# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 04:32:22 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: 6-deoxy-6-(methylamino)-D-galactitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC[C@@H](O)[C@H](O)[C@H](O)[C@@H](O)CO
#
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
 XPS  XPS  "6-deoxy-6-(methylamino)-D-galactitol"
  ligand  30  13  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XPS
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
 XPS  C1   C  CH1   0  -0.011  133.0683  131.8073  104.4897
 XPS  C2   C  CH1   0   0.002  135.2689  132.6210  103.5084
 XPS  C3   C  CH1   0  -0.049  131.8291  132.1208  105.3585
 XPS  C4   C  CH2   0  -0.303  136.3374  133.7148  103.5493
 XPS  C5   C  CH2   0  -0.169  131.1077  133.4314  105.0721
 XPS  C6   C  CH3   0  -0.524  137.1323  133.5671  101.2452
 XPS  N    N  NH1   0  -0.585  137.4627  133.5239  102.6549
 XPS  C    C  CH1   0   0.036  134.0778  132.9592  104.4116
 XPS  O    O  OH1   0  -0.698  134.5510  133.2959  105.6963
 XPS  O1   O  OH1   0  -0.663  132.7163  131.4620  103.1740
 XPS  O2   O  OH1   0  -0.677  135.8963  131.4040  103.8658
 XPS  O3   O  OH1   0  -0.668  132.2004  132.2008  106.7286
 XPS  O4   O  OH1   0  -0.661  130.6180  133.4263  103.7552
 XPS  H1   H  HCH1  0   0.211  133.5733  130.9608  104.9853
 XPS  H2   H  HCH1  0   0.217  134.8789  132.5643  102.4855
 XPS  H3   H  HCH1  0   0.238  131.1133  131.2980  105.2116
 XPS  H4   H  HCH2  0   0.230  136.7284  133.8017  104.5656
 XPS  H5   H  HCH2  0   0.217  135.8658  134.6741  103.3127
 XPS  H6   H  HCH2  0   0.199  131.7884  134.2753  105.2520
 XPS  H7   H  HCH2  0   0.217  130.2954  133.5242  105.8049
 XPS  H8   H  HCH3  0   0.229  138.0405  133.4420  100.6547
 XPS  H9   H  HCH3  0   0.196  136.4140  132.8102  100.9043
 XPS  H10  H  HCH3  0   0.218  136.7149  134.5452  100.9967
 XPS  H11  H  HNH1  0   0.338  137.9060  132.6403  102.8696
 XPS  H13  H  HCH1  0   0.198  133.5766  133.8228  103.9432
 XPS  H14  H  HOH1  0   0.442  133.8462  133.1314  106.3380
 XPS  H15  H  HOH1  0   0.452  132.1225  130.7054  103.2011
 XPS  H16  H  HOH1  0   0.450  135.4189  130.6816  103.4485
 XPS  H17  H  HOH1  0   0.465  132.4751  131.3268  107.0274
 XPS  H18  H  HOH1  0   0.454  130.1275  134.2420  103.6217

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
 XPS  C6  N    single  1.449  0.020  1.449
 XPS  N   C4   single  1.450  0.020  1.450
 XPS  O4  C5   single  1.405  0.020  1.405
 XPS  C4  C2   single  1.530  0.020  1.530
 XPS  O1  C1   single  1.405  0.020  1.405
 XPS  C2  O2   single  1.415  0.020  1.415
 XPS  C2  C    single  1.533  0.020  1.533
 XPS  C5  C3   single  1.523  0.020  1.523
 XPS  C   C1   single  1.534  0.020  1.534
 XPS  C   O    single  1.410  0.020  1.410
 XPS  C1  C3   single  1.546  0.020  1.546
 XPS  C3  O3   single  1.422  0.020  1.422
 XPS  C1  H1   single  0.970  0.020  1.090
 XPS  C2  H2   single  0.970  0.020  1.090
