# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 12:11:27 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 2,2,2-trifluoro-N-[(1R,2R,3R,4R,5R,6R)-2,3,5,6-tetrahydroxy-4-(hydroxymethyl)cyclohexyl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H]1[C@@H](O)[C@H](O)[C@@H](NC(=O)C(F)(F)F)[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
 H9J  H9J  2,2,2-trifluoro-N-[(1R,2R,3R,4R,5R,6R)-2,3,5,6-tetrahydroxy-4-(hydroxymethyl)cyclohexyl]acetamide  ligand  33  19  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H9J
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
 H9J  C1   C  CH1   0  -0.003  -0.8809  -1.3990   0.0574
 H9J  C2   C  CH1   0  -0.118  -0.0586  -0.1535  -0.2526
 H9J  C3   C  CH1   0   0.055  -0.6587   1.0884   0.4040
 H9J  C4   C  CH1   0   0.043  -2.1148   1.2775  -0.0284
 H9J  C5   C  CH1   0  -0.339  -2.9509   0.0392   0.2963
 H9J  C6   C  CH2   0  -0.126  -4.4099   0.2453  -0.0930
 H9J  C8   C  CT    0   0.946   3.7154  -0.3618   0.1077
 H9J  C9   C  CH1   0   0.012  -2.3449  -1.2021  -0.3575
 H9J  F81  F  F     0  -0.308   3.9615  -1.6755   0.0757
 H9J  F82  F  F     0  -0.291   4.7077   0.2563  -0.5156
 H9J  F83  F  F     0  -0.304   3.7314   0.0191   1.3887
 H9J  N2   N  NH1   0  -0.640   1.3097  -0.3512   0.1757
 H9J  O3   O  OH1   0  -0.668   0.1368   2.1893   0.0331
 H9J  O4   O  OH1   0  -0.678  -2.6731   2.3914   0.6412
 H9J  O6   O  OH1   0  -0.676  -5.1347  -0.9290   0.2050
 H9J  O7   O  O     0  -0.458   2.3670   0.3630  -1.7132
 H9J  O9   O  OH1   0  -0.672  -2.4393  -1.0609  -1.7586
 H9J  H1   H  HCH1  0   0.246  -0.4647  -2.2360  -0.5218
 H9J  H2   H  HCH1  0   0.277  -0.0534  -0.0154  -1.3351
 H9J  H3   H  HCH1  0   0.214  -0.6423   0.9544   1.4954
 H9J  H4   H  HCH1  0   0.216  -2.1314   1.4449  -1.1142
 H9J  H5   H  HCH1  0   0.245  -2.9099  -0.1234   1.3801
 H9J  H62  H  HCH2  0   0.210  -4.8073   1.1009   0.4617
 H9J  H61  H  HCH2  0   0.190  -4.4758   0.4979  -1.1592
 H9J  H7   H  HCH1  0   0.238  -2.9032  -2.0854  -0.0200
 H9J  HN2  H  HNH1  0   0.413   1.4383  -0.6724   1.1246
 H9J  HO3  H  HOH1  0   0.453  -0.0213   2.9034   0.6576
 H9J  HO4  H  HOH1  0   0.454  -2.4598   3.1870   0.1463
 H9J  HO6  H  HOH1  0   0.454  -6.0546  -0.7770  -0.0281
 H9J  H02  H  HOH1  0   0.455  -2.1771  -1.8903  -2.1703
 H9J  O1   O  OH1   0  -0.673  -0.7671  -1.6521   1.4397
 H9J  H6   H  HOH1  0   0.463  -1.0807  -2.5442   1.6179
 H9J  C7   C  C     0   0.368   2.3682  -0.0567  -0.5747

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
 H9J  F81  C8   single  1.337  0.020  1.337
 H9J  O9   C9   single  1.411  0.020  1.411
 H9J  C8   C7   single  1.541  0.020  1.541
 H9J  C8   F82  single  1.325  0.020  1.325
 H9J  C8   F83  single  1.337  0.020  1.337
 H9J  O7   C7   double  1.213  0.020  1.213
 H9J  C1   C9   single  1.534  0.020  1.534
 H9J  C1   C2   single  1.524  0.020  1.524
 H9J  C7   N2   single  1.330  0.020  1.330
 H9J  C9   C5   single  1.528  0.020  1.528
 H9J  N2   C2   single  1.447  0.020  1.447
 H9J  O6   C6   single  1.412  0.020  1.412
 H9J  C2   C3   single  1.528  0.020  1.528
 H9J  C5   C6   single  1.524  0.020  1.524
 H9J  C5   C4   single  1.529  0.020  1.529
 H9J  C3   C4   single  1.531  0.020  1.531
 H9J  C3   O3   single  1.408  0.020  1.408
 H9J  C4   O4   single  1.414  0.020  1.414
 H9J  C1   H1   single  0.970  0.020  1.090
