# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 16:23:42 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: piperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)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
 MN1  MN1  'piperidine-4-carboxylic acid'  ligand  19  9  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MN1
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
 MN1  N1   N  NH1    0  -0.595   0.0508   0.3444  -2.5110
 MN1  C2   C  CH2    0  -0.292  -1.0696  -0.4015  -1.9641
 MN1  C3   C  CH2    0  -0.403  -1.2462  -0.0794  -0.4867
 MN1  C4   C  CH1    0  -0.381   0.0282  -0.3796   0.2934
 MN1  C    C  C      0   0.422  -0.0531  -0.0577   1.7990
 MN1  O1   O  O      0  -0.604  -1.1460   0.3330   2.2560
 MN1  O2   O  OC    -1  -0.624   0.9978  -0.2252   2.4545
 MN1  C5   C  CH2    0  -0.413   1.2148   0.3271  -0.3658
 MN1  C6   C  CH2    0  -0.289   1.2961  -0.0021  -1.8488
 MN1  HN1  H  HNH1   0   0.345   0.1322   0.1508  -3.5006
 MN1  H21  H  HCH2   0   0.176  -0.9392  -1.4921  -2.0760
 MN1  H22  H  HCH2   0   0.221  -1.9725  -0.1346  -2.5189
 MN1  H31  H  HCH2   0   0.212  -2.0865  -0.6525  -0.0891
 MN1  H32  H  HCH2   0   0.199  -1.5068   0.9776  -0.3794
 MN1  H4   H  HCH1   0   0.207   0.2191  -1.4609   0.2129
 MN1  H51  H  HCH2   0   0.202   1.1107   1.4114  -0.2455
 MN1  H52  H  HCH2   0   0.218   2.1450   0.0378   0.1246
 MN1  H61  H  HCH2   0   0.177   1.5436  -1.0726  -1.9570
 MN1  H62  H  HCH2   0   0.222   2.1107   0.5581  -2.3148

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
 MN1  N1  C2   single  1.453  0.020  1.453
 MN1  N1  C6   single  1.452  0.020  1.452
 MN1  N1  HN1  single  0.890  0.020  1.040
 MN1  C2  C3   single  1.522  0.020  1.522
 MN1  C2  H21  single  0.970  0.020  1.090
 MN1  C2  H22  single  0.970  0.020  1.090
 MN1  C3  C4   single  1.524  0.020  1.524
 MN1  C3  H31  single  0.970  0.020  1.090
 MN1  C3  H32  single  0.970  0.020  1.090
 MN1  C4  C    single  1.542  0.020  1.542
 MN1  C4  C5   single  1.530  0.020  1.530
 MN1  C4  H4   single  0.970  0.020  1.090
 MN1  C   O1   deloc   1.247  0.020  1.247
 MN1  C   O2   deloc   1.250  0.020  1.250
 MN1  C5  C6   single  1.521  0.020  1.521
 MN1  C5  H51  single  0.970  0.020  1.090
 MN1  C5  H52  single  0.970  0.020  1.090
 MN1  C6  H61  single  0.970  0.020  1.090
 MN1  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
 MN1  HN1  N1  C6   109.35  3.000
 MN1  HN1  N1  C2   109.39  3.000
 MN1  C6   N1  C2   111.54  3.000
 MN1  H22  C2  H21  106.70  3.000
 MN1  H22  C2  C3   110.19  3.000
 MN1  H21  C2  C3   108.73  3.000
 MN1  H22  C2  N1   108.70  3.000
 MN1  H21  C2  N1   112.20  3.000
 MN1  C3   C2  N1   110.25  3.000
 MN1  H32  C3  H31  106.74  3.000
 MN1  H32  C3  C4   109.84  3.000
 MN1  H31  C3  C4   110.71  3.000
 MN1  H32  C3  C2   109.10  3.000
 MN1  H31  C3  C2   109.36  3.000
 MN1  C4   C3  C2   110.98  3.000
 MN1  H4   C4  C5   106.72  3.000
 MN1  H4   C4  C    106.60  3.000
 MN1  C5   C4  C    111.42  3.000
 MN1  H4   C4  C3   107.52  3.000
 MN1  C5   C4  C3   109.69  3.000
 MN1  C    C4  C3   114.49  3.000
 MN1  O2   C   O1   125.91  3.000
 MN1  O2   C   C4   116.09  3.000
 MN1  O1   C   C4   117.99  3.000
 MN1  H52  C5  H51  107.10  3.000
 MN1  H52  C5  C6   109.60  3.000
 MN1  H51  C5  C6   109.04  3.000
 MN1  H52  C5  C4   110.19  3.000
 MN1  H51  C5  C4   109.63  3.000
 MN1  C6   C5  C4   111.19  3.000
 MN1  H62  C6  H61  106.75  3.000
 MN1  H62  C6  C5   110.16  3.000
 MN1  H61  C6  C5   108.50  3.000
 MN1  H62  C6  N1   108.81  3.000
 MN1  H61  C6  N1   112.26  3.000
 MN1  C5   C6  N1   110.30  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
 MN1  Var_01  C4  C3  C2  N1  -57.16  30.0  1
 MN1  Var_02  C4  C5  C6  N1   56.42  30.0  1
 MN1  Var_03  C5  C6  N1  C2  -60.89  30.0  1
 MN1  Var_04  C6  N1  C2  C3   61.26  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
 MN1  chir_01  C4  C3  C  C5  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
 MN1  plan-1  C4  0.020
 MN1  plan-1  C   0.020
 MN1  plan-1  O1  0.020
 MN1  plan-1  O2  0.020

