# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:23:10 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (1~{S},2~{R},3~{R},4~{R},6~{S})-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
 GDQ  GDQ  (1~{S},2~{R},3~{R},4~{R},6~{S})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol  ligand  24  11  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GDQ
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
 GDQ  C7   C  CH2   0  -0.459  -0.0997  -1.6905   0.5185
 GDQ  C4   C  CH1   0   0.088   0.4035   0.7292   0.3646
 GDQ  C2   C  CH1   0  -0.189  -2.0019  -0.0151   0.0166
 GDQ  C1   C  CH1   0  -0.116  -1.5649  -1.3888   0.3483
 GDQ  O4   O  OH1   0  -0.666   1.3494   1.6983  -0.0133
 GDQ  C5   C  CH1   0  -0.341   0.8367  -0.6535  -0.1091
 GDQ  C6   C  CH2   0  -0.124   2.2683  -1.0131   0.2739
 GDQ  O6   O  OH1   0  -0.666   3.1942  -0.4036  -0.5935
 GDQ  C3   C  CH1   0   0.007  -0.9762   1.0920  -0.1815
 GDQ  O3   O  OH1   0  -0.679  -1.3677   2.2741   0.4859
 GDQ  N2   N  NH1   0  -0.586  -2.1068  -1.0851  -0.9651
 GDQ  H1   H  HCH2  0   0.236   0.1094  -1.7560   1.5916
 GDQ  H2   H  HCH2  0   0.251   0.1189  -2.6786   0.1038
 GDQ  H3   H  HCH1  0   0.196   0.3189   0.6818   1.4649
 GDQ  H4   H  HCH1  0   0.255  -2.9607   0.3314   0.3938
 GDQ  H5   H  HCH1  0   0.249  -2.2187  -2.0042   0.9598
 GDQ  H6   H  HOH1  0   0.443   1.0207   2.5521   0.2890
 GDQ  H7   H  HCH1  0   0.233   0.7657  -0.7130  -1.2037
 GDQ  H8   H  HCH2  0   0.188   2.4379  -0.7290   1.3226
 GDQ  H9   H  HCH2  0   0.201   2.3630  -2.1069   0.2308
 GDQ  H10  H  HOH1  0   0.450   4.0691  -0.7265  -0.3599
 GDQ  H11  H  HCH1  0   0.222  -0.8686   1.2847  -1.2599
 GDQ  H12  H  HOH1  0   0.458  -2.0757   2.6920  -0.0138
 GDQ  H13  H  HNH1  0   0.349  -1.3707  -1.0132  -1.6598

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
 GDQ  C6  O6   single  1.408  0.020  1.408
 GDQ  C6  C5   single  1.525  0.020  1.525
 GDQ  C5  C7   single  1.532  0.020  1.532
 GDQ  C5  C4   single  1.524  0.020  1.524
 GDQ  C7  C1   single  1.506  0.020  1.506
 GDQ  N2  C1   single  1.453  0.020  1.453
 GDQ  N2  C2   single  1.456  0.020  1.456
 GDQ  C1  C2   single  1.479  0.020  1.479
 GDQ  O4  C4   single  1.406  0.020  1.406
 GDQ  C4  C3   single  1.528  0.020  1.528
 GDQ  C2  C3   single  1.522  0.020  1.522
 GDQ  C3  O3   single  1.413  0.020  1.413
 GDQ  C7  H1   single  0.970  0.020  1.090
 GDQ  C7  H2   single  0.970  0.020  1.090
 GDQ  C4  H3   single  0.970  0.020  1.090
 GDQ  C2  H4   single  0.970  0.020  1.090
 GDQ  C1  H5   single  0.970  0.020  1.090
 GDQ  O4  H6   single  0.850  0.020  0.980
 GDQ  C5  H7   single  0.970  0.020  1.090
 GDQ  C6  H8   single  0.970  0.020  1.090
 GDQ  C6  H9   single  0.970  0.020  1.090
 GDQ  O6  H10  single  0.850  0.020  0.980
 GDQ  C3  H11  single  0.970  0.020  1.090
 GDQ  O3  H12  single  0.850  0.020  0.980
 GDQ  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
 GDQ  H2   C7  H1  106.22  3.000
 GDQ  H2   C7  C5  109.52  3.000
 GDQ  H1   C7  C5  108.98  3.000
 GDQ  H2   C7  C1  109.43  3.000
 GDQ  H1   C7  C1  107.97  3.000
 GDQ  C5   C7  C1  114.39  3.000
 GDQ  H3   C4  C3  107.29  3.000
 GDQ  H3   C4  C5  107.00  3.000
 GDQ  C3   C4  C5  111.16  3.000
 GDQ  H3   C4  O4  110.42  3.000
 GDQ  C3   C4  O4  110.36  3.000
 GDQ  C5   C4  O4  110.51  3.000
 GDQ  H4   C2  N2  113.87  3.000
 GDQ  H4   C2  C3  114.06  3.000
 GDQ  N2   C2  C3  119.69  3.000
 GDQ  H4   C2  C1  118.61  3.000
 GDQ  C3   C2  C1  120.37  3.000
 GDQ  N2   C2  C1   59.33  3.000
 GDQ  H5   C1  N2  113.76  3.000
 GDQ  H5   C1  C2  118.33  3.000
 GDQ  N2   C1  C2   59.53  3.000
 GDQ  H5   C1  C7  114.11  3.000
 GDQ  C2   C1  C7  119.93  3.000
 GDQ  N2   C1  C7  120.47  3.000
 GDQ  H6   O4  C4  107.27  3.000
 GDQ  H7   C5  C6  107.35  3.000
 GDQ  H7   C5  C4  109.90  3.000
 GDQ  C6   C5  C4  113.74  3.000
 GDQ  H7   C5  C7  109.40  3.000
 GDQ  C4   C5  C7  108.24  3.000
 GDQ  C6   C5  C7  108.14  3.000
 GDQ  H9   C6  H8  106.34  3.000
 GDQ  H9   C6  O6  110.50  3.000
 GDQ  H8   C6  O6  111.98  3.000
 GDQ  H9   C6  C5  107.81  3.000
 GDQ  H8   C6  C5  108.87  3.000
 GDQ  O6   C6  C5  111.14  3.000
 GDQ  H10  O6  C6  107.66  3.000
 GDQ  H11  C3  O3  110.08  3.000
 GDQ  H11  C3  C2  108.70  3.000
 GDQ  O3   C3  C2  111.12  3.000
 GDQ  H11  C3  C4  107.67  3.000
 GDQ  O3   C3  C4  106.27  3.000
 GDQ  C2   C3  C4  112.92  3.000
 GDQ  H12  O3  C3  108.79  3.000
 GDQ  H13  N2  C1  111.29  3.000
 GDQ  H13  N2  C2  110.94  3.000
 GDQ  C1   N2  C2   61.13  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
 GDQ  Var_01  C2  N2  C1  C7  -109.00  30.0  1
 GDQ  Var_02  C5  C7  C1  C2   -19.06  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
 GDQ  chir_01  C4  C5  O4  C3  negativ
 GDQ  chir_04  C5  C6  C7  C4  negativ
 GDQ  chir_05  C3  O3  C4  C2  negativ
 GDQ  chir_06  C2  N2  C1  C3  both
 GDQ  chir_07  C1  N2  C2  C7  both

