# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 21:56:46 2022
#   Inital geometry file: a 45 line input string
#   Ligand name: (3R,4R)-piperidine-3,4-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCNC[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
 XIF  XIF  (3R,4R)-piperidine-3,4-diol  ligand  19  8  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XIF
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
 XIF  N1   N  NH1   0  -0.599   1.8805  -0.5883  -0.3215
 XIF  C2   C  CH2   0  -0.334   0.7643  -1.3768   0.1592
 XIF  C3   C  CH1   0   0.050  -0.5556  -0.7313  -0.2623
 XIF  O3   O  OH1   0  -0.672  -1.6600  -1.4630   0.2188
 XIF  C4   C  CH1   0   0.048  -0.6290   0.6776   0.3001
 XIF  O4   O  OH1   0  -0.672  -1.8200   1.2810  -0.1545
 XIF  C5   C  CH2   0  -0.482   0.6101   1.4652  -0.1173
 XIF  C6   C  CH2   0  -0.299   1.8861   0.7362   0.2730
 XIF  HN1  H  HNH1  0   0.356   2.7472  -1.0640  -0.1096
 XIF  H21  H  HCH2  0   0.237   0.8290  -2.3808  -0.2691
 XIF  H22  H  HCH2  0   0.192   0.7604  -1.4945   1.2563
 XIF  H3   H  HCH1  0   0.196  -0.5691  -0.6657  -1.3611
 XIF  HO3  H  HOH1  0   0.449  -1.6395  -2.3357  -0.1860
 XIF  H4   H  HCH1  0   0.187  -0.6317   0.5972   1.4001
 XIF  HO4  H  HOH1  0   0.448  -1.8206   2.1965   0.1420
 XIF  H51  H  HCH2  0   0.224   0.5937   1.6137  -1.2014
 XIF  H52  H  HCH2  0   0.238   0.5918   2.4545   0.3488
 XIF  H61  H  HCH2  0   0.193   1.9682   0.7062   1.3721
 XIF  H62  H  HCH2  0   0.237   2.7545   1.2866  -0.0935

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
 XIF  N1  C2   single  1.449  0.020  1.449
 XIF  N1  C6   single  1.452  0.020  1.452
 XIF  N1  HN1  single  0.890  0.020  1.040
 XIF  C2  C3   single  1.529  0.020  1.529
 XIF  C2  H21  single  0.970  0.020  1.090
 XIF  C2  H22  single  0.970  0.020  1.090
 XIF  C3  O3   single  1.409  0.020  1.409
 XIF  C3  C4   single  1.519  0.020  1.519
 XIF  C3  H3   single  0.970  0.020  1.090
 XIF  O3  HO3  single  0.850  0.020  0.980
 XIF  C4  O4   single  1.410  0.020  1.410
 XIF  C4  C5   single  1.526  0.020  1.526
 XIF  C4  H4   single  0.970  0.020  1.090
 XIF  O4  HO4  single  0.850  0.020  0.980
 XIF  C5  C6   single  1.520  0.020  1.520
 XIF  C5  H51  single  0.970  0.020  1.090
 XIF  C5  H52  single  0.970  0.020  1.090
 XIF  C6  H61  single  0.970  0.020  1.090
 XIF  C6  H62  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
 XIF  HN1  N1  C6   109.88  3.000
 XIF  HN1  N1  C2   109.56  3.000
 XIF  C6   N1  C2   111.32  3.000
 XIF  H22  C2  H21  106.96  3.000
 XIF  H22  C2  C3   108.43  3.000
 XIF  H21  C2  C3   109.32  3.000
 XIF  H22  C2  N1   113.00  3.000
 XIF  H21  C2  N1   108.91  3.000
 XIF  C3   C2  N1   110.12  3.000
 XIF  H3   C3  C4   108.29  3.000
 XIF  H3   C3  O3   111.22  3.000
 XIF  C4   C3  O3   108.49  3.000
 XIF  H3   C3  C2   108.12  3.000
 XIF  C4   C3  C2   109.35  3.000
 XIF  O3   C3  C2   111.30  3.000
 XIF  HO3  O3  C3   108.09  3.000
 XIF  H4   C4  C5   108.20  3.000
 XIF  H4   C4  O4   110.52  3.000
 XIF  C5   C4  O4   112.13  3.000
 XIF  H4   C4  C3   107.57  3.000
 XIF  C5   C4  C3   109.76  3.000
 XIF  O4   C4  C3   108.56  3.000
 XIF  HO4  O4  C4   107.95  3.000
 XIF  H52  C5  H51  107.41  3.000
 XIF  H52  C5  C6   109.78  3.000
 XIF  H51  C5  C6   109.38  3.000
 XIF  H52  C5  C4   109.67  3.000
 XIF  H51  C5  C4   109.19  3.000
 XIF  C6   C5  C4   111.33  3.000
 XIF  H62  C6  H61  106.81  3.000
 XIF  H62  C6  C5   109.86  3.000
 XIF  H61  C6  C5   109.36  3.000
 XIF  H62  C6  N1   109.00  3.000
 XIF  H61  C6  N1   112.56  3.000
 XIF  C5   C6  N1   109.21  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
 XIF  Var_01  C4  C5  C6  N1   56.81  30.0  1
 XIF  Var_02  C5  C6  N1  C2  -61.47  30.0  1
 XIF  Var_03  C6  N1  C2  C3   63.23  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
 XIF  chir_01  C3  C2  O3  C4  negativ
 XIF  chir_02  C4  O4  C3  C5  negativ

