# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 11:59:14 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (1R,2R,3S,4R,5S)-2-(hydroxymethyl)-8-azabicyclo[3.2.1]octane-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@H](O)[C@H](O)[C@@H]2CC[C@H]1N2
#
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
 DZX  DZX  (1R,2R,3S,4R,5S)-2-(hydroxymethyl)-8-azabicyclo[3.2.1]octane-3,4-diol  ligand  27  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DZX
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
 DZX  O1    O  OH1   0  -0.675   3.2744   0.7300  -0.2616
 DZX  C6    C  CH2   0  -0.131   2.4720  -0.3635   0.1285
 DZX  C5    C  CH1   0  -0.275   1.1090  -0.2445  -0.5323
 DZX  C4    C  CH1   0   0.017   0.3873   1.0693  -0.2081
 DZX  O5    O  OH1   0  -0.671   0.4976   1.3501   1.1686
 DZX  C3    C  CH1   0   0.044  -1.0923   1.0073  -0.6404
 DZX  O7    O  OH1   0  -0.674  -1.8332   2.0299  -0.0008
 DZX  C2    C  CH1   0  -0.164  -1.7434  -0.3407  -0.3407
 DZX  C7    C  CH2   0  -0.452  -1.6545  -0.7885   1.1313
 DZX  C8    C  CH2   0  -0.448  -0.3118  -1.5466   1.1993
 DZX  C1    C  CH1   0  -0.145   0.2273  -1.4658  -0.2455
 DZX  N1    N  NH1   0  -0.580  -0.9655  -1.3301  -1.0843
 DZX  H1    H  HOH1  0   0.452   4.0908   0.6970   0.2443
 DZX  H61C  H  HCH2  0   0.196   2.9224  -1.3155  -0.1864
 DZX  H62C  H  HCH2  0   0.197   2.3662  -0.4132   1.2177
 DZX  H5    H  HCH1  0   0.237   1.2710  -0.2520  -1.6164
 DZX  H4    H  HCH1  0   0.205   0.8630   1.8773  -0.7851
 DZX  HA    H  HCH1  0   0.234   0.7753  -2.3679  -0.5287
 DZX  HB    H  HOH1  0   0.441  -0.2148   1.9662   1.3785
 DZX  H3    H  HCH1  0   0.221  -1.1254   1.1304  -1.7302
 DZX  H7    H  HOH1  0   0.458  -1.6465   2.8650  -0.4417
 DZX  H2    H  HCH1  0   0.239  -2.7731  -0.3160  -0.7048
 DZX  H71C  H  HCH2  0   0.231  -1.7247   0.0302   1.8460
 DZX  H72C  H  HCH2  0   0.230  -2.4854  -1.4636   1.3450
 DZX  HC    H  HNH1  0   0.350  -1.4711  -2.2096  -1.0842
 DZX  H81C  H  HCH2  0   0.234   0.3690  -1.1327   1.9408
 DZX  H82C  H  HCH2  0   0.229  -0.4752  -2.5928   1.4645

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
 DZX  O1  C6    single  1.411  0.020  1.411
 DZX  C6  C5    single  1.519  0.020  1.519
 DZX  C5  C4    single  1.534  0.020  1.534
 DZX  C5  C1    single  1.533  0.020  1.533
 DZX  C4  O5    single  1.409  0.020  1.409
 DZX  C4  C3    single  1.543  0.020  1.543
 DZX  C3  O7    single  1.416  0.020  1.416
 DZX  C3  C2    single  1.527  0.020  1.527
 DZX  C2  C7    single  1.541  0.020  1.541
 DZX  C2  N1    single  1.462  0.020  1.462
 DZX  C7  C8    single  1.543  0.020  1.543
 DZX  C8  C1    single  1.544  0.020  1.544
 DZX  C1  N1    single  1.464  0.020  1.464
 DZX  O1  H1    single  0.850  0.020  0.980
 DZX  C6  H61C  single  0.970  0.020  1.090
 DZX  C6  H62C  single  0.970  0.020  1.090
