# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 23:57:27 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (3R,4R,5R)-3-(hydroxymethyl)hexahydropyridazine-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
 AZF  AZF  (3R,4R,5R)-3-(hydroxymethyl)hexahydropyridazine-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_AZF
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
 AZF  O4    O  OH1   0  -0.676   0.9043  -2.0244   3.4733
 AZF  C4    C  CH1   0   0.061   0.3343  -1.6223   2.2509
 AZF  C3    C  CH1   0   0.020   1.3680  -1.0002   1.3206
 AZF  O3    O  OH1   0  -0.675   1.8361   0.1824   1.9323
 AZF  C2    C  CH2   0  -0.318   0.7362  -0.7351  -0.0400
 AZF  N     N  NH1   0  -0.493   0.2265  -1.9909  -0.5597
 AZF  C5    C  CH1   0  -0.148  -0.2917  -2.8410   1.5771
 AZF  C6    C  CH2   0  -0.159  -1.4079  -3.4389   2.4250
 AZF  O6    O  OH1   0  -0.667  -2.0075  -4.5610   1.8120
 AZF  N2    N  NH1   0  -0.503  -0.8497  -2.4126   0.3036
 AZF  H4    H  HOH1  0   0.450   1.3473  -1.2609   3.8577
 AZF  HA    H  HCH1  0   0.193  -0.4654  -0.8795   2.4106
 AZF  H3    H  HCH1  0   0.203   2.1835  -1.7260   1.1887
 AZF  H5    H  HCH1  0   0.207   0.5008  -3.5971   1.4378
 AZF  HB    H  HOH1  0   0.457   2.6448   0.4564   1.4893
 AZF  H2C1  H  HCH2  0   0.201  -0.0474   0.0289   0.0707
 AZF  H2C2  H  HCH2  0   0.241   1.4875  -0.3525  -0.7348
 AZF  H     H  HNH1  0   0.365  -0.2098  -1.8003  -1.4541
 AZF  H2    H  HNH1  0   0.357  -1.2439  -3.2341  -0.1401
 AZF  H6C1  H  HCH2  0   0.215  -2.1963  -2.6925   2.5502
 AZF  H6C2  H  HCH2  0   0.218  -1.0234  -3.6823   3.4196
 AZF  H6    H  HOH1  0   0.450  -1.3828  -5.2918   1.8501

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
 AZF  O4  C4    single  1.407  0.020  1.407
 AZF  O4  H4    single  0.850  0.020  0.980
 AZF  C4  C3    single  1.523  0.020  1.523
 AZF  C4  C5    single  1.527  0.020  1.527
 AZF  C4  HA    single  0.970  0.020  1.090
 AZF  C3  O3    single  1.411  0.020  1.411
 AZF  C3  C2    single  1.523  0.020  1.523
 AZF  C3  H3    single  0.970  0.020  1.090
 AZF  O3  HB    single  0.850  0.020  0.980
 AZF  C2  N     single  1.452  0.020  1.452
 AZF  C2  H2C1  single  0.970  0.020  1.090
 AZF  C2  H2C2  single  0.970  0.020  1.090
 AZF  N   N2    single  1.443  0.020  1.443
 AZF  N   H     single  0.860  0.020  1.020
 AZF  C5  C6    single  1.524  0.020  1.524
 AZF  C5  N2    single  1.455  0.020  1.455
 AZF  C5  H5    single  0.970  0.020  1.090
 AZF  C6  O6    single  1.412  0.020  1.412
 AZF  C6  H6C1  single  0.970  0.020  1.090
 AZF  C6  H6C2  single  0.970  0.020  1.090
 AZF  O6  H6    single  0.850  0.020  0.980
 AZF  N2  H2    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
 AZF  H4    O4  C4    107.85  3.000
 AZF  HA    C4  C5    107.71  3.000
 AZF  HA    C4  C3    107.77  3.000
 AZF  C5    C4  C3    109.55  3.000
 AZF  HA    C4  O4    111.12  3.000
 AZF  C5    C4  O4    108.74  3.000
 AZF  C3    C4  O4    111.85  3.000
 AZF  H3    C3  C2    108.38  3.000
 AZF  H3    C3  O3    111.04  3.000
 AZF  C2    C3  O3    112.26  3.000
 AZF  H3    C3  C4    107.88  3.000
 AZF  C2    C3  C4    109.58  3.000
 AZF  O3    C3  C4    107.61  3.000
 AZF  HB    O3  C3    108.54  3.000
 AZF  H2C2  C2  H2C1  108.10  3.000
 AZF  H2C2  C2  N     108.46  3.000
 AZF  H2C1  C2  N     112.76  3.000
 AZF  H2C2  C2  C3    110.11  3.000
 AZF  H2C1  C2  C3    109.05  3.000
 AZF  N     C2  C3    108.35  3.000
 AZF  H     N   N2    105.19  3.000
 AZF  H     N   C2    107.73  3.000
 AZF  N2    N   C2    107.49  3.000
 AZF  H5    C5  N2    111.50  3.000
 AZF  H5    C5  C6    109.10  3.000
 AZF  N2    C5  C6    108.76  3.000
 AZF  H5    C5  C4    107.94  3.000
 AZF  N2    C5  C4    107.97  3.000
 AZF  C6    C5  C4    111.59  3.000
 AZF  H6C2  C6  H6C1  107.55  3.000
 AZF  H6C2  C6  O6    111.54  3.000
 AZF  H6C1  C6  O6    106.63  3.000
 AZF  H6C2  C6  C5    109.62  3.000
 AZF  H6C1  C6  C5    108.91  3.000
 AZF  O6    C6  C5    112.41  3.000
 AZF  H6    O6  C6    108.10  3.000
 AZF  H2    N2  C5    107.08  3.000
 AZF  H2    N2  N     105.38  3.000
 AZF  C5    N2  N     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
 AZF  Var_01  N2  N   C2  C3   65.84  30.0  1
 AZF  Var_02  C5  N2  N   C2  -71.21  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
 AZF  chir_01  C4  O4  C3  C5  negativ
 AZF  chir_02  C3  O3  C4  C2  negativ
 AZF  chir_03  C5  N2  C6  C4  positiv

