# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 08:40:52 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(3R,4S,5R,6R,7R)-3,5,6-trihydroxy-7-(hydroxymethyl)azepan-4-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)CN[C@H](CO)[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
 HQ6  HQ6  N-[(3R,4S,5R,6R,7R)-3,5,6-trihydroxy-7-(hydroxymethyl)azepan-4-yl]acetamide  ligand  34  16  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_HQ6
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
 HQ6  O9    O  O     0  -0.514   3.2133   0.4217   1.5611
 HQ6  C9    C  C     0   0.520   3.2959  -0.1316   0.4713
 HQ6  C10   C  CH3   0  -0.782   4.6299  -0.5387  -0.1070
 HQ6  N2    N  NH1   0  -0.602   2.2355  -0.4221  -0.2968
 HQ6  C5    C  CH1   0  -0.116   0.8808  -0.0443   0.0201
 HQ6  C6    C  CH1   0   0.043   0.4527   1.1928  -0.8002
 HQ6  O6    O  OH1   0  -0.659   1.5898   1.9829  -1.0579
 HQ6  C4    C  CH1   0   0.048  -0.0365  -1.2384  -0.2853
 HQ6  O4    O  OH1   0  -0.668   0.5576  -2.3855   0.2744
 HQ6  C3    C  CH1   0   0.046  -1.4805  -1.1379   0.2186
 HQ6  O3    O  OH1   0  -0.681  -2.1211  -2.2768  -0.3363
 HQ6  C2    C  CH1   0  -0.150  -2.2128   0.1686  -0.1117
 HQ6  C8    C  CH2   0  -0.167  -3.6776   0.0616   0.2882
 HQ6  O8    O  OH1   0  -0.670  -4.3092   1.2926   0.0126
 HQ6  N1    N  NH1   0  -0.621  -1.5666   1.2284   0.6456
 HQ6  C7    C  CH2   0  -0.315  -0.6083   2.0274  -0.0832
 HQ6  H101  H  HCH3  0   0.260   5.2344  -1.0131   0.6644
 HQ6  H102  H  HCH3  0   0.246   4.5480  -1.2181  -0.9535
 HQ6  H103  H  HCH3  0   0.265   5.1650   0.3525  -0.4386
 HQ6  H2    H  HNH1  0   0.393   2.4071  -0.8369  -1.1992
 HQ6  H5    H  HCH1  0   0.256   0.8495   0.1882   1.0860
 HQ6  H6    H  HCH1  0   0.201   0.0404   0.8293  -1.7539
 HQ6  H4    H  HCH1  0   0.201  -0.0846  -1.3307  -1.3851
 HQ6  HA    H  HOH1  0   0.452   1.3123   2.7297  -1.5984
 HQ6  H71C  H  HCH2  0   0.231  -0.0916   2.6682   0.6370
 HQ6  H72C  H  HCH2  0   0.209  -1.0819   2.6905  -0.8251
 HQ6  HB    H  HOH1  0   0.446  -0.0432  -3.1212   0.1092
 HQ6  H3    H  HCH1  0   0.212  -1.4516  -1.2057   1.3152
 HQ6  HC    H  HOH1  0   0.462  -2.7958  -2.5882   0.2734
 HQ6  HD    H  HCH1  0   0.221  -2.1816   0.3550  -1.1975
 HQ6  H81C  H  HCH2  0   0.212  -4.1483  -0.7551  -0.2683
 HQ6  H82C  H  HCH2  0   0.199  -3.7395  -0.1876   1.3574
 HQ6  H1    H  HNH1  0   0.363  -2.2602   1.8456   1.0444
 HQ6  H8    H  HOH1  0   0.458  -5.1976   1.2608   0.3782

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
 HQ6  O9   C9    double  1.225  0.020  1.225
 HQ6  C9   C10   single  1.510  0.020  1.510
 HQ6  C9   N2    single  1.341  0.020  1.341
 HQ6  N2   C5    single  1.442  0.020  1.442
 HQ6  C5   C6    single  1.545  0.020  1.545
 HQ6  C5   C4    single  1.536  0.020  1.536
 HQ6  C6   O6    single  1.408  0.020  1.408
 HQ6  C6   C7    single  1.529  0.020  1.529
 HQ6  C4   O4    single  1.408  0.020  1.408
 HQ6  C4   C3    single  1.533  0.020  1.533
 HQ6  C3   O3    single  1.420  0.020  1.420
 HQ6  C3   C2    single  1.534  0.020  1.534
 HQ6  C2   C8    single  1.522  0.020  1.522
 HQ6  C2   N1    single  1.454  0.020  1.454
 HQ6  C8   O8    single  1.411  0.020  1.411
 HQ6  N1   C7    single  1.445  0.020  1.445
 HQ6  C10  H101  single  0.970  0.020  1.090
 HQ6  C10  H102  single  0.970  0.020  1.090
 HQ6  C10  H103  single  0.970  0.020  1.090
 HQ6  N2   H2    single  0.860  0.020  1.020
 HQ6  C5   H5    single  0.970  0.020  1.090
 HQ6  C6   H6    single  0.970  0.020  1.090
