# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 07:56:59 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: (3R)-1-acetyl-3-hydroxypiperidine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC[C@@](O)(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
 VWM  VWM  '(3R)-1-acetyl-3-hydroxypiperidine-3-carboxylic acid'  ligand  25  13  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_VWM
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
 VWM  N1   N  NT     0  -0.434  -29.2121  14.4376  -21.7436
 VWM  C4   C  CH2    0  -0.427  -28.6393  14.7771  -24.1020
 VWM  C5   C  CH2    0  -0.442  -29.9039  15.6134  -24.2694
 VWM  C6   C  CT     0   0.087  -30.9802  15.2076  -23.2564
 VWM  C7   C  CH2    0  -0.302  -30.3799  15.2924  -21.8467
 VWM  C8   C  C      0   0.418  -32.2131  16.1450  -23.3482
 VWM  C1   C  CH3    0  -0.805  -28.0196  12.4075  -21.0772
 VWM  C2   C  C      0   0.505  -29.2415  13.2992  -21.0174
 VWM  O1   O  O      0  -0.505  -30.1979  12.9910  -20.3154
 VWM  C3   C  CH2    0  -0.313  -28.1504  14.8169  -22.6593
 VWM  O2   O  OH1    0  -0.701  -31.4052  13.8900  -23.5068
 VWM  O3   O  O      0  -0.580  -32.0421  17.3550  -23.1394
 VWM  O4   O  OC    -1  -0.599  -33.2860  15.5595  -23.6249
 VWM  H7   H  HCH2   0   0.232  -27.8481  15.1515  -24.7555
 VWM  H6   H  HCH2   0   0.223  -28.8249  13.7397  -24.3920
 VWM  H9   H  HCH2   0   0.217  -29.6605  16.6695  -24.1265
 VWM  H8   H  HCH2   0   0.229  -30.2943  15.5142  -25.2860
 VWM  H12  H  HCH2   0   0.234  -30.0774  16.3226  -21.6386
 VWM  H11  H  HCH2   0   0.253  -31.1111  15.0010  -21.0958
 VWM  H2   H  HCH3   0   0.263  -28.1765  11.5511  -20.4267
 VWM  H1   H  HCH3   0   0.260  -27.8352  12.0409  -22.0880
 VWM  H3   H  HCH3   0   0.261  -27.1183  12.9268  -20.7498
 VWM  H4   H  HCH2   0   0.236  -27.8313  15.8347  -22.4085
 VWM  H5   H  HCH2   0   0.267  -27.2819  14.1771  -22.5305
 VWM  H10  H  HOH1   0   0.424  -32.3632  14.0204  -23.6568

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
 VWM  C1  C2   single  1.514  0.020  1.514
 VWM  C2  O1   double  1.226  0.020  1.226
 VWM  C2  N1   single  1.351  0.020  1.351
 VWM  N1  C3   single  1.452  0.020  1.452
 VWM  C3  C4   single  1.524  0.020  1.524
 VWM  C4  C5   single  1.525  0.020  1.525
 VWM  C5  C6   single  1.533  0.020  1.533
 VWM  C6  O2   single  1.407  0.020  1.407
 VWM  C6  C7   single  1.535  0.020  1.535
 VWM  C6  C8   single  1.551  0.020  1.551
 VWM  C8  O3   deloc   1.240  0.020  1.240
 VWM  C8  O4   deloc   1.253  0.020  1.253
 VWM  N1  C7   single  1.451  0.020  1.451
 VWM  C4  H7   single  0.970  0.020  1.090
 VWM  C4  H6   single  0.970  0.020  1.090
 VWM  C5  H9   single  0.970  0.020  1.090
 VWM  C5  H8   single  0.970  0.020  1.090
 VWM  C7  H12  single  0.970  0.020  1.090
