# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 16:03:37 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1CNC[C@H](O)[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
 2CZ  2CZ  N-[(3S,4R,5R,6S)-4,5,6-trihydroxyazepan-3-yl]acetamide  ligand  30  14  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2CZ
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
 2CZ  N1   N  NH1   0  -0.599  -0.5619   2.2620  -0.2775
 2CZ  C2   C  CH2   0  -0.328   0.3720   1.3037  -0.8262
 2CZ  N2   N  NH1   0  -0.629   2.0190  -0.4422  -0.3469
 2CZ  C3   C  CH1   0  -0.095   0.7081   0.0574   0.0190
 2CZ  C4   C  CH1   0   0.030  -0.3018  -1.0636  -0.2188
 2CZ  O4   O  OH1   0  -0.670   0.1771  -2.2210   0.4270
 2CZ  C5   C  CH1   0   0.021  -1.7224  -0.7717   0.2640
 2CZ  O5   O  OH1   0  -0.683  -2.4718  -1.8904  -0.1586
 2CZ  C6   C  CH1   0   0.004  -2.3632   0.5278  -0.2306
 2CZ  O6   O  OH1   0  -0.682  -3.7178   0.4223   0.1697
 2CZ  C7   C  CH2   0  -0.319  -1.7357   1.7617   0.4154
 2CZ  C8   C  C     0   0.523   3.1615   0.0519   0.1546
 2CZ  O8   O  O     0  -0.512   3.1864   0.9436   0.9948
 2CZ  C9   C  CH3   0  -0.779   4.4273  -0.5684  -0.3830
 2CZ  H02  H  HNH1  0   0.357  -0.0695   2.8930   0.3385
 2CZ  H14  H  HCH2  0   0.222   0.0259   0.9639  -1.8095
 2CZ  H03  H  HCH2  0   0.260   1.2976   1.8475  -1.0144
 2CZ  H04  H  HNH1  0   0.399   2.0750  -1.1580  -1.0529
 2CZ  H05  H  HCH1  0   0.253   0.7325   0.3252   1.0800
 2CZ  H06  H  HCH1  0   0.212  -0.3546  -1.2243  -1.3093
 2CZ  H07  H  HOH1  0   0.451  -0.4584  -2.9289   0.2746
 2CZ  H08  H  HCH1  0   0.206  -1.6966  -0.7177   1.3657
 2CZ  H09  H  HOH1  0   0.453  -3.3889  -1.7458   0.0980
 2CZ  H10  H  HCH1  0   0.224  -2.2899   0.5951  -1.3255
 2CZ  H11  H  HOH1  0   0.460  -4.2249   1.1108  -0.2710
 2CZ  H15  H  HCH2  0   0.206  -1.5458   1.5303   1.4747
 2CZ  H12  H  HCH2  0   0.239  -2.4857   2.5586   0.4141
 2CZ  H16  H  HCH3  0   0.248   4.2542  -1.3569  -1.1130
 2CZ  H13  H  HCH3  0   0.265   5.0376   0.2046  -0.8501
 2CZ  H01  H  HCH3  0   0.265   5.0061  -0.9835   0.4420

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
 2CZ  C2  N1   single  1.446  0.020  1.446
 2CZ  C2  C3   single  1.543  0.020  1.543
 2CZ  N1  C7   single  1.452  0.020  1.452
 2CZ  C9  C8   single  1.509  0.020  1.509
 2CZ  O8  C8   double  1.225  0.020  1.225
 2CZ  C8  N2   single  1.342  0.020  1.342
 2CZ  N2  C3   single  1.450  0.020  1.450
 2CZ  O6  C6   single  1.416  0.020  1.416
 2CZ  C7  C6   single  1.528  0.020  1.528
 2CZ  C3  C4   single  1.527  0.020  1.527
 2CZ  C6  C5   single  1.531  0.020  1.531
 2CZ  C4  C5   single  1.529  0.020  1.529
 2CZ  C4  O4   single  1.409  0.020  1.409
 2CZ  C5  O5   single  1.411  0.020  1.411
 2CZ  N1  H02  single  0.890  0.020  1.040
 2CZ  C2  H14  single  0.970  0.020  1.090
 2CZ  C2  H03  single  0.970  0.020  1.090
 2CZ  N2  H04  single  0.860  0.020  1.020
 2CZ  C3  H05  single  0.970  0.020  1.090
 2CZ  C4  H06  single  0.970  0.020  1.090
 2CZ  O4  H07  single  0.850  0.020  0.980
 2CZ  C5  H08  single  0.970  0.020  1.090
 2CZ  O5  H09  single  0.850  0.020  0.980
 2CZ  C6  H10  single  0.970  0.020  1.090
 2CZ  O6  H11  single  0.850  0.020  0.980
 2CZ  C7  H15  single  0.970  0.020  1.090
 2CZ  C7  H12  single  0.970  0.020  1.090
 2CZ  C9  H16  single  0.970  0.020  1.090
 2CZ  C9  H13  single  0.970  0.020  1.090
 2CZ  C9  H01  single  0.970  0.020  1.090

