# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:01:22 2020
#   Inital geometry file: a 45 line input string
#   Ligand name: (3R)-2,3,4,5-tetrahydropyridin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]1CCC=NC1
#
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
 XBB  XBB  (3R)-2,3,4,5-tetrahydropyridin-3-amine  ligand  17  7  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XBB
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
 XBB  C2    C  C1    0  -0.054   0.1821   0.0648  -1.7986
 XBB  N1    N  N     0  -0.348   1.2761  -0.0431  -1.1742
 XBB  C3    C  CH2   0  -0.520  -1.1991   0.0945  -1.2161
 XBB  C6    C  CH2   0  -0.306   1.2591  -0.1368   0.2731
 XBB  C5    C  CH1   0  -0.105  -0.0220   0.3322   0.9534
 XBB  C4    C  CH2   0  -0.441  -1.2083  -0.3081   0.2512
 XBB  N7    N  NH2   0  -0.803   0.0136  -0.0477   2.3561
 XBB  HC2   H  H     0   0.240   0.2443   0.1444  -2.8847
 XBB  HC31  H  HCH2  0   0.260  -1.8435  -0.5539  -1.8144
 XBB  HC32  H  HCH2  0   0.257  -1.5977   1.1063  -1.3502
 XBB  HC61  H  HCH2  0   0.234   2.1152   0.4299   0.6521
 XBB  HC62  H  HCH2  0   0.229   1.4477  -1.1803   0.5487
 XBB  HC5   H  HCH1  0   0.202  -0.0994   1.4230   0.8110
 XBB  HC41  H  HCH2  0   0.226  -1.1335  -1.3956   0.3460
 XBB  HC42  H  HCH2  0   0.242  -2.1481  -0.0090   0.7219
 XBB  HN71  H  HNH2  0   0.344   0.7877   0.4179   2.8156
 XBB  HN72  H  HNH2  0   0.344  -0.8199   0.2966   2.8179

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
 XBB  C2  N1    double  1.264  0.020  1.264
 XBB  C2  C3    single  1.499  0.020  1.499
 XBB  C2  HC2   single  0.930  0.020  1.080
 XBB  N1  C6    single  1.450  0.020  1.450
 XBB  C3  C4    single  1.522  0.020  1.522
 XBB  C3  HC31  single  0.970  0.020  1.090
 XBB  C3  HC32  single  0.970  0.020  1.090
 XBB  C6  C5    single  1.524  0.020  1.524
 XBB  C6  HC61  single  0.970  0.020  1.090
 XBB  C6  HC62  single  0.970  0.020  1.090
 XBB  C5  C4    single  1.520  0.020  1.520
 XBB  C5  N7    single  1.454  0.020  1.454
 XBB  C5  HC5   single  0.970  0.020  1.090
 XBB  C4  HC41  single  0.970  0.020  1.090
 XBB  C4  HC42  single  0.970  0.020  1.090
 XBB  N7  HN71  single  0.890  0.020  1.040
 XBB  N7  HN72  single  0.890  0.020  1.040

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
 XBB  HC2   C2  C3    115.98  3.000
 XBB  HC2   C2  N1    116.65  3.000
 XBB  C3    C2  N1    127.37  3.000
 XBB  C6    N1  C2    119.22  3.000
 XBB  HC32  C3  HC31  105.45  3.000
 XBB  HC32  C3  C4    111.11  3.000
 XBB  HC31  C3  C4    111.56  3.000
 XBB  HC32  C3  C2    107.81  3.000
 XBB  HC31  C3  C2    108.59  3.000
 XBB  C4    C3  C2    112.03  3.000
 XBB  HC62  C6  HC61  105.74  3.000
 XBB  HC62  C6  C5    108.99  3.000
 XBB  HC61  C6  C5    110.09  3.000
 XBB  HC62  C6  N1    108.09  3.000
 XBB  HC61  C6  N1    107.64  3.000
 XBB  C5    C6  N1    115.81  3.000
 XBB  HC5   C5  N7    112.63  3.000
 XBB  HC5   C5  C4    107.59  3.000
 XBB  N7    C5  C4    110.78  3.000
 XBB  HC5   C5  C6    107.80  3.000
 XBB  N7    C5  C6    109.25  3.000
 XBB  C4    C5  C6    108.67  3.000
 XBB  HC42  C4  HC41  107.07  3.000
 XBB  HC42  C4  C5    110.91  3.000
 XBB  HC41  C4  C5    108.99  3.000
 XBB  HC42  C4  C3    110.37  3.000
 XBB  HC41  C4  C3    110.25  3.000
 XBB  C5    C4  C3    109.22  3.000
 XBB  HN72  N7  HN71  105.39  3.000
 XBB  HN72  N7  C5    109.32  3.000
 XBB  HN71  N7  C5    109.64  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
 XBB  Var_01  C5   C6  N1  C2  -18.40  30.0  1
 XBB  Var_02  C5   C4  C3  C2   41.60  30.0  1
 XBB  Var_03  C4   C3  C2  N1  -11.78  30.0  1
 XBB  Var_04  HC2  C2  N1  C6  179.28  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
 XBB  chir_01  C5  C6  C4  N7  negativ

