# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 00:49:08 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2R,4R)-4-methylpiperidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CCN[C@H](C1)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
 MCP  MCP  '(2R,4R)-4-methylpiperidine-2-carboxylic acid'  ligand  22  10  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MCP
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
 MCP  N    N  NH1    0  -0.600  -1.3596  -0.1862   0.0375
 MCP  C1   C  CH1    0  -0.219  -0.0026  -0.2398  -0.4759
 MCP  C2   C  CH2    0  -0.400   0.8389   0.7834   0.2785
 MCP  C3   C  CH1    0  -0.247   0.8127   0.5490   1.7943
 MCP  C4   C  CH2    0  -0.415  -0.6335   0.3984   2.2783
 MCP  C5   C  CH2    0  -0.292  -1.4223  -0.5886   1.4278
 MCP  C6   C  C      0   0.413   0.0322  -0.0515  -2.0068
 MCP  O1   O  O      0  -0.610  -1.0253  -0.2759  -2.6297
 MCP  O2   O  OC    -1  -0.612   1.1308   0.2636  -2.5055
 MCP  C7   C  CH3    0  -0.663   1.6819  -0.6390   2.2037
 MCP  HN   H  HNH1   0   0.333  -1.9521  -0.7723  -0.5343
 MCP  H1   H  HCH1   0   0.189   0.4432  -1.2396  -0.2956
 MCP  H21  H  HCH2   0   0.206   0.4477   1.7832   0.0607
 MCP  H22  H  HCH2   0   0.212   1.8678   0.7595  -0.0835
 MCP  H3   H  HCH1   0   0.219   1.2368   1.4355   2.2780
 MCP  H41  H  HCH2   0   0.214  -0.6515   0.0870   3.3267
 MCP  H42  H  HCH2   0   0.213  -1.1343   1.3705   2.2305
 MCP  H51  H  HCH2   0   0.179  -1.0366  -1.6097   1.5897
 MCP  H52  H  HCH2   0   0.221  -2.4668  -0.5989   1.7500
 MCP  H71  H  HCH3   0   0.221   1.6786  -0.7684   3.2879
 MCP  H72  H  HCH3   0   0.218   1.3455  -1.5793   1.7639
 MCP  H73  H  HCH3   0   0.222   2.7174  -0.4883   1.8919

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
 MCP  N   C1   single  1.452  0.020  1.452
 MCP  N   C5   single  1.449  0.020  1.449
 MCP  N   HN   single  0.890  0.020  1.040
 MCP  C1  C2   single  1.525  0.020  1.525
 MCP  C1  C6   single  1.543  0.020  1.543
 MCP  C1  H1   single  0.970  0.020  1.090
 MCP  C2  C3   single  1.534  0.020  1.534
 MCP  C2  H21  single  0.970  0.020  1.090
 MCP  C2  H22  single  0.970  0.020  1.090
 MCP  C3  C4   single  1.532  0.020  1.532
 MCP  C3  C7   single  1.528  0.020  1.528
 MCP  C3  H3   single  0.970  0.020  1.090
 MCP  C4  C5   single  1.523  0.020  1.523
 MCP  C4  H41  single  0.970  0.020  1.090
 MCP  C4  H42  single  0.970  0.020  1.090
 MCP  C5  H51  single  0.970  0.020  1.090
 MCP  C5  H52  single  0.970  0.020  1.090
 MCP  C6  O1   deloc   1.248  0.020  1.248
 MCP  C6  O2   deloc   1.247  0.020  1.247
 MCP  C7  H71  single  0.970  0.020  1.090
 MCP  C7  H72  single  0.970  0.020  1.090
 MCP  C7  H73  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
 MCP  HN   N   C5   110.88  3.000
 MCP  HN   N   C1   109.05  3.000
 MCP  C5   N   C1   111.69  3.000
 MCP  H1   C1  C6   105.19  3.000
 MCP  H1   C1  C2   107.61  3.000
 MCP  C6   C1  C2   113.37  3.000
 MCP  H1   C1  N    110.57  3.000
 MCP  C6   C1  N    111.56  3.000
 MCP  C2   C1  N    108.43  3.000
 MCP  H22  C2  H21  106.90  3.000
 MCP  H22  C2  C3   109.92  3.000
 MCP  H21  C2  C3   109.26  3.000
 MCP  H22  C2  C1   109.98  3.000
 MCP  H21  C2  C1   108.48  3.000
 MCP  C3   C2  C1   112.15  3.000
 MCP  H3   C3  C7   106.90  3.000
 MCP  H3   C3  C4   107.79  3.000
 MCP  C7   C3  C4   112.08  3.000
 MCP  H3   C3  C2   107.82  3.000
 MCP  C7   C3  C2   111.95  3.000
 MCP  C4   C3  C2   110.07  3.000
 MCP  H42  C4  H41  106.68  3.000
 MCP  H42  C4  C5   108.31  3.000
 MCP  H41  C4  C5   110.01  3.000
 MCP  H42  C4  C3   109.31  3.000
 MCP  H41  C4  C3   110.25  3.000
 MCP  C5   C4  C3   112.09  3.000
 MCP  H52  C5  H51  106.38  3.000
 MCP  H52  C5  C4   109.66  3.000
 MCP  H51  C5  C4   109.68  3.000
 MCP  H52  C5  N    109.08  3.000
 MCP  H51  C5  N    112.49  3.000
 MCP  C4   C5  N    109.48  3.000
 MCP  O2   C6  O1   126.33  3.000
 MCP  O2   C6  C1   116.59  3.000
 MCP  O1   C6  C1   117.02  3.000
 MCP  H73  C7  H72  107.23  3.000
 MCP  H73  C7  H71  107.63  3.000
 MCP  H72  C7  H71  107.28  3.000
 MCP  H73  C7  C3   110.84  3.000
 MCP  H72  C7  C3   112.74  3.000
 MCP  H71  C7  C3   110.89  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
 MCP  Var_01  C3  C4  C5  N   -55.35  30.0  1
 MCP  Var_02  C4  C5  N   C1   63.86  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
 MCP  chir_01  C1  N   C2  C6  positiv
 MCP  chir_02  C3  C2  C4  C7  negativ

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
 MCP  plan-1  C1  0.020
 MCP  plan-1  C6  0.020
 MCP  plan-1  O1  0.020
 MCP  plan-1  O2  0.020

