# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 19:17:03 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: phenyl beta-D-galactopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](Oc2ccccc2)[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
 56N  56N  'phenyl beta-D-galactopyranoside'  D-saccharide  34  18  .  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_56N
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
 56N  O2   O  OH1   0  -0.668  -1.0516   2.6876   0.4442
 56N  O3   O  OH1   0  -0.672  -3.7163   1.6574   0.2995
 56N  O4   O  OH1   0  -0.671  -3.2373  -0.6085  -1.2282
 56N  O5   O  O2    0  -0.491  -0.5221  -0.8152  -0.3816
 56N  C1   C  CH1   0   0.268  -0.1786   0.4500   0.0977
 56N  C2   C  CH1   0  -0.020  -1.3313   1.4293  -0.1169
 56N  C3   C  CH1   0   0.003  -2.5761   0.8835   0.5751
 56N  C4   C  CH1   0   0.004  -2.8649  -0.5479   0.1258
 56N  C5   C  CH1   0  -0.021  -1.6071  -1.3822   0.3290
 56N  C6   C  CH2   0  -0.155  -1.7639  -2.8209  -0.1102
 56N  O6   O  OH1   0  -0.666  -0.6249  -3.5340   0.3090
 56N  O1'  O  O2    0  -0.502   0.9137   0.9118  -0.6288
 56N  C1'  C  CR6   0   0.358   2.1667   0.5175  -0.2709
 56N  C2'  C  CR16  0  -0.340   3.2047   1.3626  -0.6545
 56N  C3'  C  CR16  0  -0.245   4.5139   1.0377  -0.3380
 56N  C4'  C  CR16  0  -0.272   4.8002  -0.1245   0.3686
 56N  C5'  C  CR16  0  -0.245   3.7608  -0.9623   0.7436
 56N  C6'  C  CR16  0  -0.352   2.4427  -0.6573   0.4232
 56N  H1   H  HOH1  0   0.460  -0.4415   3.1575  -0.1326
 56N  H2   H  HOH1  0   0.457  -3.5151   2.5813   0.4830
 56N  H3   H  HOH1  0   0.453  -3.9654   0.0074  -1.3638
 56N  H4   H  HCH1  0   0.207   0.0713   0.3992   1.1729
 56N  H5   H  HCH1  0   0.232  -1.5229   1.5025  -1.1961
 56N  H6   H  HCH1  0   0.217  -2.3757   0.8538   1.6582
 56N  H7   H  HCH1  0   0.237  -3.6528  -0.9591   0.7744
 56N  H8   H  HCH1  0   0.234  -1.3900  -1.3814   1.4096
 56N  H9   H  HCH2  0   0.204  -2.6812  -3.2131   0.3477
 56N  H10  H  HCH2  0   0.209  -1.8986  -2.8684  -1.1968
 56N  H11  H  HOH1  0   0.457  -0.7088  -4.4400  -0.0010
 56N  H12  H  HCR6  0   0.264   2.9780   2.2725  -1.1961
 56N  H13  H  HCR6  0   0.259   5.3131   1.7028  -0.6389
 56N  H14  H  HCR6  0   0.255   5.8223  -0.3754   0.6189
 56N  H15  H  HCR6  0   0.260   3.9703  -1.8762   1.2844
 56N  H16  H  HCR6  0   0.284   1.6579  -1.3513   0.6929

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
 56N  C4'  C5'  aromatic  1.387  0.020  1.387
 56N  C4'  C3'  aromatic  1.390  0.020  1.390
 56N  C5'  C6'  aromatic  1.390  0.020  1.390
 56N  C3'  C2'  aromatic  1.386  0.020  1.386
 56N  C6'  C1'  aromatic  1.392  0.020  1.392
 56N  C2'  C1'  aromatic  1.392  0.020  1.392
 56N  C1'  O1'  single    1.361  0.020  1.361
 56N  O1'  C1   single    1.391  0.020  1.391
 56N  O2   C2   single    1.406  0.020  1.406
 56N  C1   C2   single    1.528  0.020  1.528
 56N  C1   O5   single    1.396  0.020  1.396
 56N  C2   C3   single    1.525  0.020  1.525
 56N  O5   C5   single    1.416  0.020  1.416
 56N  C3   O3   single    1.405  0.020  1.405
 56N  C3   C4   single    1.528  0.020  1.528
 56N  C5   C4   single    1.523  0.020  1.523
 56N  C5   C6   single    1.512  0.020  1.512
 56N  C4   O4   single    1.406  0.020  1.406
 56N  O6   C6   single    1.408  0.020  1.408
 56N  O2   H1   single    0.850  0.020  0.980
 56N  O3   H2   single    0.850  0.020  0.980
 56N  O4   H3   single    0.850  0.020  0.980
 56N  C1   H4   single    0.970  0.020  1.090
 56N  C2   H5   single    0.970  0.020  1.090
 56N  C3   H6   single    0.970  0.020  1.090
 56N  C4   H7   single    0.970  0.020  1.090
 56N  C5   H8   single    0.970  0.020  1.090
 56N  C6   H9   single    0.970  0.020  1.090
 56N  C6   H10  single    0.970  0.020  1.090
