# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 15:53:07 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  22  10  .  2022-03-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

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  -0.472  -0.7469   0.0599  -0.2765
 ODS  C    C  C     0   0.683  -2.0252   0.1537   0.1311
 ODS  O    O  O     0  -0.531  -2.6195   1.1990   0.3295
 ODS  C2   C  CH2   0  -0.301   0.0321   1.2498  -0.5582
 ODS  C3   C  CH2   0  -0.277   1.3605   1.1937   0.1749
 ODS  N4   N  NT    0  -0.417   2.0807  -0.0195  -0.1552
 ODS  CM   C  CH3   0  -0.516   3.3803  -0.0557   0.4754
 ODS  C5   C  CH2   0  -0.275   1.2941  -1.1890   0.1788
 ODS  C6   C  CH2   0  -0.304  -0.0384  -1.1771  -0.5509
 ODS  OXT  O  OH1   0  -0.622  -2.6051  -1.0395   0.3053
 ODS  H21  H  HCH2  0   0.237   0.2111   1.3185  -1.6365
 ODS  H22  H  HCH2  0   0.265  -0.5199   2.1348  -0.2548
 ODS  H31  H  HCH2  0   0.243   1.9600   2.0571  -0.1228
 ODS  H32  H  HCH2  0   0.196   1.1794   1.2827   1.2604
 ODS  HM1  H  HCH3  0   0.194   3.3278  -0.0586   1.5752
 ODS  HM2  H  HCH3  0   0.234   3.9216  -0.9506   0.1649
 ODS  HM3  H  HCH3  0   0.234   3.9668   0.8127   0.1717
 ODS  H51  H  HCH2  0   0.243   1.8426  -2.0858  -0.1185
 ODS  H52  H  HCH2  0   0.196   1.1102  -1.2656   1.2649
 ODS  H61  H  HCH2  0   0.271  -0.6243  -2.0376  -0.2437
 ODS  H62  H  HCH2  0   0.237   0.1351  -1.2606  -1.6291
 ODS  HXT  H  HOH1  0   0.484  -3.5114  -0.8964   0.6070

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  1.345  0.020  1.345
 ODS  N1   C2   single  1.450  0.020  1.450
 ODS  N1   C6   single  1.452  0.020  1.452
 ODS  C    O    double  1.231  0.020  1.231
 ODS  C    OXT  single  1.338  0.020  1.338
 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  1.445  0.020  1.445
 ODS  N4   C5   single  1.448  0.020  1.448
 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  1.519  0.020  1.519
 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
 ODS  OXT  HXT  single  0.850  0.020  0.980

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   113.60  3.000
 ODS  C6   N1   C    125.49  3.000
 ODS  C2   N1   C    120.82  3.000
 ODS  OXT  C    O    122.16  3.000
 ODS  OXT  C    N1   112.90  3.000
 ODS  O    C    N1   124.94  3.000
 ODS  H22  C2   H21  107.87  3.000
 ODS  H22  C2   C3   109.87  3.000
 ODS  H21  C2   C3   109.55  3.000
 ODS  H22  C2   N1   109.96  3.000
 ODS  H21  C2   N1   109.31  3.000
 ODS  C3   C2   N1   110.24  3.000
 ODS  H32  C3   H31  107.11  3.000
 ODS  H32  C3   N4   111.90  3.000
 ODS  H31  C3   N4   109.08  3.000
 ODS  H32  C3   C2   109.16  3.000
 ODS  H31  C3   C2   108.62  3.000
 ODS  N4   C3   C2   110.84  3.000
 ODS  C5   N4   CM   111.56  3.000
 ODS  C5   N4   C3   110.71  3.000
 ODS  CM   N4   C3   111.63  3.000
 ODS  HM3  CM   HM2  107.87  3.000
 ODS  HM3  CM   HM1  107.80  3.000
 ODS  HM2  CM   HM1  107.81  3.000
 ODS  HM3  CM   N4   110.00  3.000
 ODS  HM2  CM   N4   110.04  3.000
 ODS  HM1  CM   N4   113.15  3.000
 ODS  H52  C5   H51  107.12  3.000
 ODS  H52  C5   C6   109.08  3.000
 ODS  H51  C5   C6   108.42  3.000
 ODS  H52  C5   N4   111.92  3.000
 ODS  H51  C5   N4   109.12  3.000
 ODS  C6   C5   N4   111.05  3.000
 ODS  H62  C6   H61  107.68  3.000
 ODS  H62  C6   C5   109.47  3.000
 ODS  H61  C6   C5   109.35  3.000
 ODS  H62  C6   N1   109.16  3.000
 ODS  H61  C6   N1   111.01  3.000
 ODS  C5   C6   N1   110.11  3.000
 ODS  HXT  OXT  C    108.37  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  CONST_01  HXT  OXT  C   N1  180.00   0.0  0
 ODS  Var_01    N4   C3   C2  N1   55.32  30.0  1
 ODS  Var_02    N4   C5   C6  N1  -54.98  30.0  1
 ODS  Var_03    C5   C6   N1  C2   53.71  30.0  1
 ODS  Var_04    C6   N1   C2  C3  -53.97  30.0  1
 ODS  Var_05    C6   C5   N4  C3   58.20  30.0  1
 ODS  Var_06    C2   N1   C   O    -1.94  30.0  3
 ODS  Var_07    HM1  CM   N4  C3   62.55  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
 ODS  plan-1  HXT  0.020