 XPS  C3  H3   single  0.970  0.020  1.090
 XPS  C4  H4   single  0.970  0.020  1.090
 XPS  C4  H5   single  0.970  0.020  1.090
 XPS  C5  H6   single  0.970  0.020  1.090
 XPS  C5  H7   single  0.970  0.020  1.090
 XPS  C6  H8   single  0.970  0.020  1.090
 XPS  C6  H9   single  0.970  0.020  1.090
 XPS  C6  H10  single  0.970  0.020  1.090
 XPS  N   H11  single  0.890  0.020  1.040
 XPS  C   H13  single  0.970  0.020  1.090
 XPS  O   H14  single  0.850  0.020  0.980
 XPS  O1  H15  single  0.850  0.020  0.980
 XPS  O2  H16  single  0.850  0.020  0.980
 XPS  O3  H17  single  0.850  0.020  0.980
 XPS  O4  H18  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
 XPS  H1   C1  O1  110.29  3.000
 XPS  H1   C1  C   107.33  3.000
 XPS  O1   C1  C   107.56  3.000
 XPS  H1   C1  C3  105.67  3.000
 XPS  C    C1  C3  113.83  3.000
 XPS  O1   C1  C3  112.05  3.000
 XPS  H2   C2  O2  110.42  3.000
 XPS  H2   C2  C   106.55  3.000
 XPS  O2   C2  C   112.68  3.000
 XPS  H2   C2  C4  108.09  3.000
 XPS  C    C2  C4  111.67  3.000
 XPS  O2   C2  C4  107.37  3.000
 XPS  H3   C3  O3  109.91  3.000
 XPS  H3   C3  C5  108.07  3.000
 XPS  O3   C3  C5  104.86  3.000
 XPS  H3   C3  C1  107.14  3.000
 XPS  O3   C3  C1  110.11  3.000
 XPS  C5   C3  C1  116.65  3.000
 XPS  H5   C4  H4  106.59  3.000
 XPS  H5   C4  N   108.44  3.000
 XPS  H4   C4  N   107.85  3.000
 XPS  H5   C4  C2  108.66  3.000
 XPS  H4   C4  C2  109.38  3.000
 XPS  N    C4  C2  115.56  3.000
 XPS  H7   C5  H6  106.50  3.000
 XPS  H7   C5  O4  111.59  3.000
 XPS  H6   C5  O4  111.84  3.000
 XPS  H7   C5  C3  107.32  3.000
 XPS  H6   C5  C3  109.66  3.000
 XPS  O4   C5  C3  109.77  3.000
 XPS  H10  C6  H9  107.26  3.000
 XPS  H10  C6  H8  107.33  3.000
 XPS  H9   C6  H8  107.31  3.000
 XPS  H10  C6  N   109.60  3.000
 XPS  H9   C6  N   115.52  3.000
 XPS  H8   C6  N   109.49  3.000
 XPS  H11  N   C6  109.43  3.000
 XPS  H11  N   C4  108.91  3.000
 XPS  C6   N   C4  114.79  3.000
 XPS  H13  C   O   110.64  3.000
 XPS  H13  C   C2  106.01  3.000
 XPS  O    C   C2  109.20  3.000
 XPS  H13  C   C1  108.10  3.000
 XPS  O    C   C1  110.72  3.000
 XPS  C2   C   C1  112.08  3.000
 XPS  H14  O   C   108.62  3.000
 XPS  H15  O1  C1  108.75  3.000
 XPS  H16  O2  C2  108.45  3.000
 XPS  H17  O3  C3  108.80  3.000
 XPS  H18  O4  C5  107.76  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
 XPS  Var_01  C6   N   C4  C2    65.09  30.0  1
 XPS  Var_02  H11  N   C4  C2   -57.97  30.0  1
 XPS  Var_03  H8   C6  N   C4   178.47  30.0  3
 XPS  Var_04  H9   C6  N   C4   -60.28  30.0  3
 XPS  Var_05  H10  C6  N   C4    60.99  30.0  3
 XPS  Var_06  H4   C4  N   C6  -172.20  30.0  3
 XPS  Var_07  H5   C4  N   C6   -57.13  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
 XPS  chir_01  C1  O1  C   C3  negativ
 XPS  chir_02  C2  O2  C   C4  negativ
 XPS  chir_03  C3  O3  C5  C1  negativ
 XPS  chir_04  C   O   C1  C2  positiv

