3  0   0.240  44.2995  11.8000  32.0155
 IPT  H2'2  H  HCH3  0   0.229  43.5317  11.0426  33.4045
 IPT  H2'3  H  HCH3  0   0.236  42.5461  11.8411  32.1689
 IPT  H3'1  H  HCH3  0   0.224  45.7679  13.2220  33.4958
 IPT  H3'2  H  HCH3  0   0.230  45.0482  14.2970  34.6932
 IPT  H3'3  H  HCH3  0   0.234  45.0552  12.5534  34.9640

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
 IPT  C1   C2    single  1.531  0.020  1.531
 IPT  C1   O5    single  1.396  0.020  1.396
 IPT  C1   S1    single  1.815  0.020  1.815
 IPT  C1   H1    single  0.970  0.020  1.090
 IPT  C2   O2    single  1.404  0.020  1.404
 IPT  C2   C3    single  1.526  0.020  1.526
 IPT  C2   H2    single  0.970  0.020  1.090
 IPT  O2   HO2   single  0.850  0.020  0.980
 IPT  C3   O3    single  1.406  0.020  1.406
 IPT  C3   C4    single  1.526  0.020  1.526
 IPT  C3   H3    single  0.970  0.020  1.090
 IPT  O3   HO3   single  0.850  0.020  0.980
 IPT  C4   O4    single  1.406  0.020  1.406
 IPT  C4   C5    single  1.530  0.020  1.530
 IPT  C4   H4    single  0.970  0.020  1.090
 IPT  O4   HO4   single  0.850  0.020  0.980
 IPT  C5   O5    single  1.416  0.020  1.416
 IPT  C5   C6    single  1.521  0.020  1.521
 IPT  C5   H5    single  0.970  0.020  1.090
 IPT  C6   O6    single  1.407  0.020  1.407
 IPT  C6   H61   single  0.970  0.020  1.090
 IPT  C6   H62   single  0.970  0.020  1.090
 IPT  O6   HO6   single  0.850  0.020  0.980
 IPT  S1   C1'   single  1.837  0.020  1.837
 IPT  C1'  C2'   single  1.520  0.020  1.520
 IPT  C1'  C3'   single  1.522  0.020  1.522
 IPT  C1'  H1'   single  0.970  0.020  1.090
 IPT  C2'  H2'1  single  0.970  0.020  1.090
 IPT  C2'  H2'2  single  0.970  0.020  1.090
 IPT  C2'  H2'3  single  0.970  0.020  1.090
 IPT  C3'  H3'1  single  0.970  0.020  1.090
 IPT  C3'  H3'2  single  0.970  0.020  1.090
 IPT  C3'  H3'3  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
 IPT  H1    C1   S1    103.14  3.000
 IPT  H1    C1   O5    110.81  3.000
 IPT  S1    C1   O5    109.47  3.000
 IPT  H1    C1   C2    106.95  3.000
 IPT  S1    C1   C2    113.96  3.000
 IPT  O5    C1   C2    112.12  3.000
 IPT  H2    C2   C3    108.85  3.000
 IPT  H2    C2   O2    111.06  3.000
 IPT  C3    C2   O2    111.45  3.000
 IPT  H2    C2   C1    109.73  3.000
 IPT  C3    C2   C1    108.79  3.000
 IPT  O2    C2   C1    106.92  3.000
 IPT  HO2   O2   C2    107.72  3.000
 IPT  H3    C3   C4    106.64  3.000
 IPT  H3    C3   O3    110.74  3.000
 IPT  C4    C3   O3    113.44  3.000
 IPT  H3    C3   C2    107.62  3.000
 IPT  C4    C3   C2    111.08  3.000
 IPT  O3    C3   C2    107.20  3.000
 IPT  HO3   O3   C3    108.91  3.000
 IPT  H4    C4   C5    107.96  3.000
 IPT  H4    C4   O4    111.18  3.000
 IPT  C5    C4   O4    112.62  3.000
 IPT  H4    C4   C3    108.22  3.000
 IPT  C5    C4   C3    107.61  3.000
 IPT  O4    C4   C3    109.09  3.000
 IPT  HO4   O4   C4    108.65  3.000
 IPT  H5    C5   C6    108.97  3.000
 IPT  H5    C5   O5    109.88  3.000
 IPT  C6    C5   O5    105.44  3.000
 IPT  H5    C5   C4    107.52  3.000
 IPT  C6    C5   C4    113.98  3.000
 IPT  O5    C5   C4    111.02  3.000
 IPT  C5    O5   C1    114.72  3.000
 IPT  H62   C6   H61   106.92  3.000
 IPT  H62   C6   O6    111.87  3.000
 IPT  H61   C6   O6    111.96  3.000
 IPT  H62   C6   C5    108.67  3.000
 IPT  H61   C6   C5    109.20  3.000
 IPT  O6    C6   C5    108.15  3.000
 IPT  HO6   O6   C6    108.32  3.000
 IPT  C1'   S1   C1    107.35  3.000
 IPT  H1'   C1'  C3'   107.86  3.000
 IPT  H1'   C1'  C2'   107.80  3.000
 IPT  C3'   C1'  C2'   112.33  3.000
 IPT  H1'   C1'  S1    100.04  3.000
 IPT  C3'   C1'  S1    112.56  3.000
 IPT  C2'   C1'  S1    115.16  3.000
 IPT  H2'3  C2'  H2'2  108.74  3.000
 IPT  H2'3  C2'  H2'1  107.62  3.000
 IPT  H2'2  C2'  H2'1  107.48  3.000
 IPT  H2'3  C2'  C1'   111.89  3.000
 IPT  H2'2  C2'  C1'   111.88  3.000
 IPT  H2'1  C2'  C1'   109.05  3.000
 IPT  H3'3  C3'  H3'2  108.25  3.000
 IPT  H3'3  C3'  H3'1  107.97  3.000
 IPT  H3'2  C3'  H3'1  107.79  3.000
 IPT  H3'3  C3'  C1'   111.79  3.000
 IPT  H3'2  C3'  C1'   111.33  3.000
 IPT  H3'1  C3'  C1'   109.56  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
 IPT  Var_01  C2'   C1'  S1   C1    47.43  30.0  3
 IPT  Var_02  H2'1  C2'  C1'  S1   170.89  30.0  3
 IPT  Var_03  H3'1  C3'  C1'  S1  -169.91  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
 IPT  chir_01  C1  C2  O5  S1  negativ
 IPT  chir_02  C2  O2  C1  C3  negativ
 IPT  chir_03  C3  O3  C2  C4  positiv
 IPT  chir_04  C4  O4  C5  C3  negativ
 IPT  chir_05  C5  O5  C4  C6  negativ

