# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 14:25:06 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (3R,4S,5R)-3-(hydroxymethyl)-1,2-diazinane-4,5-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1NNC[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
 AGK  AGK  (3R,4S,5R)-3-(hydroxymethyl)-1,2-diazinane-4,5-diol  ligand  22  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AGK
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
 AGK  O2    O  OH1   0  -0.679   0.3770   1.4466  -1.0419
 AGK  C4    C  CH1   0   0.005   0.3308   0.9134   0.2633
 AGK  C3    C  CH1   0   0.037   1.5838   0.0960   0.5721
 AGK  O1    O  OH1   0  -0.676   2.6956   0.9260   0.3202
 AGK  C2    C  CH2   0  -0.335   1.6051  -1.1836  -0.2592
 AGK  N1    N  NH1   0  -0.487   0.3712  -1.9028   0.0070
 AGK  C5    C  CH1   0  -0.149  -0.9046   0.0112   0.3707
 AGK  C6    C  CH2   0  -0.139  -2.1711   0.7656   0.0053
 AGK  O     O  OH1   0  -0.671  -3.2899  -0.0016   0.3873
 AGK  N     N  NH1   0  -0.467  -0.7732  -1.1980  -0.4243
 AGK  H2    H  HOH1  0   0.449   1.2467   1.8410  -1.1697
 AGK  H4    H  HCH1  0   0.218   0.2454   1.7189   1.0093
 AGK  H3    H  HCH1  0   0.206   1.5371  -0.1952   1.6313
 AGK  H5    H  HCH1  0   0.241  -0.9833  -0.2966   1.4195
 AGK  H1    H  HOH1  0   0.456   3.5006   0.4046   0.4003
 AGK  H21C  H  HCH2  0   0.205   1.7453  -0.9422  -1.3238
 AGK  H22C  H  HCH2  0   0.240   2.4447  -1.8142   0.0464
 AGK  HA    H  HNH1  0   0.364   0.3721  -2.8054  -0.4466
 AGK  H     H  HNH1  0   0.329  -0.6686  -0.9251  -1.4030
 AGK  H61C  H  HCH2  0   0.200  -2.1527   1.7346   0.5218
 AGK  H62C  H  HCH2  0   0.197  -2.1833   0.9801  -1.0706
 AGK  HB    H  HOH1  0   0.453  -4.0798   0.4916   0.1494

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
 AGK  O2  C4    single  1.411  0.020  1.411
 AGK  C4  C3    single  1.528  0.020  1.528
 AGK  C4  C5    single  1.534  0.020  1.534
 AGK  C3  O1    single  1.410  0.020  1.410
 AGK  C3  C2    single  1.526  0.020  1.526
 AGK  C2  N1    single  1.453  0.020  1.453
 AGK  N1  N     single  1.411  0.020  1.411
 AGK  C5  C6    single  1.519  0.020  1.519
 AGK  C5  N     single  1.453  0.020  1.453
 AGK  C6  O     single  1.409  0.020  1.409
 AGK  O2  H2    single  0.850  0.020  0.980
 AGK  C4  H4    single  0.970  0.020  1.090
 AGK  C3  H3    single  0.970  0.020  1.090
 AGK  C5  H5    single  0.970  0.020  1.090
 AGK  O1  H1    single  0.850  0.020  0.980
 AGK  C2  H21C  single  0.970  0.020  1.090
 AGK  C2  H22C  single  0.970  0.020  1.090
 AGK  N1  HA    single  0.890  0.020  1.040
 AGK  N   H     single  0.860  0.020  1.020
 AGK  C6  H61C  single  0.970  0.020  1.090
 AGK  C6  H62C  single  0.970  0.020  1.090
 AGK  O   HB    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
 AGK  H2    O2  C4    107.88  3.000
 AGK  H4    C4  C5    108.69  3.000
 AGK  H4    C4  C3    108.55  3.000
 AGK  C5    C4  C3    109.38  3.000
 AGK  H4    C4  O2    110.66  3.000
 AGK  C5    C4  O2    108.27  3.000
 AGK  C3    C4  O2    111.25  3.000
 AGK  H3    C3  C2    107.66  3.000
 AGK  H3    C3  O1    111.19  3.000
 AGK  C2    C3  O1    112.66  3.000
 AGK  H3    C3  C4    107.55  3.000
 AGK  C2    C3  C4    110.48  3.000
 AGK  O1    C3  C4    107.20  3.000
 AGK  H1    O1  C3    109.00  3.000
 AGK  H22C  C2  H21C  107.40  3.000
 AGK  H22C  C2  N1    108.39  3.000
 AGK  H21C  C2  N1    113.20  3.000
 AGK  H22C  C2  C3    110.00  3.000
 AGK  H21C  C2  C3    110.17  3.000
 AGK  N1    C2  C3    107.67  3.000
 AGK  HA    N1  N     108.05  3.000
 AGK  HA    N1  C2    111.06  3.000
 AGK  N     N1  C2    112.67  3.000
 AGK  H5    C5  N     107.24  3.000
 AGK  H5    C5  C6    108.05  3.000
 AGK  N     C5  C6    110.92  3.000
 AGK  H5    C5  C4    106.87  3.000
 AGK  N     C5  C4    112.23  3.000
 AGK  C6    C5  C4    111.27  3.000
 AGK  H62C  C6  H61C  106.79  3.000
 AGK  H62C  C6  O     111.31  3.000
 AGK  H61C  C6  O     111.48  3.000
 AGK  H62C  C6  C5    110.02  3.000
 AGK  H61C  C6  C5    108.13  3.000
 AGK  O     C6  C5    109.05  3.000
 AGK  HB    O   C6    107.82  3.000
 AGK  H     N   C5    108.13  3.000
 AGK  H     N   N1    110.07  3.000
 AGK  C5    N   N1    108.77  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
 AGK  Var_01  N   N1  C2  C3   64.36  30.0  1
 AGK  Var_02  C5  N   N1  C2  -65.75  30.0  1

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
 AGK  chir_01  C4  O2  C3  C5  positiv
 AGK  chir_02  C3  O1  C4  C2  negativ
 AGK  chir_03  C5  N   C6  C4  positiv

