# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 03:52:24 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: 1-deoxy-1-(methylamino)-D-allitol
#   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
 XPJ  XPJ  "1-deoxy-1-(methylamino)-D-allitol"
  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_XPJ
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
 XPJ  C1   C  CH1   0   0.008  133.8240  133.4033  108.8236
 XPJ  C2   C  CH1   0   0.027  133.8376  132.3896  106.4704
 XPJ  C3   C  CH1   0  -0.008  133.2052  133.3026  110.2296
 XPJ  C4   C  CH2   0  -0.315  134.0028  133.7157  105.7251
 XPJ  C5   C  CH2   0  -0.182  133.8645  134.2530  111.2290
 XPJ  C6   C  CH3   0  -0.523  136.1044  133.2709  104.5657
 XPJ  N    N  NH1   0  -0.587  134.7102  133.6494  104.4612
 XPJ  C    C  CH1   0   0.006  133.0790  132.5300  107.7971
 XPJ  O    O  OH1   0  -0.690  131.7979  133.0393  107.5178
 XPJ  O1   O  OH1   0  -0.692  135.1640  132.9764  108.8603
 XPJ  O2   O  OH1   0  -0.676  133.1491  131.5121  105.5982
 XPJ  O3   O  OH1   0  -0.679  131.8319  133.6418  110.1418
 XPJ  O4   O  OH1   0  -0.671  135.2240  133.8908  111.4016
 XPJ  H1   H  HCH1  0   0.198  133.7483  134.4550  108.4982
 XPJ  H2   H  HCH1  0   0.215  134.8294  131.9849  106.7002
 XPJ  H3   H  HCH1  0   0.227  133.3269  132.2664  110.5755
 XPJ  H4   H  HCH2  0   0.225  134.5337  134.4221  106.3697
 XPJ  H5   H  HCH2  0   0.228  133.0167  134.1484  105.5390
 XPJ  H6   H  HCH2  0   0.215  133.7675  135.2790  110.8545
 XPJ  H7   H  HCH2  0   0.221  133.3227  134.1970  112.1816
 XPJ  H8   H  HCH3  0   0.228  136.5616  133.2896  103.5759
 XPJ  H9   H  HCH3  0   0.217  136.6359  133.9980  105.1836
 XPJ  H10  H  HCH3  0   0.195  136.2940  132.2783  104.9947
 XPJ  H11  H  HNH1  0   0.339  134.2317  133.0067  103.8439
 XPJ  H13  H  HCH1  0   0.192  133.0093  131.5147  108.2306
 XPJ  H14  H  HOH1  0   0.448  131.3902  133.2394  108.3721
 XPJ  H15  H  HOH1  0   0.450  135.5661  133.3382  109.6654
 XPJ  H16  H  HOH1  0   0.445  133.2516  130.6141  105.9270
 XPJ  H17  H  HOH1  0   0.469  131.3706  133.2892  110.9099
 XPJ  H18  H  HOH1  0   0.470  135.6910  134.6223  111.8171

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
 XPJ  N   C4   single  1.450  0.020  1.450
 XPJ  N   C6   single  1.448  0.020  1.448
 XPJ  O2  C2   single  1.416  0.020  1.416
 XPJ  C4  C2   single  1.530  0.020  1.530
 XPJ  C2  C    single  1.535  0.020  1.535
 XPJ  O   C    single  1.407  0.020  1.407
 XPJ  C   C1   single  1.540  0.020  1.540
 XPJ  O1  C1   single  1.407  0.020  1.407
 XPJ  C1  C3   single  1.539  0.020  1.539
 XPJ  C3  O3   single  1.417  0.020  1.417
 XPJ  C3  C5   single  1.529  0.020  1.529
 XPJ  C5  O4   single  1.418  0.020  1.418
 XPJ  C1  H1   single  0.970  0.020  1.090
 XPJ  C2  H2   single  0.970  0.020  1.090
 XPJ  C3  H3   single  0.970  0.020  1.090
