# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:01:39 2021
#   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  23  10  .  2021-08-14  2022-11-17
;
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  -0.573  -34.9886  -28.7846  43.0140
 MCP  C1   C  CH1   0  -0.259  -33.7480  -29.0911  42.3297
 MCP  C2   C  CH2   0  -0.413  -32.5115  -28.4552  42.9717
 MCP  C3   C  CH1   0  -0.243  -32.6848  -26.9536  43.1891
 MCP  C4   C  CH2   0  -0.418  -33.9785  -26.6986  43.9580
 MCP  C5   C  CH2   0  -0.326  -35.1663  -27.3625  43.2700
 MCP  C6   C  C     0   0.550  -33.8284  -28.7702  40.8440
 MCP  O1   O  O     0  -0.447  -32.8648  -28.5353  40.1558
 MCP  O2   O  OH1   0  -0.580  -35.0583  -28.8347  40.3548
 MCP  C7   C  CH3   0  -0.650  -31.4781  -26.3528  43.8952
 MCP  HN   H  HNH1  0   0.352  -35.0014  -29.2889  43.8915
 MCP  H1   H  HCH1  0   0.299  -33.6252  -30.1814  42.3594
 MCP  H21  H  HCH2  0   0.227  -32.3558  -28.9385  43.9426
 MCP  H22  H  HCH2  0   0.236  -31.6193  -28.6622  42.3778
 MCP  H3   H  HCH1  0   0.218  -32.7766  -26.4712  42.2077
 MCP  H41  H  HCH2  0   0.208  -33.8773  -27.0901  44.9773
 MCP  H42  H  HCH2  0   0.225  -34.1594  -25.6237  44.0513
 MCP  H51  H  HCH2  0   0.219  -35.3579  -26.8601  42.3153
 MCP  H52  H  HCH2  0   0.240  -36.0725  -27.2382  43.8657
 MCP  HO2  H  HOH1  0   0.476  -35.0281  -28.6688  39.4004
 MCP  H71  H  HCH3  0   0.225  -31.5958  -25.2763  44.0326
 MCP  H72  H  HCH3  0   0.213  -31.3385  -26.7989  44.8828
 MCP  H73  H  HCH3  0   0.224  -30.5613  -26.5168  43.3256

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  1.450  0.020  1.450
 MCP  N   C5   single  1.456  0.020  1.456
 MCP  N   HN   single  0.890  0.020  1.040
 MCP  C1  C2   single  1.531  0.020  1.531
 MCP  C1  C6   single  1.522  0.020  1.522
 MCP  C1  H1   single  0.970  0.020  1.090
 MCP  C2  C3   single  1.527  0.020  1.527
 MCP  C2  H21  single  0.970  0.020  1.090
 MCP  C2  H22  single  0.970  0.020  1.090
 MCP  C3  C4   single  1.526  0.020  1.526
 MCP  C3  C7   single  1.522  0.020  1.522
 MCP  C3  H3   single  0.970  0.020  1.090
 MCP  C4  C5   single  1.525  0.020  1.525
 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   double  1.207  0.020  1.207
 MCP  C6  O2   single  1.325  0.020  1.325
 MCP  O2  HO2  single  0.850  0.020  0.980
 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   109.43  3.000
 MCP  HN   N   C1   108.35  3.000
 MCP  C5   N   C1   113.20  3.000
 MCP  H1   C1  C6   103.99  3.000
 MCP  H1   C1  C2   108.10  3.000
 MCP  C6   C1  C2   111.36  3.000
 MCP  H1   C1  N    107.04  3.000
 MCP  C6   C1  N    111.78  3.000
 MCP  C2   C1  N    113.91  3.000
 MCP  H22  C2  H21  106.40  3.000
 MCP  H22  C2  C3   110.90  3.000
 MCP  H21  C2  C3   108.89  3.000
 MCP  H22  C2  C1   110.68  3.000
 MCP  H21  C2  C1   107.64  3.000
 MCP  C3   C2  C1   112.11  3.000
 MCP  H3   C3  C7   107.92  3.000
 MCP  H3   C3  C4   107.83  3.000
 MCP  C7   C3  C4   111.86  3.000
 MCP  H3   C3  C2   108.32  3.000
 MCP  C7   C3  C2   111.37  3.000
 MCP  C4   C3  C2   109.40  3.000
 MCP  H42  C4  H41  106.67  3.000
 MCP  H42  C4  C5   109.72  3.000
 MCP  H41  C4  C5   109.63  3.000
 MCP  H42  C4  C3   110.32  3.000
 MCP  H41  C4  C3   109.29  3.000
 MCP  C5   C4  C3   111.11  3.000
 MCP  H52  C5  H51  106.15  3.000
 MCP  H52  C5  C4   110.54  3.000
 MCP  H51  C5  C4   109.25  3.000
 MCP  H52  C5  N    107.97  3.000
 MCP  H51  C5  N    108.42  3.000
 MCP  C4   C5  N    114.18  3.000
 MCP  O2   C6  O1   122.67  3.000
 MCP  O2   C6  C1   113.52  3.000
 MCP  O1   C6  C1   123.73  3.000
 MCP  HO2  O2  C6   109.05  3.000
 MCP  H73  C7  H72  107.64  3.000
 MCP  H73  C7  H71  107.72  3.000
 MCP  H72  C7  H71  107.61  3.000
 MCP  H73  C7  C3   111.38  3.000
 MCP  H72  C7  C3   111.07  3.000
 MCP  H71  C7  C3   111.24  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  CONST_01  HO2  O2  C6  C1  180.00   0.0  0
 MCP  Var_01    C3   C4  C5  N    53.79  30.0  1
 MCP  Var_02    C4   C5  N   C1  -51.41  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
 MCP  plan-1  HO2  0.020

