# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:48:51 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1CC[C@@H](N)[C@@H](O)O1
#
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
 GE1  GE1  2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranose  D-saccharide  24  10  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GE1
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
 GE1  C5    C  CH1   0   0.035   9.4729   1.8263  -2.7501
 GE1  O     O  O2    0  -0.503   8.1623   1.7980  -3.3058
 GE1  C1    C  CH1   0   0.299   7.1838   2.5047  -2.6141
 GE1  O1    O  OH1   0  -0.680   7.4291   3.8779  -2.6934
 GE1  C2    C  CH1   0  -0.157   7.0823   2.0734  -1.1414
 GE1  N2    N  NH2   0  -0.812   6.1929   3.0126  -0.4735
 GE1  C3    C  CH2   0  -0.453   8.4572   2.0956  -0.4864
 GE1  C4    C  CH2   0  -0.456   9.4572   1.3085  -1.3218
 GE1  C6    C  CH2   0  -0.307  10.3604   0.9912  -3.6627
 GE1  N1    N  NH2   0  -0.788  10.4921   1.4563  -5.0316
 GE1  H5    H  HCH1  0   0.200   9.8525   2.8581  -2.7466
 GE1  H1    H  HCH1  0   0.202   6.2454   2.2531  -3.1309
 GE1  HO1   H  HOH1  0   0.441   7.0513   4.2460  -1.8764
 GE1  H2    H  HCH1  0   0.222   6.7101   1.0396  -1.1269
 GE1  HN21  H  HNH2  0   0.356   5.2282   2.8257  -0.7201
 GE1  HN22  H  HNH2  0   0.361   6.2559   2.9040   0.5310
 GE1  H31   H  HCH2  0   0.223   8.7951   3.1312  -0.3795
 GE1  H32   H  HCH2  0   0.243   8.3873   1.6834   0.5235
 GE1  H41   H  HCH2  0   0.238  10.4596   1.3916  -0.8961
 GE1  H42   H  HCH2  0   0.221   9.1965   0.2446  -1.3187
 GE1  H61   H  HCH2  0   0.215   9.9865  -0.0376  -3.6753
 GE1  H62   H  HCH2  0   0.223  11.3558   0.9489  -3.2126
 GE1  HN11  H  HNH2  0   0.338  10.8812   2.3914  -5.0355
 GE1  HN12  H  HNH2  0   0.339   9.5748   1.5375  -5.4517

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
 GE1  C5  O     single  1.424  0.020  1.424
 GE1  C5  C4    single  1.519  0.020  1.519
 GE1  C5  C6    single  1.522  0.020  1.522
 GE1  C5  H5    single  0.970  0.020  1.090
 GE1  O   C1    single  1.391  0.020  1.391
 GE1  C1  O1    single  1.397  0.020  1.397
 GE1  C1  C2    single  1.538  0.020  1.538
 GE1  C1  H1    single  0.970  0.020  1.090
 GE1  O1  HO1   single  0.850  0.020  0.980
 GE1  C2  N2    single  1.456  0.020  1.456
 GE1  C2  C3    single  1.523  0.020  1.523
 GE1  C2  H2    single  0.970  0.020  1.090
 GE1  N2  HN21  single  0.890  0.020  1.040
 GE1  N2  HN22  single  0.890  0.020  1.040
 GE1  C3  C4    single  1.522  0.020  1.522
 GE1  C3  H31   single  0.970  0.020  1.090
 GE1  C3  H32   single  0.970  0.020  1.090
 GE1  C4  H41   single  0.970  0.020  1.090
 GE1  C4  H42   single  0.970  0.020  1.090
 GE1  C6  N1    single  1.452  0.020  1.452
 GE1  C6  H61   single  0.970  0.020  1.090
 GE1  C6  H62   single  0.970  0.020  1.090
 GE1  N1  HN11  single  0.890  0.020  1.040
 GE1  N1  HN12  single  0.890  0.020  1.040

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
 GE1  H5    C5  C6    108.39  3.000
 GE1  H5    C5  C4    108.69  3.000
 GE1  C6    C5  C4    112.50  3.000
 GE1  H5    C5  O     109.74  3.000
 GE1  C6    C5  O     106.96  3.000
 GE1  C4    C5  O     110.52  3.000
 GE1  C1    O   C5    116.32  3.000
 GE1  H1    C1  C2    109.23  3.000
 GE1  H1    C1  O1    110.35  3.000
 GE1  C2    C1  O1    109.97  3.000
 GE1  H1    C1  O     104.49  3.000
 GE1  C2    C1  O     112.34  3.000
 GE1  O1    C1  O     110.34  3.000
 GE1  HO1   O1  C1    104.84  3.000
 GE1  H2    C2  C3    108.29  3.000
 GE1  H2    C2  N2    113.20  3.000
 GE1  C3    C2  N2    110.17  3.000
 GE1  H2    C2  C1    107.38  3.000
 GE1  C3    C2  C1    110.38  3.000
 GE1  N2    C2  C1    107.38  3.000
 GE1  HN22  N2  HN21  106.32  3.000
 GE1  HN22  N2  C2    110.37  3.000
 GE1  HN21  N2  C2    110.56  3.000
 GE1  H32   C3  H31   106.63  3.000
 GE1  H32   C3  C4    110.74  3.000
 GE1  H31   C3  C4    109.88  3.000
 GE1  H32   C3  C2    109.52  3.000
 GE1  H31   C3  C2    109.54  3.000
 GE1  C4    C3  C2    110.46  3.000
 GE1  H42   C4  H41   106.93  3.000
 GE1  H42   C4  C3    110.13  3.000
 GE1  H41   C4  C3    110.47  3.000
 GE1  H42   C4  C5    109.64  3.000
 GE1  H41   C4  C5    109.33  3.000
 GE1  C3    C4  C5    110.27  3.000
 GE1  H62   C6  H61   106.22  3.000
 GE1  H62   C6  N1    108.55  3.000
 GE1  H61   C6  N1    108.74  3.000
 GE1  H62   C6  C5    107.77  3.000
 GE1  H61   C6  C5    108.86  3.000
 GE1  N1    C6  C5    116.26  3.000
 GE1  HN12  N1  HN11  105.82  3.000
 GE1  HN12  N1  C6    109.56  3.000
 GE1  HN11  N1  C6    109.52  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
 GE1  Var_01  C2    C3  C4  C5  54.45  30.0  1
 GE1  Var_02  HN11  N1  C6  C5  59.58  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
 GE1  chir_01  C5  O   C4  C6  negativ
 GE1  chir_02  C1  O   O1  C2  positiv
 GE1  chir_03  C2  N2  C3  C1  positiv

