# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:04:19 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1~{R},2~{R},3~{R},4~{R},6~{R})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1C[C@H]2N[C@H]2[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
 E9K  E9K  (1~{R},2~{R},3~{R},4~{R},6~{R})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol  ligand  24  11  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E9K
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
 E9K  C7   C  C     0  -0.446   0.0360   1.7950  -0.0112
 E9K  C4   C  CR16  0   0.059  -0.3350  -0.6515   0.3490
 E9K  C2   C  CR16  0  -0.173   1.9275   0.0782  -0.4861
 E9K  C1   C  CR16  0  -0.136   1.4874   1.4751  -0.2883
 E9K  O4   O  OH1   0  -0.672  -1.2787  -1.6959   0.2936
 E9K  C5   C  CR16  0  -0.301  -0.9229   0.6221  -0.2504
 E9K  C6   C  CH2   0  -0.131  -2.2901   0.9998   0.3086
 E9K  O6   O  OH1   0  -0.667  -3.3114   0.2234  -0.2727
 E9K  C3   C  CR16  0   0.036   0.9296  -1.0449  -0.4124
 E9K  O3   O  OH1   0  -0.679   1.4689  -2.1875   0.2269
 E9K  N2   N  NH1   0  -0.598   2.2122   0.7680   0.7595
 E9K  H1   H  H     0   0.232  -0.0582   2.1422   1.0233
 E9K  H2   H  H     0   0.243  -0.2733   2.6301  -0.6426
 E9K  H3   H  HCR6  0   0.193  -0.0604  -0.4423   1.3957
 E9K  H4   H  HCR6  0   0.256   2.7571  -0.0904  -1.1686
 E9K  H5   H  HCR6  0   0.257   2.0397   2.2345  -0.8326
 E9K  H6   H  HOH1  0   0.441  -0.8307  -2.4971   0.5862
 E9K  H7   H  HCR6  0   0.232  -1.0280   0.4839  -1.3346
 E9K  H8   H  HCH2  0   0.186  -2.2704   0.8983   1.4038
 E9K  H9   H  HCH2  0   0.199  -2.4539   2.0668   0.1023
 E9K  H10  H  HOH1  0   0.449  -4.1525   0.5560   0.0529
 E9K  H11  H  HCR6  0   0.206   0.6269  -1.2901  -1.4408
 E9K  H12  H  HOH1  0   0.455   2.0572  -2.6360  -0.3876
 E9K  H13  H  HNH1  0   0.360   3.1803   1.0623   0.7912

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
 E9K  C6  C5   single  1.525  0.020  1.525
 E9K  C6  O6   single  1.408  0.020  1.408
 E9K  C7  C5   single  1.534  0.020  1.534
 E9K  C7  C1   single  1.512  0.020  1.512
 E9K  C5  C4   single  1.525  0.020  1.525
 E9K  C1  C2   single  1.478  0.020  1.478
 E9K  C1  N2   single  1.457  0.020  1.457
 E9K  O4  C4   single  1.409  0.020  1.409
 E9K  C4  C3   single  1.528  0.020  1.528
 E9K  C3  C2   single  1.504  0.020  1.504
 E9K  C3  O3   single  1.416  0.020  1.416
 E9K  C2  N2   single  1.452  0.020  1.452
 E9K  C7  H1   single  0.970  0.020  1.090
 E9K  C7  H2   single  0.970  0.020  1.090
 E9K  C4  H3   single  0.970  0.020  1.090
 E9K  C2  H4   single  0.970  0.020  1.090
 E9K  C1  H5   single  0.970  0.020  1.090
 E9K  O4  H6   single  0.850  0.020  0.980
 E9K  C5  H7   single  0.970  0.020  1.090
 E9K  C6  H8   single  0.970  0.020  1.090
 E9K  C6  H9   single  0.970  0.020  1.090
 E9K  O6  H10  single  0.850  0.020  0.980
 E9K  C3  H11  single  0.970  0.020  1.090
 E9K  O3  H12  single  0.850  0.020  0.980
 E9K  N2  H13  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
 E9K  H2   C7  H1  106.23  3.000
 E9K  H2   C7  C5  108.52  3.000
 E9K  H1   C7  C5  109.63  3.000
 E9K  H2   C7  C1  109.14  3.000
 E9K  H1   C7  C1  108.83  3.000
 E9K  C5   C7  C1  114.19  3.000
 E9K  H3   C4  C3  108.42  3.000
 E9K  H3   C4  C5  108.10  3.000
 E9K  C3   C4  C5  109.77  3.000
 E9K  H3   C4  O4  110.18  3.000
 E9K  C3   C4  O4  110.12  3.000
 E9K  C5   C4  O4  110.20  3.000
 E9K  H4   C2  N2  117.54  3.000
 E9K  H4   C2  C3  114.91  3.000
 E9K  N2   C2  C3  116.28  3.000
 E9K  H4   C2  C1  117.24  3.000
 E9K  N2   C2  C1   59.64  3.000
 E9K  C3   C2  C1  120.11  3.000
 E9K  H5   C1  N2  116.55  3.000
 E9K  H5   C1  C2  116.28  3.000
 E9K  N2   C1  C2   59.30  3.000
 E9K  H5   C1  C7  115.62  3.000
 E9K  N2   C1  C7  116.64  3.000
 E9K  C2   C1  C7  120.69  3.000
 E9K  H6   O4  C4  107.04  3.000
 E9K  H7   C5  C6  107.90  3.000
 E9K  H7   C5  C4  108.65  3.000
 E9K  C6   C5  C4  114.10  3.000
 E9K  H7   C5  C7  108.06  3.000
 E9K  C4   C5  C7  109.65  3.000
 E9K  C6   C5  C7  108.30  3.000
 E9K  H9   C6  H8  106.21  3.000
 E9K  H9   C6  O6  110.46  3.000
 E9K  H8   C6  O6  111.90  3.000
 E9K  H9   C6  C5  107.78  3.000
 E9K  H8   C6  C5  109.03  3.000
 E9K  O6   C6  C5  111.25  3.000
 E9K  H10  O6  C6  107.70  3.000
 E9K  H11  C3  O3  110.31  3.000
 E9K  H11  C3  C2  107.65  3.000
 E9K  O3   C3  C2  111.84  3.000
 E9K  H11  C3  C4  107.20  3.000
 E9K  O3   C3  C4  107.34  3.000
 E9K  C2   C3  C4  112.41  3.000
 E9K  H12  O3  C3  108.71  3.000
 E9K  H13  N2  C1  110.92  3.000
 E9K  H13  N2  C2  110.64  3.000
 E9K  C1   N2  C2   61.06  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
 E9K  Var_01  C3  C2  C1  C7   -0.04  30.0  1
 E9K  Var_02  C5  C7  C1  C2  -12.20  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
 E9K  chir_01  C4  C5  O4  C3  negativ
 E9K  chir_04  C5  C6  C7  C4  negativ
 E9K  chir_05  C3  O3  C4  C2  negativ
 E9K  chir_06  C2  C1  C3  N2  both
 E9K  chir_07  C1  N2  C7  C2  both