 DZX  C5  H5    single  0.970  0.020  1.090
 DZX  C4  H4    single  0.970  0.020  1.090
 DZX  C1  HA    single  0.970  0.020  1.090
 DZX  O5  HB    single  0.850  0.020  0.980
 DZX  C3  H3    single  0.970  0.020  1.090
 DZX  O7  H7    single  0.850  0.020  0.980
 DZX  C2  H2    single  0.970  0.020  1.090
 DZX  C7  H71C  single  0.970  0.020  1.090
 DZX  C7  H72C  single  0.970  0.020  1.090
 DZX  N1  HC    single  0.890  0.020  1.040
 DZX  C8  H81C  single  0.970  0.020  1.090
 DZX  C8  H82C  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
 DZX  H1    O1  C6    108.11  3.000
 DZX  H62C  C6  H61C  106.56  3.000
 DZX  H62C  C6  C5    110.45  3.000
 DZX  H61C  C6  C5    108.11  3.000
 DZX  H62C  C6  O1    111.40  3.000
 DZX  H61C  C6  O1    111.03  3.000
 DZX  C5    C6  O1    109.22  3.000
 DZX  H5    C5  C1    105.34  3.000
 DZX  H5    C5  C4    106.53  3.000
 DZX  C1    C5  C4    111.85  3.000
 DZX  H5    C5  C6    107.28  3.000
 DZX  C1    C5  C6    111.85  3.000
 DZX  C4    C5  C6    113.41  3.000
 DZX  H4    C4  C3    107.28  3.000
 DZX  H4    C4  O5    109.39  3.000
 DZX  C3    C4  O5    110.91  3.000
 DZX  H4    C4  C5    108.33  3.000
 DZX  C3    C4  C5    110.95  3.000
 DZX  O5    C4  C5    109.90  3.000
 DZX  HB    O5  C4    106.38  3.000
 DZX  H3    C3  C2    106.34  3.000
 DZX  H3    C3  O7    110.60  3.000
 DZX  C2    C3  O7    109.02  3.000
 DZX  H3    C3  C4    107.62  3.000
 DZX  C2    C3  C4    112.93  3.000
 DZX  O7    C3  C4    110.26  3.000
 DZX  H7    O7  C3    108.56  3.000
 DZX  H2    C2  N1    110.32  3.000
 DZX  H2    C2  C7    112.29  3.000
 DZX  N1    C2  C7    104.98  3.000
 DZX  H2    C2  C3    108.46  3.000
 DZX  N1    C2  C3    105.70  3.000
 DZX  C7    C2  C3    114.80  3.000
 DZX  H72C  C7  H71C  106.70  3.000
 DZX  H72C  C7  C8    110.47  3.000
 DZX  H71C  C7  C8    113.36  3.000
 DZX  H72C  C7  C2    108.83  3.000
 DZX  H71C  C7  C2    113.87  3.000
 DZX  C8    C7  C2    103.59  3.000
 DZX  H82C  C8  H81C  107.01  3.000
 DZX  H82C  C8  C1    109.25  3.000
 DZX  H81C  C8  C1    113.52  3.000
 DZX  H82C  C8  C7    110.56  3.000
 DZX  H81C  C8  C7    112.79  3.000
 DZX  C1    C8  C7    103.69  3.000
 DZX  HA    C1  N1    109.66  3.000
 DZX  HA    C1  C8    111.98  3.000
 DZX  N1    C1  C8    104.86  3.000
 DZX  HA    C1  C5    108.70  3.000
 DZX  N1    C1  C5    106.70  3.000
 DZX  C8    C1  C5    114.67  3.000
 DZX  HC    N1  C1    109.00  3.000
 DZX  HC    N1  C2    108.75  3.000
 DZX  C1    N1  C2    101.82  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
 DZX  Var_01  C1  C8  C7  C2  -0.44  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
 DZX  chir_01  C5  C6  C4  C1  positiv
 DZX  chir_02  C4  O5  C5  C3  negativ
 DZX  chir_03  C3  O7  C4  C2  negativ
 DZX  chir_04  C2  N1  C7  C3  negativ
 DZX  chir_05  C1  N1  C8  C5  positiv

