# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:54:55 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1[C@@H](O)[C@@H](O)OC[C@]1(C)O
#
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
 GE3  GE3  3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranose  L-saccharide  27  12  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GE3
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
 GE3  C     C  CH2   0  -0.175  -1.1971  -0.4400  -1.4208
 GE3  C1    C  CT    0   0.138  -1.2594  -0.0741   0.0610
 GE3  O11   O  OH1   0  -0.678  -1.7138   1.2614   0.2157
 GE3  C2    C  CH1   0  -0.081   0.1591  -0.1105   0.6623
 GE3  C3    C  CH1   0   0.041   1.1164   0.7070  -0.2082
 GE3  C4    C  CH1   0   0.221   1.0360   0.2810  -1.6783
 GE3  O4    O  OH1   0  -0.667   1.5642  -1.0012  -1.7962
 GE3  O3    O  O2    0  -0.496  -0.2861   0.3623  -2.1419
 GE3  OH    O  OH1   0  -0.666   2.4155   0.5453   0.3014
 GE3  N1    N  NH1   0  -0.604   0.2070   0.3482   2.0397
 GE3  C31   C  CH3   0  -0.527   0.4503  -0.6805   3.0270
 GE3  C41   C  CH3   0  -0.681  -2.1935  -1.0459   0.7734
 GE3  H1    H  HCH2  0   0.237  -2.1775  -0.2799  -1.8782
 GE3  H2A   H  HCH2  0   0.209  -0.9638  -1.5053  -1.5295
 GE3  HOB   H  HOH1  0   0.449  -2.6417   1.3027  -0.0385
 GE3  H2    H  HCH1  0   0.236   0.4891  -1.1557   0.6288
 GE3  H3    H  HCH1  0   0.210   0.8081   1.7600  -0.1648
 GE3  H4    H  HCH1  0   0.225   1.5913   0.9928  -2.3037
 GE3  HO4   H  HOH1  0   0.458   1.6521  -1.2169  -2.7308
 GE3  HOH   H  HOH1  0   0.449   2.9915   1.1890  -0.1220
 GE3  HN1   H  HNH1  0   0.345  -0.6309   0.8654   2.2670
 GE3  H311  H  HCH3  0   0.227   0.4419  -0.2356   4.0228
 GE3  H312  H  HCH3  0   0.193  -0.2746  -1.5065   3.0287
 GE3  H313  H  HCH3  0   0.223   1.4394  -1.1163   2.8772
 GE3  H411  H  HCH3  0   0.237  -3.1898  -1.0239   0.3241
 GE3  H412  H  HCH3  0   0.233  -1.8285  -2.0712   0.7105
 GE3  H413  H  HCH3  0   0.243  -2.3029  -0.7877   1.8272

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
 GE3  C    C1    single  1.528  0.020  1.528
 GE3  C    O3    single  1.412  0.020  1.412
 GE3  C    H1    single  0.970  0.020  1.090
 GE3  C    H2A   single  0.970  0.020  1.090
 GE3  C1   O11   single  1.419  0.020  1.419
 GE3  C1   C2    single  1.541  0.020  1.541
 GE3  C1   C41   single  1.525  0.020  1.525
 GE3  O11  HOB   single  0.850  0.020  0.980
 GE3  C2   C3    single  1.530  0.020  1.530
 GE3  C2   N1    single  1.453  0.020  1.453
 GE3  C2   H2    single  0.970  0.020  1.090
 GE3  C3   C4    single  1.533  0.020  1.533
 GE3  C3   OH    single  1.405  0.020  1.405
 GE3  C3   H3    single  0.970  0.020  1.090
 GE3  C4   O4    single  1.392  0.020  1.392
 GE3  C4   O3    single  1.403  0.020  1.403
 GE3  C4   H4    single  0.970  0.020  1.090
 GE3  O4   HO4   single  0.850  0.020  0.980
 GE3  OH   HOH   single  0.850  0.020  0.980
 GE3  N1   C31   single  1.447  0.020  1.447
 GE3  N1   HN1   single  0.890  0.020  1.040
 GE3  C31  H311  single  0.970  0.020  1.090
 GE3  C31  H312  single  0.970  0.020  1.090
 GE3  C31  H313  single  0.970  0.020  1.090
 GE3  C41  H411  single  0.970  0.020  1.090
 GE3  C41  H412  single  0.970  0.020  1.090
 GE3  C41  H413  single  0.970  0.020  1.090

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
 GE3  H2A   C    H1    106.95  3.000
 GE3  H2A   C    O3    111.36  3.000
 GE3  H1    C    O3    106.36  3.000
 GE3  H2A   C    C1    109.74  3.000
 GE3  H1    C    C1    109.52  3.000
 GE3  O3    C    C1    112.68  3.000
 GE3  C41   C1   C2    111.51  3.000
 GE3  C41   C1   O11   110.65  3.000
 GE3  C2    C1   O11   105.93  3.000
 GE3  C41   C1   C     109.00  3.000
 GE3  C2    C1   C     109.59  3.000
 GE3  O11   C1   C     110.13  3.000
 GE3  HOB   O11  C1    108.67  3.000
 GE3  H2    C2   N1    108.67  3.000
 GE3  H2    C2   C3    107.67  3.000
 GE3  N1    C2   C3    110.49  3.000
 GE3  H2    C2   C1    106.71  3.000
 GE3  N1    C2   C1    113.13  3.000
 GE3  C3    C2   C1    109.95  3.000
 GE3  H3    C3   OH    110.84  3.000
 GE3  H3    C3   C4    106.84  3.000
 GE3  OH    C3   C4    111.38  3.000
 GE3  H3    C3   C2    108.31  3.000
 GE3  OH    C3   C2    108.09  3.000
 GE3  C4    C3   C2    111.37  3.000
 GE3  H4    C4   O3    104.52  3.000
 GE3  H4    C4   O4    110.92  3.000
 GE3  O3    C4   O4    112.51  3.000
 GE3  H4    C4   C3    109.85  3.000
 GE3  O3    C4   C3    110.50  3.000
 GE3  O4    C4   C3    108.50  3.000
 GE3  HO4   O4   C4    108.85  3.000
 GE3  C4    O3   C     113.97  3.000
 GE3  HOH   OH   C3    108.48  3.000
 GE3  HN1   N1   C31   110.48  3.000
 GE3  HN1   N1   C2    110.34  3.000
 GE3  C31   N1   C2    115.35  3.000
 GE3  H313  C31  H312  107.34  3.000
 GE3  H313  C31  H311  107.17  3.000
 GE3  H312  C31  H311  107.47  3.000
 GE3  H313  C31  N1    110.05  3.000
 GE3  H312  C31  N1    115.13  3.000
 GE3  H311  C31  N1    109.38  3.000
 GE3  H413  C41  H412  108.18  3.000
 GE3  H413  C41  H411  107.52  3.000
 GE3  H412  C41  H411  107.48  3.000
 GE3  H413  C41  C1    111.23  3.000
 GE3  H412  C41  C1    111.56  3.000
 GE3  H411  C41  C1    110.71  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
 GE3  Var_01  H1    C    O3  C4   179.75  30.0  1
 GE3  Var_02  H311  C31  N1  C2  -178.60  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
 GE3  chir_01  C1  C   C2  C41  positiv
 GE3  chir_02  C2  N1  C3  C1   positiv
 GE3  chir_03  C3  OH  C2  C4   positiv
 GE3  chir_04  C4  O3  O4  C3   positiv

