# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 20:34:32 2022
#   Inital geometry file: a 63 line input string
#   Ligand name: (1~{R},2~{S},3~{R},4~{S},5~{R},6~{R})-5-azanyl-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)[C@H]1CO
#
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
 JIW  JIW  "beta-D-manno-configured cyclophellitol aziridine, reacted form"  ligand  28  13  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JIW
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
 JIW  C1   C  CH1   0   0.071  26.5451  46.4828  -3.0124
 JIW  C2   C  CH1   0  -0.019  27.5672  46.5001  -1.8844
 JIW  C3   C  CH1   0  -0.020  28.7457  47.4213  -2.1956
 JIW  C4   C  CH1   0   0.021  28.2619  48.8296  -2.5474
 JIW  C5   C  CH1   0  -0.300  27.2030  48.8400  -3.6546
 JIW  C6   C  CH2   0  -0.140  27.8030  48.6350  -5.0484
 JIW  C7   C  CH1   0  -0.094  26.0417  47.8912  -3.3106
 JIW  O8   O  OH1   0  -0.675  28.0141  45.1663  -1.7054
 JIW  O9   O  OH1   0  -0.663  29.5073  46.9357  -3.2750
 JIW  O10  O  OH1   0  -0.667  27.6830  49.4406  -1.4125
 JIW  O11  O  OH1   0  -0.671  27.0885  49.4391  -5.9679
 JIW  N12  N  NH2   0  -0.797  25.0780  47.8327  -4.3993
 JIW  O1   O  OH1   0  -0.678  25.4283  45.6925  -2.6629
 JIW  H1   H  HCH1  0   0.196  27.0224  46.0843  -3.9198
 JIW  H2   H  HCH1  0   0.217  27.0728  46.8658  -0.9755
 JIW  H3   H  HCH1  0   0.215  29.3734  47.4906  -1.2898
 JIW  H4   H  HCH1  0   0.225  29.1289  49.4115  -2.8930
 JIW  H5   H  HCH1  0   0.251  26.8000  49.8605  -3.6588
 JIW  H6   H  HCH2  0   0.198  27.7730  47.5809  -5.3413
 JIW  H7   H  HCH2  0   0.195  28.8605  48.9264  -5.0356
 JIW  H8   H  HCH1  0   0.211  25.5875  48.2704  -2.3819
 JIW  H9   H  HOH1  0   0.457  28.4037  45.0856  -0.8288
 JIW  H10  H  HOH1  0   0.446  29.6419  45.9914  -3.1329
 JIW  H11  H  HOH1  0   0.449  28.3507  49.4985  -0.7214
 JIW  H12  H  HOH1  0   0.446  27.3784  49.2028  -6.8533
 JIW  H13  H  HNH2  0   0.342  24.2450  47.3553  -4.0803
 JIW  H14  H  HNH2  0   0.340  24.7879  48.7706  -4.6445
 JIW  H16  H  HOH1  0   0.444  25.7432  44.8035  -2.4710

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
 JIW  O11  C6   single  1.415  0.020  1.415
 JIW  C6   C5   single  1.531  0.020  1.531
 JIW  N12  C7   single  1.455  0.020  1.455
 JIW  C5   C7   single  1.539  0.020  1.539
 JIW  C5   C4   single  1.532  0.020  1.532
 JIW  C7   C1   single  1.525  0.020  1.525
 JIW  O9   C3   single  1.407  0.020  1.407
 JIW  C1   C2   single  1.522  0.020  1.522
 JIW  C4   C3   single  1.530  0.020  1.530
 JIW  C4   O10  single  1.413  0.020  1.413
 JIW  C3   C2   single  1.528  0.020  1.528
 JIW  C2   O8   single  1.418  0.020  1.418
 JIW  C1   O1   single  1.412  0.020  1.412
 JIW  C1   H1   single  0.970  0.020  1.090
 JIW  C2   H2   single  0.970  0.020  1.090
 JIW  C3   H3   single  0.970  0.020  1.090
 JIW  C4   H4   single  0.970  0.020  1.090
 JIW  C5   H5   single  0.970  0.020  1.090
 JIW  C6   H6   single  0.970  0.020  1.090
 JIW  C6   H7   single  0.970  0.020  1.090
 JIW  C7   H8   single  0.970  0.020  1.090
 JIW  O8   H9   single  0.850  0.020  0.980
 JIW  O9   H10  single  0.850  0.020  0.980
 JIW  O10  H11  single  0.850  0.020  0.980
 JIW  O11  H12  single  0.850  0.020  0.980
 JIW  N12  H13  single  0.890  0.020  1.040
 JIW  N12  H14  single  0.890  0.020  1.040
 JIW  O1   H16  single  0.850  0.020  0.980

