# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:43:23 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 4-aminophenyl alpha-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(O[C@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)cc1
#
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
 GAT  GAT  '4-aminophenyl alpha-D-galactopyranoside'  D-saccharide  36  19  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GAT
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
 GAT  C1    C  CH1   0   0.234  -0.6026   0.5166  -0.5785
 GAT  C2    C  CH1   0  -0.015  -1.3373   0.1906  -1.8825
 GAT  C3    C  CH1   0   0.003  -0.5908  -0.8856  -2.6603
 GAT  C4    C  CH1   0  -0.001   0.8603  -0.4587  -2.8715
 GAT  C5    C  CH1   0  -0.015   1.4767  -0.1326  -1.5191
 GAT  C6    C  CH2   0  -0.159   2.9027   0.3636  -1.6270
 GAT  C7    C  CR6   0   0.301  -0.5726  -0.3410   1.6180
 GAT  C8    C  CR16  0  -0.325   0.6680  -0.1004   2.1963
 GAT  C9    C  CR16  0  -0.319   0.7701   0.1177   3.5617
 GAT  C10   C  CR6   0   0.293  -0.3609   0.1017   4.3851
 GAT  C11   C  CR16  0  -0.321  -1.6020  -0.1452   3.7882
 GAT  C12   C  CR16  0  -0.317  -1.7037  -0.3578   2.4228
 GAT  N1    N  NH2   0  -0.861  -0.2623   0.3735   5.7372
 GAT  O1    O  O2    0  -0.516  -0.7114  -0.5926   0.2768
 GAT  O2    O  OH1   0  -0.667  -2.6500  -0.2583  -1.6618
 GAT  O3    O  OH1   0  -0.676  -1.1623  -1.1036  -3.9282
 GAT  O4    O  OH1   0  -0.673   0.9571   0.6692  -3.7064
 GAT  O5    O  O2    0  -0.488   0.7231   0.8575  -0.8332
 GAT  O6    O  OH1   0  -0.665   3.4651   0.3814  -0.3354
 GAT  H1    H  HCH1  0   0.241  -1.0481   1.3997  -0.1046
 GAT  H2    H  HCH1  0   0.232  -1.3325   1.1117  -2.4793
 GAT  H3    H  HCH1  0   0.220  -0.5851  -1.8149  -2.0714
 GAT  H4    H  HCH1  0   0.235   1.4160  -1.3108  -3.2918
 GAT  H5    H  HCH1  0   0.235   1.4922  -1.0678  -0.9433
 GAT  H61   H  HCH2  0   0.203   3.4478  -0.3154  -2.2958
 GAT  H62   H  HCH2  0   0.207   2.9186   1.3566  -2.0906
 GAT  H8    H  HCR6  0   0.268   1.5639  -0.0872   1.5887
 GAT  H9    H  HCR6  0   0.256   1.7455   0.3041   3.9959
 GAT  H11   H  HCR6  0   0.257  -2.4966  -0.1662   4.3997
 GAT  H12   H  HCR6  0   0.257  -2.6730  -0.5491   1.9786
 GAT  HN11  H  HNH2  0   0.376  -1.0112   0.0075   6.3034
 GAT  HN12  H  HNH2  0   0.376   0.6350   0.1747   6.1504
 GAT  HO2   H  HOH1  0   0.460  -3.2130   0.5004  -1.4812
 GAT  HO3   H  HOH1  0   0.454  -2.1175  -1.1736  -3.8240
 GAT  HO4   H  HOH1  0   0.452   0.4342   0.4964  -4.4971
 GAT  HO6   H  HOH1  0   0.457   4.3519   0.7470  -0.3994

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
 GAT  C1   C2    single    1.532  0.020  1.532
 GAT  C1   O1    single    1.405  0.020  1.405
