# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:20:24 2020
#   Inital geometry file: a 41 line input string
#   Ligand name: piperidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CCNCC1
#
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
 PIP  PIP  'piperidine               '  ligand  17  6  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PIP
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
 PIP  N1   N  NH1   0  -0.597   0.0223   0.2583   1.3631
 PIP  C2   C  CH2   0  -0.288  -1.1800  -0.2478   0.7233
 PIP  C3   C  CH2   0  -0.427  -1.2358   0.2222  -0.7234
 PIP  C4   C  CH2   0  -0.439   0.0203  -0.2069  -1.4757
 PIP  C5   C  CH2   0  -0.427   1.2745   0.2346  -0.7275
 PIP  C6   C  CH2   0  -0.288   1.2271  -0.2367   0.7191
 PIP  HN1  H  HNH1  0   0.348   0.0254  -0.0130   2.3374
 PIP  H21  H  HCH2  0   0.226  -2.0513   0.1164   1.2722
 PIP  H22  H  HCH2  0   0.181  -1.2320  -1.3502   0.7395
 PIP  H31  H  HCH2  0   0.211  -1.3253   1.3127  -0.7437
 PIP  H32  H  HCH2  0   0.224  -2.1295  -0.1792  -1.2067
 PIP  H41  H  HCH2  0   0.208   0.0259  -1.2985  -1.5700
 PIP  H42  H  HCH2  0   0.228   0.0162   0.1931  -2.4922
 PIP  H51  H  HCH2  0   0.224   2.1705  -0.1584  -1.2137
 PIP  H52  H  HCH2  0   0.211   1.3533   1.3261  -0.7475
 PIP  H61  H  HCH2  0   0.226   2.0968   0.1341   1.2662
 PIP  H62  H  HCH2  0   0.181   1.2883  -1.3387   0.7340

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
 PIP  N1  C2   single  1.453  0.020  1.453
 PIP  N1  C6   single  1.453  0.020  1.453
 PIP  N1  HN1  single  0.890  0.020  1.040
 PIP  C2  C3   single  1.522  0.020  1.522
 PIP  C2  H21  single  0.970  0.020  1.090
 PIP  C2  H22  single  0.970  0.020  1.090
 PIP  C3  C4   single  1.526  0.020  1.526
 PIP  C3  H31  single  0.970  0.020  1.090
 PIP  C3  H32  single  0.970  0.020  1.090
 PIP  C4  C5   single  1.526  0.020  1.526
 PIP  C4  H41  single  0.970  0.020  1.090
 PIP  C4  H42  single  0.970  0.020  1.090
 PIP  C5  C6   single  1.522  0.020  1.522
 PIP  C5  H51  single  0.970  0.020  1.090
 PIP  C5  H52  single  0.970  0.020  1.090
 PIP  C6  H61  single  0.970  0.020  1.090
 PIP  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
 PIP  HN1  N1  C6   109.45  3.000
 PIP  HN1  N1  C2   109.47  3.000
 PIP  C6   N1  C2   111.86  3.000
 PIP  H22  C2  H21  106.74  3.000
 PIP  H22  C2  C3   108.70  3.000
 PIP  H21  C2  C3   110.21  3.000
 PIP  H22  C2  N1   112.36  3.000
 PIP  H21  C2  N1   108.82  3.000
 PIP  C3   C2  N1   109.96  3.000
 PIP  H32  C3  H31  106.92  3.000
 PIP  H32  C3  C4   110.61  3.000
 PIP  H31  C3  C4   109.78  3.000
 PIP  H32  C3  C2   109.70  3.000
 PIP  H31  C3  C2   109.17  3.000
 PIP  C4   C3  C2   110.59  3.000
 PIP  H42  C4  H41  106.54  3.000
 PIP  H42  C4  C5   110.70  3.000
 PIP  H41  C4  C5   109.04  3.000
 PIP  H42  C4  C3   110.66  3.000
 PIP  H41  C4  C3   109.08  3.000
 PIP  C5   C4  C3   110.71  3.000
 PIP  H52  C5  H51  106.95  3.000
 PIP  H52  C5  C6   109.17  3.000
 PIP  H51  C5  C6   109.70  3.000
 PIP  H52  C5  C4   109.81  3.000
 PIP  H51  C5  C4   110.60  3.000
 PIP  C6   C5  C4   110.54  3.000
 PIP  H62  C6  H61  106.74  3.000
 PIP  H62  C6  C5   108.67  3.000
 PIP  H61  C6  C5   110.25  3.000
 PIP  H62  C6  N1   112.34  3.000
 PIP  H61  C6  N1   108.82  3.000
 PIP  C5   C6  N1   109.97  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
 PIP  Var_01  C4  C3  C2  N1   56.46  30.0  1
 PIP  Var_02  C4  C5  C6  N1  -56.52  30.0  1
 PIP  Var_03  C5  C6  N1  C2   61.81  30.0  1
 PIP  Var_04  C5  C4  C3  C2  -52.66  30.0  1
 PIP  Var_05  C6  N1  C2  C3  -61.76  30.0  1
 PIP  Var_06  C6  C5  C4  C3   52.67  30.0  1