 VWM  C7  H11  single  0.970  0.020  1.090
 VWM  C1  H2   single  0.970  0.020  1.090
 VWM  C1  H1   single  0.970  0.020  1.090
 VWM  C1  H3   single  0.970  0.020  1.090
 VWM  C3  H4   single  0.970  0.020  1.090
 VWM  C3  H5   single  0.970  0.020  1.090
 VWM  O2  H10  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
 VWM  C3   N1  C2   125.10  3.000
 VWM  C3   N1  C7   112.94  3.000
 VWM  C2   N1  C7   121.15  3.000
 VWM  H6   C4  H7   106.82  3.000
 VWM  H6   C4  C3   109.30  3.000
 VWM  H7   C4  C3   108.97  3.000
 VWM  H6   C4  C5   110.52  3.000
 VWM  H7   C4  C5   110.30  3.000
 VWM  C3   C4  C5   110.83  3.000
 VWM  H8   C5  H9   106.78  3.000
 VWM  H8   C5  C6   109.85  3.000
 VWM  H9   C5  C6   109.01  3.000
 VWM  H8   C5  C4   110.39  3.000
 VWM  H9   C5  C4   109.32  3.000
 VWM  C6   C5  C4   111.38  3.000
 VWM  O2   C6  C8   108.38  3.000
 VWM  C8   C6  C7   109.38  3.000
 VWM  O2   C6  C7   109.48  3.000
 VWM  C8   C6  C5   111.04  3.000
 VWM  C7   C6  C5   108.53  3.000
 VWM  O2   C6  C5   110.03  3.000
 VWM  H11  C7  H12  107.87  3.000
 VWM  H11  C7  C6   110.87  3.000
 VWM  H12  C7  C6   109.58  3.000
 VWM  H11  C7  N1   109.52  3.000
 VWM  H12  C7  N1   108.60  3.000
 VWM  C6   C7  N1   110.34  3.000
 VWM  O4   C8  O3   127.68  3.000
 VWM  O4   C8  C6   114.27  3.000
 VWM  O3   C8  C6   118.05  3.000
 VWM  H3   C1  H1   107.37  3.000
 VWM  H3   C1  H2   108.35  3.000
 VWM  H1   C1  H2   108.31  3.000
 VWM  H3   C1  C2   112.01  3.000
 VWM  H1   C1  C2   111.78  3.000
 VWM  H2   C1  C2   108.90  3.000
 VWM  O1   C2  C1   120.29  3.000
 VWM  O1   C2  N1   122.47  3.000
 VWM  C1   C2  N1   117.23  3.000
 VWM  H5   C3  H4   106.68  3.000
 VWM  H5   C3  C4   110.69  3.000
 VWM  H4   C3  C4   109.53  3.000
 VWM  H5   C3  N1   110.85  3.000
 VWM  H4   C3  N1   108.13  3.000
 VWM  C4   C3  N1   110.83  3.000
 VWM  H10  O2  C6   101.44  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
 VWM  CONST_01  C1  C2  N1  C7  180.00   0.0  0
 VWM  CONST_02  O1  C2  N1  C7    0.00   0.0  0
 VWM  CONST_03  C3  N1  C2  C1    0.00   0.0  0
 VWM  CONST_04  C3  N1  C2  O1  180.00   0.0  0
 VWM  Var_01    C5  C4  C3  N1   53.46  30.0  1
 VWM  Var_02    C7  N1  C3  C4  -58.58  30.0  1
 VWM  Var_03    C3  C4  C5  C6  -53.05  30.0  1
 VWM  Var_04    C3  N1  C7  C6   61.34  30.0  1
 VWM  Var_05    H2  C1  C2  N1  178.43  30.0  3

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
 VWM  chir_01  C6  C5  C7  C8  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
 VWM  plan-1  N1  0.020
 VWM  plan-1  C7  0.020
 VWM  plan-1  C1  0.020
 VWM  plan-1  C2  0.020
 VWM  plan-1  O1  0.020
 VWM  plan-1  C3  0.020
 VWM  plan-2  C6  0.020
 VWM  plan-2  C8  0.020
 VWM  plan-2  O3  0.020
 VWM  plan-2  O4  0.020

