# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 15:15:02 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: octyl 3-amino-3-deoxy-beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCO[C@@H]1O[C@H](CO)[C@H](O)[C@H](N)[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
 AOG  AOG  'octyl 3-amino-3-deoxy-beta-D-galactopyranoside'  D-saccharide  49  20  .  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_AOG
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
 AOG  C1    C  CH1   0   0.323  17.8054  63.4483  45.5060
 AOG  O1    O  O2    0  -0.488  17.6526  64.6180  44.8007
 AOG  C2    C  CH1   0   0.040  17.8959  62.2827  44.5319
 AOG  O2    O  OH1   0  -0.673  16.6916  62.1623  43.8209
 AOG  C3    C  CH1   0  -0.168  18.1667  60.9968  45.3165
 AOG  C4    C  CH1   0   0.003  19.4117  61.1463  46.1909
 AOG  O4    O  OH1   0  -0.671  20.5419  61.2191  45.3496
 AOG  C5    C  CH1   0   0.002  19.2432  62.3964  47.0582
 AOG  O5    O  O2    0  -0.501  18.9920  63.5327  46.2567
 AOG  C6    C  CH2   0  -0.165  20.4565  62.6796  47.9168
 AOG  O6    O  OH1   0  -0.665  20.1395  63.7058  48.8264
 AOG  N3    N  NH2   0  -0.803  18.1672  59.8884  44.3818
 AOG  C1'   C  CH2   0  -0.156  17.2247  65.7430  45.5491
 AOG  C2'   C  CH2   0  -0.464  16.7019  66.8208  44.6193
 AOG  C3'   C  CH2   0  -0.429  15.4363  66.4574  43.8386
 AOG  C4'   C  CH2   0  -0.431  15.6702  65.6672  42.5530
 AOG  C5'   C  CH2   0  -0.419  14.3882  65.3529  41.7865
 AOG  C6'   C  CH2   0  -0.410  13.4690  64.3629  42.4956
 AOG  C7'   C  CH2   0  -0.415  12.2499  63.9824  41.6649
 AOG  C8'   C  CH3   0  -0.659  11.3327  62.9954  42.3736
 AOG  H1    H  HCH1  0   0.174  16.9492  63.2822  46.1899
 AOG  H2    H  HCH1  0   0.201  18.7394  62.4738  43.8493
 AOG  HO2   H  HOH1  0   0.441  16.6798  61.2467  43.5048
 AOG  H3    H  HCH1  0   0.246  17.3208  60.8480  45.9984
 AOG  H4    H  HCH1  0   0.231  19.4716  60.2752  46.8573
 AOG  HO4   H  HOH1  0   0.458  21.3063  60.8683  45.8144
 AOG  H5    H  HCH1  0   0.214  18.3862  62.2081  47.7275
 AOG  H61   H  HCH2  0   0.201  20.7295  61.7496  48.4340
 AOG  H62   H  HCH2  0   0.200  21.3041  62.9529  47.2759
 AOG  HO6   H  HOH1  0   0.453  20.9319  63.9170  49.3278
 AOG  HN31  H  HNH2  0   0.358  18.0574  59.0101  44.8717
 AOG  HN32  H  HNH2  0   0.348  19.0570  59.8444  43.8987
 AOG  H1'1  H  HCH2  0   0.199  16.4302  65.4488  46.2487
 AOG  H1'2  H  HCH2  0   0.214  18.0503  66.1436  46.1478
 AOG  H2'1  H  HCH2  0   0.233  16.4942  67.6877  45.2527
 AOG  H2'2  H  HCH2  0   0.222  17.4947  67.1368  43.9336
 AOG  H3'1  H  HCH2  0   0.214  14.7546  65.9163  44.5030
 AOG  H3'2  H  HCH2  0   0.216  14.9148  67.3825  43.5732
 AOG  H4'1  H  HCH2  0   0.209  16.3389  66.2480  41.9093
 AOG  H4'2  H  HCH2  0   0.224  16.1909  64.7340  42.7692
 AOG  H5'1  H  HCH2  0   0.202  13.8399  66.2803  41.5855
 AOG  H5'2  H  HCH2  0   0.212  14.6539  64.9419  40.8072
 AOG  H6'1  H  HCH2  0   0.201  14.0370  63.4585  42.7428
 AOG  H6'2  H  HCH2  0   0.210  13.1348  64.7778  43.4517
 AOG  H7'1  H  HCH2  0   0.208  11.6889  64.8873  41.4111
 AOG  H7'2  H  HCH2  0   0.208  12.5806  63.5556  40.7129
 AOG  H8'1  H  HCH3  0   0.224  10.4666  62.7395  41.7621
 AOG  H8'2  H  HCH3  0   0.214  11.8581  62.0671  42.6058