 GAT  C1   O5    single    1.392  0.020  1.392
 GAT  C1   H1    single    0.970  0.020  1.090
 GAT  C2   C3    single    1.523  0.020  1.523
 GAT  C2   O2    single    1.405  0.020  1.405
 GAT  C2   H2    single    0.970  0.020  1.090
 GAT  C3   C4    single    1.527  0.020  1.527
 GAT  C3   O3    single    1.408  0.020  1.408
 GAT  C3   H3    single    0.970  0.020  1.090
 GAT  C4   C5    single    1.522  0.020  1.522
 GAT  C4   O4    single    1.407  0.020  1.407
 GAT  C4   H4    single    0.970  0.020  1.090
 GAT  C5   C6    single    1.514  0.020  1.514
 GAT  C5   O5    single    1.421  0.020  1.421
 GAT  C5   H5    single    0.970  0.020  1.090
 GAT  C6   O6    single    1.409  0.020  1.409
 GAT  C6   H61   single    0.970  0.020  1.090
 GAT  C6   H62   single    0.970  0.020  1.090
 GAT  C7   C8    aromatic  1.390  0.020  1.390
 GAT  C7   C12   aromatic  1.388  0.020  1.388
 GAT  C7   O1    single    1.372  0.020  1.372
 GAT  C8   C9    aromatic  1.386  0.020  1.386
 GAT  C8   H8    single    0.930  0.020  1.080
 GAT  C9   C10   aromatic  1.399  0.020  1.399
 GAT  C9   H9    single    0.930  0.020  1.080
 GAT  C10  C11   aromatic  1.399  0.020  1.399
 GAT  C10  N1    single    1.383  0.020  1.383
 GAT  C11  C12   aromatic  1.386  0.020  1.386
 GAT  C11  H11   single    0.930  0.020  1.080
 GAT  C12  H12   single    0.930  0.020  1.080
 GAT  N1   HN11  single    0.890  0.020  1.040
 GAT  N1   HN12  single    0.890  0.020  1.040
 GAT  O2   HO2   single    0.850  0.020  0.980
 GAT  O3   HO3   single    0.850  0.020  0.980
 GAT  O4   HO4   single    0.850  0.020  0.980
 GAT  O6   HO6   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
 GAT  H1    C1   O5    105.59  3.000
 GAT  H1    C1   O1    109.95  3.000
 GAT  O5    C1   O1    112.24  3.000
 GAT  H1    C1   C2    110.14  3.000
 GAT  O5    C1   C2    110.67  3.000
 GAT  O1    C1   C2    108.25  3.000
 GAT  H2    C2   O2    110.96  3.000
 GAT  H2    C2   C3    108.25  3.000
 GAT  O2    C2   C3    108.20  3.000
 GAT  H2    C2   C1    106.39  3.000
 GAT  O2    C2   C1    112.48  3.000
 GAT  C3    C2   C1    110.48  3.000
 GAT  H3    C3   O3    110.69  3.000
 GAT  H3    C3   C4    107.77  3.000
 GAT  O3    C3   C4    107.72  3.000
 GAT  H3    C3   C2    109.03  3.000
 GAT  O3    C3   C2    111.74  3.000
 GAT  C4    C3   C2    109.80  3.000
 GAT  H4    C4   O4    111.06  3.000
 GAT  H4    C4   C5    107.51  3.000
 GAT  O4    C4   C5    109.14  3.000
 GAT  H4    C4   C3    108.43  3.000
 GAT  O4    C4   C3    111.81  3.000
 GAT  C5    C4   C3    108.78  3.000
 GAT  H5    C5   O5    110.35  3.000
 GAT  H5    C5   C6    107.65  3.000
 GAT  O5    C5   C6    107.80  3.000
 GAT  H5    C5   C4    106.81  3.000
 GAT  O5    C5   C4    111.32  3.000
 GAT  C6    C5   C4    112.86  3.000
