# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:18:55 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: (1~{S},2~{S},3~{S},4~{R},5~{R},6~{S})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](O)[C@H]2N[C@@H]12
#
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
 94B  94B  (1~{S},2~{S},3~{S},4~{R},5~{R},6~{S})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol  ligand  25  12  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_94B
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
 94B  C1   C  CH1   0  -0.170  -1.2113   1.4042  -0.4275
 94B  C2   C  CH1   0   0.064  -1.6857  -0.0088  -0.5897
 94B  C3   C  CH1   0  -0.042  -0.8402  -0.9582   0.2471
 94B  C4   C  CH1   0   0.070   0.6404  -0.8166  -0.1166
 94B  C5   C  CH1   0  -0.279   1.1944   0.5662   0.2415
 94B  C6   C  CH2   0  -0.152   2.4569   0.9151  -0.5387
 94B  C7   C  CH1   0  -0.139   0.1833   1.6721  -0.0189
 94B  O6   O  OH1   0  -0.664   3.4799  -0.0170  -0.2933
 94B  O4   O  OH1   0  -0.672   1.3952  -1.8024   0.5449
 94B  O2   O  OH1   0  -0.688  -1.2414  -2.2943  -0.0217
 94B  O3   O  OH1   0  -0.677  -3.0498  -0.0606  -0.2369
 94B  N12  N  NH1   0  -0.596  -0.9077   1.8205   0.9305
 94B  H1   H  HCH1  0   0.263  -1.6823   2.1300  -1.0847
 94B  H2   H  HCH1  0   0.202  -1.5526  -0.2830  -1.6479
 94B  H3   H  HCH1  0   0.230  -0.9771  -0.7244   1.3093
 94B  H4   H  HCH1  0   0.190   0.7195  -0.9403  -1.2117
 94B  H5   H  HCH1  0   0.244   1.4262   0.5731   1.3131
 94B  H6   H  HCH2  0   0.192   2.2022   0.9625  -1.6080
 94B  H7   H  HCH2  0   0.204   2.7684   1.9281  -0.2474
 94B  H8   H  HCH1  0   0.257   0.6095   2.5954  -0.4028
 94B  H9   H  HOH1  0   0.451   4.2457   0.2511  -0.8090
 94B  H10  H  HOH1  0   0.438   0.9410  -2.6405   0.4007
 94B  H11  H  HOH1  0   0.463  -1.6109  -2.6784   0.7770
 94B  H12  H  HOH1  0   0.446  -3.3706  -0.9466  -0.4335
 94B  H13  H  HNH1  0   0.364  -1.1397   2.7956   1.0712

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
 94B  O3   C2   single  1.410  0.020  1.410
 94B  C2   C1   single  1.499  0.020  1.499
 94B  C2   C3   single  1.522  0.020  1.522
 94B  C1   N12  single  1.452  0.020  1.452
 94B  C1   C7   single  1.478  0.020  1.478
 94B  N12  C7   single  1.454  0.020  1.454
 94B  O2   C3   single  1.421  0.020  1.421
 94B  C3   C4   single  1.531  0.020  1.531
 94B  C7   C5   single  1.521  0.020  1.521
 94B  C4   C5   single  1.532  0.020  1.532
 94B  C4   O4   single  1.407  0.020  1.407
 94B  C5   C6   single  1.525  0.020  1.525
 94B  O6   C6   single  1.406  0.020  1.406
 94B  C1   H1   single  0.970  0.020  1.090
 94B  C2   H2   single  0.970  0.020  1.090
 94B  C3   H3   single  0.970  0.020  1.090
 94B  C4   H4   single  0.970  0.020  1.090
 94B  C5   H5   single  0.970  0.020  1.090
 94B  C6   H6   single  0.970  0.020  1.090
 94B  C6   H7   single  0.970  0.020  1.090
 94B  C7   H8   single  0.970  0.020  1.090
 94B  O6   H9   single  0.850  0.020  0.980
 94B  O4   H10  single  0.850  0.020  0.980
 94B  O2   H11  single  0.850  0.020  0.980
 94B  O3   H12  single  0.850  0.020  0.980
 94B  N12  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
 94B  H1   C1   N12  117.69  3.000
 94B  H1   C1   C7   117.09  3.000
 94B  N12  C1   C7    59.48  3.000
 94B  H1   C1   C2   115.27  3.000
 94B  C7   C1   C2   119.96  3.000
 94B  N12  C1   C2   115.94  3.000
 94B  H2   C2   O3   110.38  3.000
 94B  H2   C2   C3   107.81  3.000
 94B  O3   C2   C3   112.15  3.000
 94B  H2   C2   C1   107.48  3.000
 94B  C3   C2   C1   110.65  3.000
 94B  O3   C2   C1   108.28  3.000
 94B  H3   C3   O2   110.41  3.000
 94B  H3   C3   C4   109.34  3.000
 94B  O2   C3   C4   108.37  3.000
 94B  H3   C3   C2   109.29  3.000
 94B  C4   C3   C2   110.42  3.000
 94B  O2   C3   C2   109.01  3.000
 94B  H4   C4   O4   110.44  3.000
 94B  H4   C4   C5   107.87  3.000
 94B  O4   C4   C5   109.18  3.000
 94B  H4   C4   C3   107.11  3.000
 94B  O4   C4   C3   110.02  3.000
 94B  C5   C4   C3   112.19  3.000
 94B  H5   C5   C7   107.65  3.000
 94B  H5   C5   C6   108.88  3.000
 94B  C7   C5   C6   107.25  3.000
 94B  H5   C5   C4   108.09  3.000
 94B  C6   C5   C4   112.73  3.000
 94B  C7   C5   C4   112.08  3.000
 94B  H7   C6   H6   106.46  3.000
 94B  H7   C6   O6   111.02  3.000
 94B  H6   C6   O6   111.51  3.000
 94B  H7   C6   C5   108.06  3.000
 94B  H6   C6   C5   108.39  3.000
 94B  O6   C6   C5   111.20  3.000
 94B  H8   C7   N12  115.98  3.000
 94B  H8   C7   C5   114.67  3.000
 94B  N12  C7   C5   117.47  3.000
 94B  H8   C7   C1   115.23  3.000
 94B  C5   C7   C1   122.89  3.000
 94B  N12  C7   C1    59.40  3.000
 94B  H9   O6   C6   107.53  3.000
 94B  H10  O4   C4   106.62  3.000
 94B  H11  O2   C3   109.12  3.000
 94B  H12  O3   C2   107.77  3.000
 94B  H13  N12  C7   111.17  3.000
 94B  H13  N12  C1   110.99  3.000
 94B  C7   N12  C1    61.12  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
 94B  Var_01  C5  C7   N12  C1  -113.79  30.0  1
 94B  Var_02  C7  N12  C1   C2   110.97  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
 94B  chir_02  C2  O3   C1   C3  negativ
 94B  chir_03  C3  O2   C2   C4  positiv
 94B  chir_04  C4  O4   C3   C5  negativ
 94B  chir_05  C5  C7   C4   C6  negativ
 94B  chir_06  C1  C2   N12  C7  both
 94B  chir_07  C7  N12  C1   C5  both