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
 JIW  H1   C1   O1   110.16  3.000
 JIW  H1   C1   C7   108.45  3.000
 JIW  O1   C1   C7   107.71  3.000
 JIW  H1   C1   C2   108.91  3.000
 JIW  O1   C1   C2   110.73  3.000
 JIW  C7   C1   C2   110.86  3.000
 JIW  H2   C2   O8   110.54  3.000
 JIW  H2   C2   C3   108.37  3.000
 JIW  O8   C2   C3   110.47  3.000
 JIW  H2   C2   C1   108.36  3.000
 JIW  O8   C2   C1   107.13  3.000
 JIW  C3   C2   C1   111.95  3.000
 JIW  H3   C3   O9   110.07  3.000
 JIW  H3   C3   C4   108.10  3.000
 JIW  O9   C3   C4   108.20  3.000
 JIW  H3   C3   C2   108.02  3.000
 JIW  C4   C3   C2   110.97  3.000
 JIW  O9   C3   C2   111.44  3.000
 JIW  H4   C4   O10  110.27  3.000
 JIW  H4   C4   C5   108.31  3.000
 JIW  O10  C4   C5   107.12  3.000
 JIW  H4   C4   C3   108.06  3.000
 JIW  O10  C4   C3   110.05  3.000
 JIW  C5   C4   C3   113.01  3.000
 JIW  H5   C5   C7   107.29  3.000
 JIW  H5   C5   C6   105.36  3.000
 JIW  C7   C5   C6   114.63  3.000
 JIW  H5   C5   C4   105.25  3.000
 JIW  C7   C5   C4   110.85  3.000
 JIW  C6   C5   C4   112.71  3.000
 JIW  H7   C6   H6   106.58  3.000
 JIW  H7   C6   O11  110.08  3.000
 JIW  H6   C6   O11  111.07  3.000
 JIW  H7   C6   C5   109.36  3.000
 JIW  H6   C6   C5   111.21  3.000
 JIW  O11  C6   C5   108.51  3.000
 JIW  H8   C7   N12  111.82  3.000
 JIW  H8   C7   C5   106.71  3.000
 JIW  N12  C7   C5   110.94  3.000
 JIW  H8   C7   C1   106.81  3.000
 JIW  C5   C7   C1   111.35  3.000
 JIW  N12  C7   C1   109.14  3.000
 JIW  H9   O8   C2   108.75  3.000
 JIW  H10  O9   C3   107.48  3.000
 JIW  H11  O10  C4   108.57  3.000
 JIW  H12  O11  C6   107.85  3.000
 JIW  H14  N12  H13  106.12  3.000
 JIW  H14  N12  C7   109.51  3.000
 JIW  H13  N12  C7   109.17  3.000
 JIW  H16  O1   C1   107.91  3.000

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
 JIW  chir_01  C1  C7   C2  O1  negativ
 JIW  chir_02  C2  O8   C1  C3  positiv
 JIW  chir_03  C3  O9   C2  C4  positiv
 JIW  chir_04  C4  O10  C3  C5  negativ
 JIW  chir_05  C5  C4   C7  C6  positiv
 JIW  chir_06  C7  N12  C1  C5  negativ