 H9J  C2   H2   single  0.970  0.020  1.090
 H9J  C3   H3   single  0.970  0.020  1.090
 H9J  C4   H4   single  0.970  0.020  1.090
 H9J  C5   H5   single  0.970  0.020  1.090
 H9J  C6   H62  single  0.970  0.020  1.090
 H9J  C6   H61  single  0.970  0.020  1.090
 H9J  C9   H7   single  0.970  0.020  1.090
 H9J  N2   HN2  single  0.860  0.020  1.020
 H9J  O3   HO3  single  0.850  0.020  0.980
 H9J  O4   HO4  single  0.850  0.020  0.980
 H9J  O6   HO6  single  0.850  0.020  0.980
 H9J  O9   H02  single  0.850  0.020  0.980
 H9J  C1   O1   single  1.410  0.020  1.410
 H9J  O1   H6   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
 H9J  O1   C1  H1   110.44  3.000
 H9J  O1   C1  C9   111.42  3.000
 H9J  H1   C1  C9   108.45  3.000
 H9J  O1   C1  C2   107.61  3.000
 H9J  H1   C1  C2   108.10  3.000
 H9J  C9   C1  C2   110.79  3.000
 H9J  H2   C2  N2   107.83  3.000
 H9J  H2   C2  C3   108.99  3.000
 H9J  N2   C2  C3   110.81  3.000
 H9J  H2   C2  C1   107.92  3.000
 H9J  C3   C2  C1   111.40  3.000
 H9J  N2   C2  C1   109.77  3.000
 H9J  H3   C3  O3   110.38  3.000
 H9J  H3   C3  C4   108.03  3.000
 H9J  O3   C3  C4   111.49  3.000
 H9J  H3   C3  C2   108.77  3.000
 H9J  O3   C3  C2   107.49  3.000
 H9J  C4   C3  C2   110.65  3.000
 H9J  H4   C4  O4   110.00  3.000
 H9J  H4   C4  C5   108.97  3.000
 H9J  O4   C4  C5   108.75  3.000
 H9J  H4   C4  C3   108.20  3.000
 H9J  O4   C4  C3   109.81  3.000
 H9J  C5   C4  C3   111.11  3.000
 H9J  H5   C5  C9   106.71  3.000
 H9J  H5   C5  C6   107.96  3.000
 H9J  C9   C5  C6   112.35  3.000
 H9J  H5   C5  C4   108.03  3.000
 H9J  C6   C5  C4   111.08  3.000
 H9J  C9   C5  C4   110.49  3.000
 H9J  H61  C6  H62  106.90  3.000
 H9J  H61  C6  O6   111.45  3.000
 H9J  H62  C6  O6   110.91  3.000
 H9J  H61  C6  C5   109.68  3.000
 H9J  H62  C6  C5   108.90  3.000
 H9J  O6   C6  C5   108.96  3.000
 H9J  F83  C8  F82  107.99  3.000
 H9J  F83  C8  F81  107.51  3.000
 H9J  F82  C8  F81  108.02  3.000
 H9J  F83  C8  C7   112.24  3.000
 H9J  F82  C8  C7   110.74  3.000
 H9J  F81  C8  C7   110.18  3.000
 H9J  H7   C9  O9   110.58  3.000
 H9J  H7   C9  C5   108.68  3.000
 H9J  O9   C9  C5   108.48  3.000
 H9J  H7   C9  C1   107.39  3.000
 H9J  C5   C9  C1   111.53  3.000
 H9J  O9   C9  C1   110.19  3.000
 H9J  HN2  N2  C7   119.93  3.000
 H9J  HN2  N2  C2   116.22  3.000
 H9J  C7   N2  C2   123.72  3.000
 H9J  HO3  O3  C3   108.46  3.000
 H9J  HO4  O4  C4   108.69  3.000
 H9J  HO6  O6  C6   107.98  3.000
 H9J  H02  O9  C9   108.68  3.000
 H9J  H6   O1  C1   108.76  3.000
 H9J  O7   C7  N2   127.22  3.000
 H9J  N2   C7  C8   113.71  3.000
 H9J  O7   C7  C8   119.01  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
 H9J  CONST_01  C8   C7  N2  C2    180.00   0.0  0
 H9J  CONST_02  O7   C7  N2  C2      0.00   0.0  0
 H9J  CONST_03  HN2  N2  C7  C8      0.00   0.0  0
 H9J  Var_01    O7   C7  C8  F81  -100.54  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
 H9J  chir_01  C1  C9  C2  O1  negativ
 H9J  chir_02  C2  N2  C3  C1  positiv
 H9J  chir_03  C3  O3  C4  C2  negativ
 H9J  chir_04  C4  O4  C5  C3  positiv
 H9J  chir_05  C5  C4  C6  C9  negativ
 H9J  chir_06  C9  O9  C5  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
 H9J  plan-1  C2   0.020
 H9J  plan-1  C8   0.020
 H9J  plan-1  N2   0.020
 H9J  plan-1  O7   0.020
 H9J  plan-1  HN2  0.020
 H9J  plan-1  C7   0.020