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
 2CZ  H02  N1  C7   108.57  3.000
 2CZ  H02  N1  C2   109.30  3.000
 2CZ  C7   N1  C2   118.34  3.000
 2CZ  H03  C2  H14  105.53  3.000
 2CZ  H03  C2  C3   108.22  3.000
 2CZ  H14  C2  C3   108.04  3.000
 2CZ  H03  C2  N1   106.46  3.000
 2CZ  H14  C2  N1   109.99  3.000
 2CZ  C3   C2  N1   117.91  3.000
 2CZ  H04  N2  C8   118.44  3.000
 2CZ  H04  N2  C3   118.18  3.000
 2CZ  C8   N2  C3   123.27  3.000
 2CZ  H05  C3  C4   110.19  3.000
 2CZ  H05  C3  N2   107.99  3.000
 2CZ  C4   C3  N2   107.79  3.000
 2CZ  H05  C3  C2   109.77  3.000
 2CZ  C4   C3  C2   111.32  3.000
 2CZ  N2   C3  C2   109.70  3.000
 2CZ  H06  C4  C5   107.18  3.000
 2CZ  H06  C4  O4   110.46  3.000
 2CZ  C5   C4  O4   109.15  3.000
 2CZ  H06  C4  C3   107.00  3.000
 2CZ  O4   C4  C3   107.86  3.000
 2CZ  C5   C4  C3   115.16  3.000
 2CZ  H07  O4  C4   107.87  3.000
 2CZ  H08  C5  C6   106.90  3.000
 2CZ  H08  C5  O5   110.50  3.000
 2CZ  C6   C5  O5   110.72  3.000
 2CZ  H08  C5  C4   107.63  3.000
 2CZ  O5   C5  C4   104.34  3.000
 2CZ  C6   C5  C4   116.69  3.000
 2CZ  H09  O5  C5   107.87  3.000
 2CZ  H10  C6  C7   110.14  3.000
 2CZ  H10  C6  O6   110.47  3.000
 2CZ  C7   C6  O6   109.48  3.000
 2CZ  H10  C6  C5   110.23  3.000
 2CZ  C7   C6  C5   112.15  3.000
 2CZ  O6   C6  C5   104.23  3.000
 2CZ  H11  O6  C6   108.74  3.000
 2CZ  H12  C7  H15  105.81  3.000
 2CZ  H12  C7  C6   107.83  3.000
 2CZ  H15  C7  C6   107.94  3.000
 2CZ  H12  C7  N1   107.61  3.000
 2CZ  H15  C7  N1   113.09  3.000
 2CZ  C6   C7  N1   114.12  3.000
 2CZ  C9   C8  O8   121.77  3.000
 2CZ  O8   C8  N2   122.78  3.000
 2CZ  C9   C8  N2   115.46  3.000
 2CZ  H01  C9  H13  107.29  3.000
 2CZ  H01  C9  H16  108.43  3.000
 2CZ  H13  C9  H16  108.38  3.000
 2CZ  H01  C9  C8   109.42  3.000
 2CZ  H13  C9  C8   109.32  3.000
 2CZ  H16  C9  C8   113.79  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
 2CZ  CONST_01  C9   C8  N2  C3  180.00   0.0  0
 2CZ  CONST_02  O8   C8  N2  C3    0.00   0.0  0
 2CZ  CONST_03  H04  N2  C8  O8  180.00   0.0  0
 2CZ  Var_01    H16  C9  C8  N2   -0.59  30.0  3

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
 2CZ  chir_01  C3  C2  N2  C4  positiv
 2CZ  chir_02  C4  O4  C3  C5  positiv
 2CZ  chir_03  C5  O5  C4  C6  negativ
 2CZ  chir_04  C6  O6  C5  C7  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
 2CZ  plan-1  N2   0.020
 2CZ  plan-1  C3   0.020
 2CZ  plan-1  C8   0.020
 2CZ  plan-1  O8   0.020
 2CZ  plan-1  C9   0.020
 2CZ  plan-1  H04  0.020