 HQ6  C4   H4    single  0.970  0.020  1.090
 HQ6  O6   HA    single  0.850  0.020  0.980
 HQ6  C7   H71C  single  0.970  0.020  1.090
 HQ6  C7   H72C  single  0.970  0.020  1.090
 HQ6  O4   HB    single  0.850  0.020  0.980
 HQ6  C3   H3    single  0.970  0.020  1.090
 HQ6  O3   HC    single  0.850  0.020  0.980
 HQ6  C2   HD    single  0.970  0.020  1.090
 HQ6  C8   H81C  single  0.970  0.020  1.090
 HQ6  C8   H82C  single  0.970  0.020  1.090
 HQ6  N1   H1    single  0.890  0.020  1.040
 HQ6  O8   H8    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
 HQ6  N2    C9   C10   114.88  3.000
 HQ6  N2    C9   O9    123.64  3.000
 HQ6  C10   C9   O9    121.48  3.000
 HQ6  H103  C10  H102  108.08  3.000
 HQ6  H103  C10  H101  107.40  3.000
 HQ6  H102  C10  H101  108.71  3.000
 HQ6  H103  C10  C9    109.24  3.000
 HQ6  H102  C10  C9    113.56  3.000
 HQ6  H101  C10  C9    109.67  3.000
 HQ6  H2    N2   C5    117.69  3.000
 HQ6  H2    N2   C9    117.85  3.000
 HQ6  C5    N2   C9    124.08  3.000
 HQ6  H5    C5   C4    110.04  3.000
 HQ6  H5    C5   C6    109.88  3.000
 HQ6  C4    C5   C6    110.57  3.000
 HQ6  H5    C5   N2    107.31  3.000
 HQ6  C4    C5   N2    108.28  3.000
 HQ6  C6    C5   N2    110.70  3.000
 HQ6  H6    C6   C7    109.07  3.000
 HQ6  H6    C6   O6    109.21  3.000
 HQ6  C7    C6   O6    109.87  3.000
 HQ6  H6    C6   C5    107.42  3.000
 HQ6  C7    C6   C5    112.36  3.000
 HQ6  O6    C6   C5    108.82  3.000
 HQ6  HA    O6   C6    107.77  3.000
 HQ6  H4    C4   C3    106.96  3.000
 HQ6  H4    C4   O4    110.25  3.000
 HQ6  C3    C4   O4    108.68  3.000
 HQ6  H4    C4   C5    106.79  3.000
 HQ6  C3    C4   C5    116.50  3.000
 HQ6  O4    C4   C5    107.59  3.000
 HQ6  HB    O4   C4    106.90  3.000
 HQ6  H3    C3   C2    106.26  3.000
 HQ6  H3    C3   O3    110.64  3.000
 HQ6  C2    C3   O3    112.57  3.000
 HQ6  H3    C3   C4    107.41  3.000
 HQ6  C2    C3   C4    115.78  3.000
 HQ6  O3    C3   C4    104.12  3.000
 HQ6  HC    O3   C3    109.19  3.000
 HQ6  HD    C2   N1    112.16  3.000
 HQ6  HD    C2   C8    107.34  3.000
 HQ6  N1    C2   C8    110.01  3.000
 HQ6  HD    C2   C3    110.04  3.000
 HQ6  N1    C2   C3    107.25  3.000
 HQ6  C8    C2   C3    110.06  3.000
 HQ6  H82C  C8   H81C  107.52  3.000
 HQ6  H82C  C8   O8    111.25  3.000
 HQ6  H81C  C8   O8    111.05  3.000
 HQ6  H82C  C8   C2    109.00  3.000
 HQ6  H81C  C8   C2    109.44  3.000
 HQ6  O8    C8   C2    108.55  3.000
 HQ6  H8    O8   C8    108.09  3.000
 HQ6  H1    N1   C7    108.45  3.000
 HQ6  H1    N1   C2    110.22  3.000
 HQ6  C7    N1   C2    115.79  3.000
 HQ6  H72C  C7   H71C  107.09  3.000
 HQ6  H72C  C7   N1    112.79  3.000
 HQ6  H71C  C7   N1    107.77  3.000
 HQ6  H72C  C7   C6    108.12  3.000
 HQ6  H71C  C7   C6    107.51  3.000
 HQ6  N1    C7   C6    113.27  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
 HQ6  CONST_01  C5    N2   C9  O9     0.00   0.0  0
 HQ6  CONST_02  C5    N2   C9  C10  180.00   0.0  0
 HQ6  CONST_03  H2    N2   C9  O9   180.00   0.0  0
 HQ6  Var_01    H101  C10  C9  O9    44.61  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
 HQ6  chir_01  C5  N2  C6  C4  negativ
 HQ6  chir_02  C6  O6  C5  C7  negativ
 HQ6  chir_03  C4  O4  C5  C3  positiv
 HQ6  chir_04  C3  O3  C4  C2  negativ
 HQ6  chir_05  C2  N1  C3  C8  negativ

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
 HQ6  plan-1  O9   0.020
 HQ6  plan-1  C9   0.020
 HQ6  plan-1  C10  0.020
 HQ6  plan-1  N2   0.020
 HQ6  plan-1  C5   0.020
 HQ6  plan-1  H2   0.020

