# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 12:08:54 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-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)c2nc[nH]c12
#
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
 AEZ  AEZ  (4~{S},5~{S},6~{R},7~{R})-7-(hydroxymethyl)-4,5,6,7-tetrahydro-1~{H}-benzimidazole-4,5,6-triol  ligand  26  14  .  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_AEZ
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
 AEZ  C4   C  CH1   0   0.055  -0.6216  -1.3869  -0.2970
 AEZ  C5   C  CH1   0  -0.382   0.7487  -1.0207   0.2831
 AEZ  C6   C  CH2   0  -0.137   1.8638  -1.8176  -0.3824
 AEZ  C7   C  CR5   0   0.332   0.9088   0.4521   0.1177
 AEZ  C10  C  CR15  0   0.072   1.7088   2.4858  -0.0063
 AEZ  C3   C  CH1   0   0.005  -1.7155  -0.4290   0.1987
 AEZ  C1   C  CR5   0   0.033  -0.0795   1.3526  -0.1503
 AEZ  C2   C  CH1   0  -0.036  -1.5105   0.9815  -0.3492
 AEZ  O2   O  OH1   0  -0.670  -2.3981   1.8455   0.3268
 AEZ  O4   O  OH1   0  -0.674  -0.9101  -2.7086   0.0807
 AEZ  O3   O  OH1   0  -0.681  -2.9506  -0.9693  -0.2138
 AEZ  O6   O  OH1   0  -0.672   3.0798  -1.4913   0.2588
 AEZ  N8   N  N     0  -0.463   0.4252   2.6185  -0.2303
 AEZ  N9   N  NR15  0  -0.625   2.0484   1.1977   0.2085
 AEZ  H1   H  HCH1  0   0.209  -0.5642  -1.2987  -1.3954
 AEZ  H2   H  HCH1  0   0.263   0.7387  -1.2729   1.3524
 AEZ  H3   H  HCH2  0   0.220   1.6499  -2.8880  -0.2965
 AEZ  H4   H  HCH2  0   0.201   1.8920  -1.5723  -1.4521
 AEZ  H5   H  HCR5  0   0.276   2.4357   3.2829   0.0111
 AEZ  H6   H  HCH1  0   0.224  -1.6564  -0.3830   1.2969
 AEZ  H7   H  HCH1  0   0.212  -1.7430   0.9667  -1.4255
 AEZ  H8   H  HOH1  0   0.453  -2.2525   2.7372  -0.0055
 AEZ  H9   H  HOH1  0   0.450  -1.8184  -2.8950  -0.1823
 AEZ  H10  H  HOH1  0   0.461  -3.6474  -0.6142   0.3455
 AEZ  H11  H  HOH1  0   0.461   3.7980  -1.9192  -0.2163
 AEZ  H12  H  HNR5  0   0.411   2.9739   0.8374   0.3814

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
 AEZ  O4   C4   single    1.405  0.020  1.405
 AEZ  O3   C3   single    1.410  0.020  1.410
 AEZ  C4   C3   single    1.536  0.020  1.536
 AEZ  C4   C5   single    1.532  0.020  1.532
 AEZ  C3   C2   single    1.527  0.020  1.527
 AEZ  C6   C5   single    1.524  0.020  1.524
 AEZ  C6   O6   single    1.413  0.020  1.413
 AEZ  C5   C7   single    1.491  0.020  1.491
 AEZ  C2   O2   single    1.411  0.020  1.411
 AEZ  C2   C1   single    1.492  0.020  1.492
 AEZ  C7   C1   aromatic  1.364  0.020  1.364
 AEZ  C7   N9   aromatic  1.365  0.020  1.365
 AEZ  C1   N8   aromatic  1.365  0.020  1.365
 AEZ  N9   C10  aromatic  1.349  0.020  1.349
 AEZ  N8   C10  aromatic  1.310  0.020  1.310
 AEZ  C4   H1   single    0.970  0.020  1.090
 AEZ  C5   H2   single    0.970  0.020  1.090
 AEZ  C6   H3   single    0.970  0.020  1.090
 AEZ  C6   H4   single    0.970  0.020  1.090
 AEZ  C10  H5   single    0.930  0.020  1.080
 AEZ  C3   H6   single    0.970  0.020  1.090
 AEZ  C2   H7   single    0.970  0.020  1.090
 AEZ  O2   H8   single    0.850  0.020  0.980
 AEZ  O4   H9   single    0.850  0.020  0.980
 AEZ  O3   H10  single    0.850  0.020  0.980
 AEZ  O6   H11  single    0.850  0.020  0.980
 AEZ  N9   H12  single    0.860  0.020  1.020