 AOG  H8'3  H  HCH3  0   0.214  10.9627  63.4070  43.3145

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
 AOG  C1   O1    single  1.374  0.020  1.374
 AOG  C1   C2    single  1.522  0.020  1.522
 AOG  C1   O5    single  1.407  0.020  1.407
 AOG  C1   H1    single  0.970  0.020  1.090
 AOG  O1   C1'   single  1.417  0.020  1.417
 AOG  C2   O2    single  1.404  0.020  1.404
 AOG  C2   C3    single  1.530  0.020  1.530
 AOG  C2   H2    single  0.970  0.020  1.090
 AOG  O2   HO2   single  0.850  0.020  0.980
 AOG  C3   C4    single  1.529  0.020  1.529
 AOG  C3   N3    single  1.450  0.020  1.450
 AOG  C3   H3    single  0.970  0.020  1.090
 AOG  C4   O4    single  1.411  0.020  1.411
 AOG  C4   C5    single  1.531  0.020  1.531
 AOG  C4   H4    single  0.970  0.020  1.090
 AOG  O4   HO4   single  0.850  0.020  0.980
 AOG  C5   O5    single  1.413  0.020  1.413
 AOG  C5   C6    single  1.513  0.020  1.513
 AOG  C5   H5    single  0.970  0.020  1.090
 AOG  C6   O6    single  1.407  0.020  1.407
 AOG  C6   H61   single  0.970  0.020  1.090
 AOG  C6   H62   single  0.970  0.020  1.090
 AOG  O6   HO6   single  0.850  0.020  0.980
 AOG  N3   HN31  single  0.890  0.020  1.040
 AOG  N3   HN32  single  0.890  0.020  1.040
 AOG  C1'  C2'   single  1.516  0.020  1.516
 AOG  C1'  H1'1  single  0.970  0.020  1.090
 AOG  C1'  H1'2  single  0.970  0.020  1.090
 AOG  C2'  C3'   single  1.531  0.020  1.531
 AOG  C2'  H2'1  single  0.970  0.020  1.090
 AOG  C2'  H2'2  single  0.970  0.020  1.090
 AOG  C3'  C4'   single  1.527  0.020  1.527
 AOG  C3'  H3'1  single  0.970  0.020  1.090
 AOG  C3'  H3'2  single  0.970  0.020  1.090
 AOG  C4'  C5'   single  1.526  0.020  1.526
 AOG  C4'  H4'1  single  0.970  0.020  1.090
 AOG  C4'  H4'2  single  0.970  0.020  1.090
 AOG  C5'  C6'   single  1.526  0.020  1.526
 AOG  C5'  H5'1  single  0.970  0.020  1.090
 AOG  C5'  H5'2  single  0.970  0.020  1.090
 AOG  C6'  C7'   single  1.524  0.020  1.524
 AOG  C6'  H6'1  single  0.970  0.020  1.090
 AOG  C6'  H6'2  single  0.970  0.020  1.090
 AOG  C7'  C8'   single  1.522  0.020  1.522
 AOG  C7'  H7'1  single  0.970  0.020  1.090
 AOG  C7'  H7'2  single  0.970  0.020  1.090
 AOG  C8'  H8'1  single  0.970  0.020  1.090
 AOG  C8'  H8'2  single  0.970  0.020  1.090
 AOG  C8'  H8'3  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
 AOG  H1    C1   O5    109.35  3.000
 AOG  H1    C1   C2    109.03  3.000
 AOG  O5    C1   C2    109.72  3.000
 AOG  H1    C1   O1    111.00  3.000
 AOG  O5    C1   O1    108.46  3.000
 AOG  C2    C1   O1    109.27  3.000
 AOG  C1'   O1   C1    115.98  3.000
 AOG  H2    C2   C3    109.14  3.000
 AOG  H2    C2   O2    110.97  3.000
 AOG  C3    C2   O2    109.84  3.000
 AOG  H2    C2   C1    108.01  3.000
 AOG  C3    C2   C1    109.02  3.000
 AOG  O2    C2   C1    109.81  3.000
 AOG  HO2   O2   C2    104.88  3.000
 AOG  H3    C3   N3    107.30  3.000
 AOG  H3    C3   C4    106.61  3.000
 AOG  N3    C3   C4    116.31  3.000
 AOG  H3    C3   C2    107.23  3.000
 AOG  N3    C3   C2    108.17  3.000
 AOG  C4    C3   C2    110.80  3.000
 AOG  H4    C4   C5    108.06  3.000
 AOG  H4    C4   O4    111.04  3.000
 AOG  C5    C4   O4    112.57  3.000