 GAT  H62   C6   H61   107.18  3.000
 GAT  H62   C6   O6    111.75  3.000
 GAT  H61   C6   O6    111.60  3.000
 GAT  H62   C6   C5    109.93  3.000
 GAT  H61   C6   C5    107.96  3.000
 GAT  O6    C6   C5    108.35  3.000
 GAT  O1    C7   C12   118.83  3.000
 GAT  O1    C7   C8    121.94  3.000
 GAT  C12   C7   C8    119.22  3.000
 GAT  H8    C8   C9    119.33  3.000
 GAT  H8    C8   C7    120.48  3.000
 GAT  C9    C8   C7    120.18  3.000
 GAT  H9    C9   C10   119.58  3.000
 GAT  H9    C9   C8    119.20  3.000
 GAT  C10   C9   C8    121.22  3.000
 GAT  N1    C10  C11   121.01  3.000
 GAT  N1    C10  C9    121.04  3.000
 GAT  C11   C10  C9    117.90  3.000
 GAT  H11   C11  C12   119.50  3.000
 GAT  H11   C11  C10   119.66  3.000
 GAT  C12   C11  C10   120.84  3.000
 GAT  H12   C12  C11   119.80  3.000
 GAT  H12   C12  C7    119.56  3.000
 GAT  C11   C12  C7    120.64  3.000
 GAT  HN12  N1   HN11  111.09  3.000
 GAT  HN12  N1   C10   115.19  3.000
 GAT  HN11  N1   C10   115.15  3.000
 GAT  C7    O1   C1    116.27  3.000
 GAT  HO2   O2   C2    108.93  3.000
 GAT  HO3   O3   C3    108.44  3.000
 GAT  HO4   O4   C4    107.82  3.000
 GAT  C5    O5   C1    115.01  3.000
 GAT  HO6   O6   C6    108.18  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
 GAT  CONST_01  C10  C9   C8   C7     0.00   0.0  0
 GAT  CONST_02  C10  C11  C12  C7     0.00   0.0  0
 GAT  CONST_03  C11  C12  C7   C8     0.00   0.0  0
 GAT  CONST_04  C11  C10  C9   C8     0.00   0.0  0
 GAT  CONST_05  C12  C7   C8   C9     0.00   0.0  0
 GAT  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 GAT  CONST_07  N1   C10  C9   C8   180.00   0.0  0
 GAT  CONST_08  O1   C7   C8   C9   180.00   0.0  0
 GAT  CONST_09  O1   C7   C12  C11  180.00   0.0  0
 GAT  CONST_10  N1   C10  C11  C12  180.00   0.0  0
 GAT  CONST_11  H9   C9   C8   C7   180.00   0.0  0
 GAT  CONST_12  H11  C11  C12  C7   180.00   0.0  0
 GAT  CONST_13  H12  C12  C7   C8   180.00   0.0  0
 GAT  CONST_14  H8   C8   C9   C10  180.00   0.0  0
 GAT  Var_01    C8   C7   O1   C1   -75.80  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
 GAT  chir_01  C1  C2  O1  O5  negativ
 GAT  chir_02  C2  O2  C1  C3  negativ
 GAT  chir_03  C3  O3  C2  C4  positiv
 GAT  chir_04  C4  O4  C3  C5  positiv
 GAT  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
 GAT  plan-1  C7    0.020
 GAT  plan-1  C8    0.020
 GAT  plan-1  C9    0.020
 GAT  plan-1  C10   0.020
 GAT  plan-1  C11   0.020
 GAT  plan-1  C12   0.020
 GAT  plan-1  N1    0.020
 GAT  plan-1  O1    0.020
 GAT  plan-1  H8    0.020
 GAT  plan-1  H9    0.020
 GAT  plan-1  H11   0.020
 GAT  plan-1  H12   0.020
 GAT  plan-2  C10   0.020
 GAT  plan-2  N1    0.020
 GAT  plan-2  HN11  0.020
 GAT  plan-2  HN12  0.020