 56N  O6   H11  single    0.850  0.020  0.980
 56N  C2'  H12  single    0.930  0.020  1.080
 56N  C3'  H13  single    0.930  0.020  1.080
 56N  C4'  H14  single    0.930  0.020  1.080
 56N  C5'  H15  single    0.930  0.020  1.080
 56N  C6'  H16  single    0.930  0.020  1.080

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
 56N  H1   O2   C2   108.91  3.000
 56N  H2   O3   C3   108.75  3.000
 56N  H3   O4   C4   107.96  3.000
 56N  C5   O5   C1   112.29  3.000
 56N  H4   C1   O1'  110.24  3.000
 56N  H4   C1   C2   109.68  3.000
 56N  O1'  C1   C2   107.84  3.000
 56N  H4   C1   O5   110.37  3.000
 56N  C2   C1   O5   110.31  3.000
 56N  O1'  C1   O5   108.35  3.000
 56N  H5   C2   C3   109.10  3.000
 56N  H5   C2   C1   108.20  3.000
 56N  C3   C2   C1   108.82  3.000
 56N  H5   C2   O2   111.54  3.000
 56N  C3   C2   O2   107.56  3.000
 56N  C1   C2   O2   111.57  3.000
 56N  H6   C3   C4   107.35  3.000
 56N  H6   C3   C2   107.89  3.000
 56N  C4   C3   C2   110.86  3.000
 56N  H6   C3   O3   110.80  3.000
 56N  C4   C3   O3   107.75  3.000
 56N  C2   C3   O3   112.09  3.000
 56N  H7   C4   C5   107.95  3.000
 56N  H7   C4   C3   108.19  3.000
 56N  C5   C4   C3   108.53  3.000
 56N  H7   C4   O4   111.22  3.000
 56N  C5   C4   O4   108.89  3.000
 56N  C3   C4   O4   111.95  3.000
 56N  H8   C5   C6   107.81  3.000
 56N  H8   C5   C4   107.04  3.000
 56N  C6   C5   C4   113.38  3.000
 56N  H8   C5   O5   109.93  3.000
 56N  C6   C5   O5   108.34  3.000
 56N  C4   C5   O5   110.28  3.000
 56N  H10  C6   H9   107.18  3.000
 56N  H10  C6   O6   111.89  3.000
 56N  H9   C6   O6   111.77  3.000
 56N  H10  C6   C5   109.99  3.000
 56N  H9   C6   C5   107.78  3.000
 56N  O6   C6   C5   108.15  3.000
 56N  H11  O6   C6   108.11  3.000
 56N  C1'  O1'  C1   119.30  3.000
 56N  C6'  C1'  C2'  120.11  3.000
 56N  C2'  C1'  O1'  115.97  3.000
 56N  C6'  C1'  O1'  123.91  3.000
 56N  H12  C2'  C3'  120.60  3.000
 56N  H12  C2'  C1'  119.45  3.000
 56N  C3'  C2'  C1'  119.95  3.000
 56N  H13  C3'  C4'  120.20  3.000
 56N  H13  C3'  C2'  119.35  3.000
 56N  C4'  C3'  C2'  120.45  3.000
 56N  H14  C4'  C5'  120.37  3.000
 56N  H14  C4'  C3'  120.41  3.000
 56N  C5'  C4'  C3'  119.22  3.000
 56N  H15  C5'  C6'  118.94  3.000
 56N  H15  C5'  C4'  120.00  3.000
 56N  C6'  C5'  C4'  121.05  3.000
 56N  H16  C6'  C5'  119.31  3.000
 56N  H16  C6'  C1'  121.45  3.000
 56N  C5'  C6'  C1'  119.21  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
 56N  CONST_01  C4'  C5'  C6'  C1'    0.00   0.0  0
 56N  CONST_02  C4'  C3'  C2'  C1'    0.00   0.0  0
 56N  CONST_03  C5'  C4'  C3'  C2'    0.00   0.0  0
 56N  CONST_04  C5'  C6'  C1'  C2'    0.00   0.0  0
 56N  CONST_05  C6'  C5'  C4'  C3'    0.00   0.0  0
 56N  CONST_06  C6'  C1'  C2'  C3'    0.00   0.0  0
 56N  CONST_07  C5'  C6'  C1'  O1'  180.00   0.0  0
 56N  CONST_08  C3'  C2'  C1'  O1'  180.00   0.0  0
 56N  CONST_09  H15  C5'  C6'  C1'  180.00   0.0  0
 56N  CONST_10  H13  C3'  C2'  C1'  180.00   0.0  0
 56N  CONST_11  H14  C4'  C3'  C2'  180.00   0.0  0
 56N  CONST_12  H16  C6'  C1'  C2'  180.00   0.0  0
 56N  CONST_13  H12  C2'  C3'  C4'  180.00   0.0  0
 56N  Var_01    C6'  C1'  O1'  C1    24.62  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
 56N  chir_01  C1  O1'  C2  O5  negativ
 56N  chir_02  C2  O2   C1  C3  negativ
 56N  chir_03  C3  O3   C2  C4  positiv
 56N  chir_04  C4  O4   C5  C3  negativ
 56N  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
 56N  plan-1  O1'  0.020
 56N  plan-1  C1'  0.020
 56N  plan-1  C2'  0.020
 56N  plan-1  C3'  0.020
 56N  plan-1  C4'  0.020
 56N  plan-1  C5'  0.020
 56N  plan-1  C6'  0.020
 56N  plan-1  H12  0.020
 56N  plan-1  H13  0.020
 56N  plan-1  H14  0.020
 56N  plan-1  H15  0.020
 56N  plan-1  H16  0.020

