# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:02:12 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: 4-methylpiperazine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)C(O)=O
#
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
 ODS  ODS  '4-methylpiperazine-1-carboxylic acid'  peptide  21  10  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ODS
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
 ODS  N1   N  NT     0  -0.495  -0.7227   0.0361  -0.0584
 ODS  C    C  C      0   0.523  -2.1356   0.0796  -0.1091
 ODS  O    O  O      0  -0.645  -2.6650   1.2108  -0.0924
 ODS  C2   C  CH2    0  -0.273   0.0355   1.2248  -0.3666
 ODS  C3   C  CH2    0  -0.281   1.4228   1.1540   0.2462
 ODS  N4   N  NT     0  -0.413   2.1165  -0.0453  -0.1775
 ODS  CM   C  CH3    0  -0.514   3.4628  -0.0984   0.3400
 ODS  C5   C  CH2    0  -0.280   1.3518  -1.2187   0.1930
 ODS  C6   C  CH2    0  -0.274  -0.0368  -1.1814  -0.4196
 ODS  OXT  O  OC    -1  -0.645  -2.7308  -1.0180  -0.1390
 ODS  H21  H  HCH2   0   0.185   0.1399   1.3684  -1.4541
 ODS  H22  H  HCH2   0   0.233  -0.4820   2.0978   0.0236
 ODS  H31  H  HCH2   0   0.227   1.9971   2.0284  -0.0716
 ODS  H32  H  HCH2   0   0.181   1.3378   1.2052   1.3470
 ODS  HM1  H  HCH3   0   0.187   3.5065  -0.1318   1.4406
 ODS  HM2  H  HCH3   0   0.229   3.9754  -0.9850  -0.0379
 ODS  HM3  H  HCH3   0   0.229   4.0255   0.7776   0.0125
 ODS  H51  H  HCH2   0   0.227   1.8738  -2.1110  -0.1630
 ODS  H52  H  HCH2   0   0.180   1.2621  -1.3128   1.2905
 ODS  H61  H  HCH2   0   0.234  -0.6046  -2.0380  -0.0647
 ODS  H62  H  HCH2   0   0.185   0.0583  -1.2848  -1.5126

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
 ODS  N1  C    single  1.414  0.020  1.414
 ODS  N1  C2   single  1.443  0.020  1.443
 ODS  N1  C6   single  1.443  0.020  1.443
 ODS  C   O    deloc   1.231  0.020  1.231
 ODS  C   OXT  deloc   1.249  0.020  1.249
 ODS  C2  C3   single  1.518  0.020  1.518
 ODS  C2  H21  single  0.970  0.020  1.090
 ODS  C2  H22  single  0.970  0.020  1.090
 ODS  C3  N4   single  1.449  0.020  1.449
 ODS  C3  H31  single  0.970  0.020  1.090
 ODS  C3  H32  single  0.970  0.020  1.090
 ODS  N4  CM   single  1.443  0.020  1.443
 ODS  N4  C5   single  1.449  0.020  1.449
 ODS  CM  HM1  single  0.970  0.020  1.090
 ODS  CM  HM2  single  0.970  0.020  1.090
 ODS  CM  HM3  single  0.970  0.020  1.090
 ODS  C5  C6   single  1.518  0.020  1.518
 ODS  C5  H51  single  0.970  0.020  1.090
 ODS  C5  H52  single  0.970  0.020  1.090
 ODS  C6  H61  single  0.970  0.020  1.090
 ODS  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
 ODS  C6   N1  C2   113.06  3.000
 ODS  C6   N1  C    119.45  3.000
 ODS  C2   N1  C    119.46  3.000
 ODS  OXT  C   O    126.45  3.000
 ODS  OXT  C   N1   116.74  3.000
 ODS  O    C   N1   116.79  3.000
 ODS  H22  C2  H21  107.13  3.000
 ODS  H22  C2  C3   109.12  3.000
 ODS  H21  C2  C3   108.53  3.000
 ODS  H22  C2  N1   109.55  3.000
 ODS  H21  C2  N1   111.58  3.000
 ODS  C3   C2  N1   110.82  3.000
 ODS  H32  C3  H31  107.02  3.000
 ODS  H32  C3  N4   111.50  3.000
 ODS  H31  C3  N4   109.00  3.000
 ODS  H32  C3  C2   109.24  3.000
 ODS  H31  C3  C2   108.98  3.000
 ODS  N4   C3  C2   110.98  3.000
 ODS  C5   N4  CM   111.77  3.000
 ODS  C5   N4  C3   110.06  3.000
 ODS  CM   N4  C3   111.85  3.000
 ODS  HM3  CM  HM2  107.81  3.000
 ODS  HM3  CM  HM1  107.67  3.000
 ODS  HM2  CM  HM1  107.61  3.000
 ODS  HM3  CM  N4   110.11  3.000
 ODS  HM2  CM  N4   110.10  3.000
 ODS  HM1  CM  N4   113.34  3.000
 ODS  H52  C5  H51  107.01  3.000
 ODS  H52  C5  C6   109.18  3.000
 ODS  H51  C5  C6   108.99  3.000
 ODS  H52  C5  N4   111.46  3.000
 ODS  H51  C5  N4   109.01  3.000
 ODS  C6   C5  N4   111.08  3.000
 ODS  H62  C6  H61  107.14  3.000
 ODS  H62  C6  C5   108.60  3.000
 ODS  H61  C6  C5   109.07  3.000
 ODS  H62  C6  N1   111.62  3.000
 ODS  H61  C6  N1   109.55  3.000
 ODS  C5   C6  N1   110.76  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
 ODS  Var_01  N4   C3  C2  N1   55.44  30.0  1
 ODS  Var_02  N4   C5  C6  N1  -55.37  30.0  1
 ODS  Var_03  C5   C6  N1  C2   53.40  30.0  1
 ODS  Var_04  C6   N1  C2  C3  -53.48  30.0  1
 ODS  Var_05  C6   C5  N4  C3   58.07  30.0  1
 ODS  Var_06  C2   N1  C   O   -17.31  30.0  2
 ODS  Var_07  HM1  CM  N4  C3   62.35  30.0  3

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
 ODS  plan-1  N1   0.020
 ODS  plan-1  C    0.020
 ODS  plan-1  O    0.020
 ODS  plan-1  OXT  0.020