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
 AEZ  H1   C4   O4   110.71  3.000
 AEZ  H1   C4   C3   107.96  3.000
 AEZ  O4   C4   C3   110.72  3.000
 AEZ  H1   C4   C5   108.13  3.000
 AEZ  C3   C4   C5   111.44  3.000
 AEZ  O4   C4   C5   107.86  3.000
 AEZ  H2   C5   C7   109.63  3.000
 AEZ  H2   C5   C6   108.16  3.000
 AEZ  C7   C5   C6   112.94  3.000
 AEZ  H2   C5   C4   107.78  3.000
 AEZ  C7   C5   C4   106.87  3.000
 AEZ  C6   C5   C4   111.35  3.000
 AEZ  H4   C6   H3   107.45  3.000
 AEZ  H4   C6   O6   111.62  3.000
 AEZ  H3   C6   O6   111.00  3.000
 AEZ  H4   C6   C5   109.12  3.000
 AEZ  H3   C6   C5   109.52  3.000
 AEZ  O6   C6   C5   108.11  3.000
 AEZ  N9   C7   C1   104.92  3.000
 AEZ  N9   C7   C5   128.47  3.000
 AEZ  C1   C7   C5   126.61  3.000
 AEZ  H5   C10  N9   122.22  3.000
 AEZ  H5   C10  N8   126.03  3.000
 AEZ  N9   C10  N8   111.75  3.000
 AEZ  H6   C3   O3   110.79  3.000
 AEZ  H6   C3   C2   108.18  3.000
 AEZ  O3   C3   C2   111.51  3.000
 AEZ  H6   C3   C4   108.05  3.000
 AEZ  C2   C3   C4   111.39  3.000
 AEZ  O3   C3   C4   106.89  3.000
 AEZ  N8   C1   C2   125.28  3.000
 AEZ  N8   C1   C7   110.85  3.000
 AEZ  C2   C1   C7   123.87  3.000
 AEZ  H7   C2   O2   110.10  3.000
 AEZ  H7   C2   C1   109.65  3.000
 AEZ  O2   C2   C1   112.78  3.000
 AEZ  H7   C2   C3   108.05  3.000
 AEZ  C1   C2   C3   108.10  3.000
 AEZ  O2   C2   C3   108.02  3.000
 AEZ  H8   O2   C2   107.86  3.000
 AEZ  H9   O4   C4   107.59  3.000
 AEZ  H10  O3   C3   108.86  3.000
 AEZ  H11  O6   C6   108.41  3.000
 AEZ  C1   N8   C10  104.97  3.000
 AEZ  H12  N9   C10  126.83  3.000
 AEZ  H12  N9   C7   125.64  3.000
 AEZ  C10  N9   C7   107.50  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
 AEZ  CONST_01  C10  N8   C1  C7     0.00  0.0  0
 AEZ  CONST_02  N8   C10  N9  C7     0.00  0.0  0
 AEZ  CONST_03  C1   C7   N9  C10    0.00  0.0  0
 AEZ  CONST_04  N9   C10  N8  C1     0.00  0.0  0
 AEZ  CONST_05  N9   C7   C1  N8     0.00  0.0  0
 AEZ  CONST_06  H12  N9   C7  C5     0.00  0.0  0
 AEZ  CONST_07  H5   C10  N9  C7   180.00  0.0  0

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
 AEZ  chir_01  C4  O4  C3  C5  negativ
 AEZ  chir_02  C5  C4  C6  C7  negativ
 AEZ  chir_03  C3  O3  C2  C4  positiv
 AEZ  chir_04  C2  O2  C3  C1  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 AEZ  plan-1  C5   0.020
 AEZ  plan-1  C7   0.020
 AEZ  plan-1  C10  0.020
 AEZ  plan-1  C1   0.020
 AEZ  plan-1  C2   0.020
 AEZ  plan-1  N8   0.020
 AEZ  plan-1  N9   0.020
 AEZ  plan-1  H5   0.020
 AEZ  plan-1  H12  0.020