 XPJ  C4  H4   single  0.970  0.020  1.090
 XPJ  C4  H5   single  0.970  0.020  1.090
 XPJ  C5  H6   single  0.970  0.020  1.090
 XPJ  C5  H7   single  0.970  0.020  1.090
 XPJ  C6  H8   single  0.970  0.020  1.090
 XPJ  C6  H9   single  0.970  0.020  1.090
 XPJ  C6  H10  single  0.970  0.020  1.090
 XPJ  N   H11  single  0.890  0.020  1.040
 XPJ  C   H13  single  0.970  0.020  1.090
 XPJ  O   H14  single  0.850  0.020  0.980
 XPJ  O1  H15  single  0.850  0.020  0.980
 XPJ  O2  H16  single  0.850  0.020  0.980
 XPJ  O3  H17  single  0.850  0.020  0.980
 XPJ  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
 XPJ  H1   C1  O1  111.24  3.000
 XPJ  H1   C1  C   108.10  3.000
 XPJ  O1   C1  C   107.83  3.000
 XPJ  H1   C1  C3  107.70  3.000
 XPJ  O1   C1  C3  109.83  3.000
 XPJ  C    C1  C3  112.17  3.000
 XPJ  H2   C2  O2  109.91  3.000
 XPJ  H2   C2  C   107.45  3.000
 XPJ  O2   C2  C   110.42  3.000
 XPJ  H2   C2  C4  108.94  3.000
 XPJ  C    C2  C4  113.27  3.000
 XPJ  O2   C2  C4  106.84  3.000
 XPJ  H3   C3  O3  110.63  3.000
 XPJ  H3   C3  C5  109.42  3.000
 XPJ  O3   C3  C5  108.03  3.000
 XPJ  H3   C3  C1  107.73  3.000
 XPJ  C5   C3  C1  112.53  3.000
 XPJ  O3   C3  C1  108.50  3.000
 XPJ  H5   C4  H4  106.42  3.000
 XPJ  H5   C4  N   108.05  3.000
 XPJ  H4   C4  N   107.85  3.000
 XPJ  H5   C4  C2  109.18  3.000
 XPJ  H4   C4  C2  108.97  3.000
 XPJ  N    C4  C2  115.95  3.000
 XPJ  H7   C5  H6  107.50  3.000
 XPJ  H7   C5  O4  110.78  3.000
 XPJ  H6   C5  O4  111.44  3.000
 XPJ  H7   C5  C3  108.84  3.000
 XPJ  H6   C5  C3  108.68  3.000
 XPJ  O4   C5  C3  109.53  3.000
 XPJ  H10  C6  H9  107.26  3.000
 XPJ  H10  C6  H8  107.32  3.000
 XPJ  H9   C6  H8  107.35  3.000
 XPJ  H10  C6  N   115.51  3.000
 XPJ  H9   C6  N   109.59  3.000
 XPJ  H8   C6  N   109.48  3.000
 XPJ  H11  N   C6  109.47  3.000
 XPJ  H11  N   C4  109.29  3.000
 XPJ  C6   N   C4  114.75  3.000
 XPJ  H13  C   O   110.65  3.000
 XPJ  H13  C   C2  106.61  3.000
 XPJ  O    C   C2  108.16  3.000
 XPJ  H13  C   C1  106.84  3.000
 XPJ  O    C   C1  111.57  3.000
 XPJ  C2   C   C1  112.89  3.000
 XPJ  H14  O   C   106.46  3.000
 XPJ  H15  O1  C1  107.66  3.000
 XPJ  H16  O2  C2  108.43  3.000
 XPJ  H17  O3  C3  109.10  3.000
 XPJ  H18  O4  C5  108.89  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
 XPJ  Var_01  C6   N   C4  C2   -65.33  30.0  1
 XPJ  Var_02  H11  N   C4  C2    58.05  30.0  1
 XPJ  Var_03  H8   C6  N   C4  -177.58  30.0  3
 XPJ  Var_04  H9   C6  N   C4   -60.09  30.0  3
 XPJ  Var_05  H10  C6  N   C4    61.16  30.0  3
 XPJ  Var_06  H4   C4  N   C6    57.12  30.0  3
 XPJ  Var_07  H5   C4  N   C6   171.79  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
 XPJ  chir_01  C1  C   O1  C3  positiv
 XPJ  chir_02  C2  O2  C   C4  positiv
 XPJ  chir_03  C3  O3  C1  C5  negativ
 XPJ  chir_04  C   O   C1  C2  positiv

