# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 08:01:00 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1S,2S,3R,5S)-3,5-diaminocyclohexane-1,2-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1C[C@@H](N)[C@H](O)[C@@H](O)C1
#
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
 PA2  PA2  (1S,2S,3R,5S)-3,5-diaminocyclohexane-1,2-diol  ligand  24  10  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PA2
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
 PA2  C1    C  CH1   0  -0.119  -1.2951  -0.2520  -0.4511
 PA2  N1    N  NH2   0  -0.784  -2.4874   0.2062  -1.1488
 PA2  C2    C  CH1   0   0.075  -0.0427   0.2631  -1.1536
 PA2  O2    O  OH1   0  -0.675  -0.0631  -0.1550  -2.4973
 PA2  C3    C  CH1   0   0.025   1.2115  -0.2401  -0.4451
 PA2  O3    O  OH1   0  -0.683   2.3204   0.2782  -1.1577
 PA2  C4    C  CH2   0  -0.482   1.2250   0.1722   1.0191
 PA2  C5    C  CH1   0  -0.093  -0.0147  -0.3375   1.7545
 PA2  N5    N  NH2   0  -0.790  -0.0806   0.0425   3.1585
 PA2  C6    C  CH2   0  -0.442  -1.2694   0.1338   1.0302
 PA2  H1    H  HCH1  0   0.219  -1.2849  -1.3474  -0.5206
 PA2  HN11  H  HNH2  0   0.344  -3.3013  -0.1962  -0.6996
 PA2  HN12  H  HNH2  0   0.333  -2.5810   1.2091  -1.0265
 PA2  H2    H  HCH1  0   0.184  -0.0453   1.3667  -1.0871
 PA2  HO2   H  HOH1  0   0.442   0.7949   0.0649  -2.8761
 PA2  H3    H  HCH1  0   0.201   1.2073  -1.3399  -0.5034
 PA2  HO3   H  HOH1  0   0.455   3.1037  -0.2186  -0.9040
 PA2  H41   H  HCH2  0   0.216   1.2672   1.2658   1.0927
 PA2  H42   H  HCH2  0   0.235   2.1290  -0.2152   1.5006
 PA2  H5    H  HCH1  0   0.218  -0.0002  -1.4338   1.7211
 PA2  HN51  H  HNH2  0   0.343   0.7448  -0.2962   3.6389
 PA2  HN52  H  HNH2  0   0.334  -0.0381   1.0535   3.2316
 PA2  H61   H  HCH2  0   0.236  -2.1541  -0.2797   1.5223
 PA2  H62   H  HCH2  0   0.210  -1.3464   1.2261   1.1144

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
 PA2  C1  N1    single  1.455  0.020  1.455
 PA2  C1  C2    single  1.526  0.020  1.526
 PA2  C1  C6    single  1.531  0.020  1.531
 PA2  C1  H1    single  0.970  0.020  1.090
 PA2  N1  HN11  single  0.890  0.020  1.040
 PA2  N1  HN12  single  0.890  0.020  1.040
 PA2  C2  O2    single  1.407  0.020  1.407
 PA2  C2  C3    single  1.526  0.020  1.526
 PA2  C2  H2    single  0.970  0.020  1.090
 PA2  O2  HO2   single  0.850  0.020  0.980
 PA2  C3  O3    single  1.416  0.020  1.416
 PA2  C3  C4    single  1.521  0.020  1.521
 PA2  C3  H3    single  0.970  0.020  1.090
 PA2  O3  HO3   single  0.850  0.020  0.980
 PA2  C4  C5    single  1.529  0.020  1.529
 PA2  C4  H41   single  0.970  0.020  1.090
 PA2  C4  H42   single  0.970  0.020  1.090
 PA2  C5  N5    single  1.456  0.020  1.456
 PA2  C5  C6    single  1.524  0.020  1.524
 PA2  C5  H5    single  0.970  0.020  1.090
 PA2  N5  HN51  single  0.890  0.020  1.040
 PA2  N5  HN52  single  0.890  0.020  1.040
 PA2  C6  H61   single  0.970  0.020  1.090
 PA2  C6  H62   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
 PA2  H1    C1  C6    108.22  3.000
 PA2  H1    C1  C2    107.47  3.000
 PA2  C6    C1  C2    110.29  3.000
 PA2  H1    C1  N1    106.94  3.000
 PA2  C6    C1  N1    113.47  3.000
 PA2  C2    C1  N1    110.21  3.000
 PA2  HN12  N1  HN11  105.37  3.000
 PA2  HN12  N1  C1    109.20  3.000
 PA2  HN11  N1  C1    108.69  3.000
 PA2  H2    C2  C3    107.65  3.000
 PA2  H2    C2  O2    110.73  3.000
 PA2  C3    C2  O2    110.93  3.000
 PA2  H2    C2  C1    107.90  3.000
 PA2  C3    C2  C1    110.46  3.000
 PA2  O2    C2  C1    109.12  3.000
 PA2  HO2   O2  C2    107.14  3.000
 PA2  H3    C3  C4    108.76  3.000
 PA2  H3    C3  O3    109.99  3.000
 PA2  C4    C3  O3    112.22  3.000
 PA2  H3    C3  C2    107.55  3.000
 PA2  C4    C3  C2    111.40  3.000
 PA2  O3    C3  C2    106.81  3.000
 PA2  HO3   O3  C3    108.42  3.000
 PA2  H42   C4  H41   106.94  3.000
 PA2  H42   C4  C5    109.88  3.000
 PA2  H41   C4  C5    109.35  3.000
 PA2  H42   C4  C3    109.55  3.000
 PA2  H41   C4  C3    109.58  3.000
 PA2  C5    C4  C3    111.43  3.000
 PA2  H5    C5  C6    107.79  3.000
 PA2  H5    C5  N5    106.91  3.000
 PA2  C6    C5  N5    109.90  3.000
 PA2  H5    C5  C4    107.93  3.000
 PA2  C6    C5  C4    109.63  3.000
 PA2  N5    C5  C4    114.43  3.000
 PA2  HN52  N5  HN51  105.36  3.000
 PA2  HN52  N5  C5    109.13  3.000
 PA2  HN51  N5  C5    109.45  3.000
 PA2  H62   C6  H61   106.55  3.000
 PA2  H62   C6  C5    109.20  3.000
 PA2  H61   C6  C5    109.60  3.000
 PA2  H62   C6  C1    108.88  3.000
 PA2  H61   C6  C1    109.06  3.000
 PA2  C5    C6  C1    113.32  3.000

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
 PA2  chir_01  C1  N1  C2  C6  negativ
 PA2  chir_02  C2  O2  C1  C3  negativ
 PA2  chir_03  C3  O3  C2  C4  positiv
 PA2  chir_04  C5  N5  C6  C4  negativ