 AOG  H4    C4   C3    108.30  3.000
 AOG  C5    C4   C3    108.32  3.000
 AOG  O4    C4   C3    108.44  3.000
 AOG  HO4   O4   C4    109.27  3.000
 AOG  H5    C5   C6    108.09  3.000
 AOG  H5    C5   O5    110.07  3.000
 AOG  C6    C5   O5    108.30  3.000
 AOG  H5    C5   C4    106.84  3.000
 AOG  C6    C5   C4    112.71  3.000
 AOG  O5    C5   C4    110.79  3.000
 AOG  C5    O5   C1    113.85  3.000
 AOG  H62   C6   H61   107.10  3.000
 AOG  H62   C6   O6    111.70  3.000
 AOG  H61   C6   O6    111.65  3.000
 AOG  H62   C6   C5    109.54  3.000
 AOG  H61   C6   C5    107.94  3.000
 AOG  O6    C6   C5    108.82  3.000
 AOG  HO6   O6   C6    108.16  3.000
 AOG  HN32  N3   HN31  106.77  3.000
 AOG  HN32  N3   C3    109.93  3.000
 AOG  HN31  N3   C3    110.57  3.000
 AOG  H1'2  C1'  H1'1  107.14  3.000
 AOG  H1'2  C1'  C2'   109.57  3.000
 AOG  H1'1  C1'  C2'   109.36  3.000
 AOG  H1'2  C1'  O1    110.56  3.000
 AOG  H1'1  C1'  O1    110.00  3.000
 AOG  C2'   C1'  O1    110.15  3.000
 AOG  H2'2  C2'  H2'1  105.75  3.000
 AOG  H2'2  C2'  C3'   110.35  3.000
 AOG  H2'1  C2'  C3'   109.06  3.000
 AOG  H2'2  C2'  C1'   109.85  3.000
 AOG  H2'1  C2'  C1'   105.89  3.000
 AOG  C3'   C2'  C1'   115.40  3.000
 AOG  H3'2  C3'  H3'1  105.56  3.000
 AOG  H3'2  C3'  C4'   107.83  3.000
 AOG  H3'1  C3'  C4'   110.52  3.000
 AOG  H3'2  C3'  C2'   108.48  3.000
 AOG  H3'1  C3'  C2'   108.82  3.000
 AOG  C4'   C3'  C2'   115.19  3.000
 AOG  H4'2  C4'  H4'1  106.19  3.000
 AOG  H4'2  C4'  C5'   108.93  3.000
 AOG  H4'1  C4'  C5'   109.08  3.000
 AOG  H4'2  C4'  C3'   110.44  3.000
 AOG  H4'1  C4'  C3'   108.30  3.000
 AOG  C5'   C4'  C3'   113.62  3.000
 AOG  H5'2  C5'  H5'1  105.97  3.000
 AOG  H5'2  C5'  C6'   108.56  3.000
 AOG  H5'1  C5'  C6'   109.45  3.000
 AOG  H5'2  C5'  C4'   108.83  3.000
 AOG  H5'1  C5'  C4'   109.76  3.000
 AOG  C6'   C5'  C4'   113.97  3.000
 AOG  H6'2  C6'  H6'1  105.90  3.000
 AOG  H6'2  C6'  C7'   109.07  3.000
 AOG  H6'1  C6'  C7'   109.37  3.000
 AOG  H6'2  C6'  C5'   110.12  3.000
 AOG  H6'1  C6'  C5'   109.14  3.000
 AOG  C7'   C6'  C5'   113.00  3.000
 AOG  H7'2  C7'  H7'1  106.00  3.000
 AOG  H7'2  C7'  C8'   109.52  3.000
 AOG  H7'1  C7'  C8'   109.59  3.000
 AOG  H7'2  C7'  C6'   109.26  3.000
 AOG  H7'1  C7'  C6'   109.28  3.000
 AOG  C8'   C7'  C6'   112.96  3.000
 AOG  H8'3  C8'  H8'2  107.48  3.000
 AOG  H8'3  C8'  H8'1  107.61  3.000
 AOG  H8'2  C8'  H8'1  107.57  3.000
 AOG  H8'3  C8'  C7'   111.16  3.000
 AOG  H8'2  C8'  C7'   111.13  3.000
 AOG  H8'1  C8'  C7'   111.68  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
 AOG  Var_01  C2'   C1'  O1   C1   -162.99  30.0  3
 AOG  Var_02  C3'   C2'  C1'  O1     65.19  30.0  3
 AOG  Var_03  C4'   C3'  C2'  C1'   -83.89  30.0  3
 AOG  Var_04  C5'   C4'  C3'  C2'  -178.62  30.0  3
 AOG  Var_05  C6'   C5'  C4'  C3'   -68.23  30.0  3
 AOG  Var_06  C7'   C6'  C5'  C4'  -175.55  30.0  3
 AOG  Var_07  C8'   C7'  C6'  C5'  -179.96  30.0  3
 AOG  Var_08  H8'1  C8'  C7'  C6'   179.86  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
 AOG  chir_01  C1  O1  C2  O5  negativ
 AOG  chir_02  C2  O2  C1  C3  negativ
 AOG  chir_03  C3  N3  C4  C2  negativ
 AOG  chir_04  C4  O4  C3  C5  positiv
 AOG  chir_05  C5  O5  C4  C6  negativ

