# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 09:21:20 2021
#   Inital geometry file: a 61 line input string
#   Ligand name: 1-carbamoylpiperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)N1CCC(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
 W3V  W3V  '1-carbamoylpiperidine-4-carboxylic acid'  ligand  24  12  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W3V
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
 W3V  N1   N  NT    0  -0.471  -0.8680  15.8575  -4.4180
 W3V  C4   C  CH2   0  -0.415   1.0620  14.6801  -3.4732
 W3V  C5   C  CH2   0  -0.316   0.5450  15.5778  -4.5894
 W3V  C6   C  C     0   0.555   0.6383  12.4244  -2.3290
 W3V  O2   O  OH1   0  -0.585   1.2312  12.9987  -1.2908
 W3V  O1   O  O     0  -0.453   0.4054  11.2406  -2.3783
 W3V  C3   C  CH1   0  -0.386   0.2434  13.3943  -3.4142
 W3V  C2   C  CH2   0  -0.428  -1.2502  13.7254  -3.2787
 W3V  C1   C  CH2   0  -0.294  -1.6943  14.6674  -4.3892
 W3V  C    C  C     0   0.659  -1.4444  17.0904  -4.4548
 W3V  O    O  O     0  -0.546  -2.6614  17.2433  -4.5217
 W3V  N    N  NH2   0  -0.845  -0.6017  18.1678  -4.4526
 W3V  H1   H  HCH2  0   0.251   2.1147  14.4581  -3.6603
 W3V  H2   H  HCH2  0   0.238   1.0047  15.2257  -2.5288
 W3V  H3   H  HCH2  0   0.241   0.6973  15.0878  -5.5590
 W3V  H4   H  HCH2  0   0.260   1.1325  16.4910  -4.6213
 W3V  H5   H  HOH1  0   0.482   1.4324  12.3320  -0.6164
 W3V  H6   H  HCH1  0   0.271   0.3742  12.8536  -4.3584
 W3V  H7   H  HCH2  0   0.240  -1.4468  14.1877  -2.3073
 W3V  H8   H  HCH2  0   0.254  -1.8467  12.8128  -3.3322
 W3V  H9   H  HCH2  0   0.268  -2.7322  14.9513  -4.2426
 W3V  H10  H  HCH2  0   0.230  -1.6327  14.1488  -5.3543
 W3V  H11  H  HNH2  0   0.393  -1.0625  19.0524  -4.3153
 W3V  H12  H  HNH2  0   0.396   0.2934  18.1133  -3.9968

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
 W3V  O   C    double  1.228  0.020  1.228
 W3V  C5  N1   single  1.451  0.020  1.451
 W3V  C5  C4   single  1.523  0.020  1.523
 W3V  C   N    single  1.368  0.020  1.368
 W3V  C   N1   single  1.361  0.020  1.361
 W3V  N1  C1   single  1.449  0.020  1.449
 W3V  C1  C2   single  1.522  0.020  1.522
 W3V  C3  C4   single  1.525  0.020  1.525
 W3V  C3  C2   single  1.536  0.020  1.536
 W3V  C3  C6   single  1.508  0.020  1.508
 W3V  O1  C6   double  1.208  0.020  1.208
 W3V  C6  O2   single  1.326  0.020  1.326
 W3V  C4  H1   single  0.970  0.020  1.090
 W3V  C4  H2   single  0.970  0.020  1.090
 W3V  C5  H3   single  0.970  0.020  1.090
 W3V  C5  H4   single  0.970  0.020  1.090
 W3V  O2  H5   single  0.850  0.020  0.980
 W3V  C3  H6   single  0.970  0.020  1.090
 W3V  C2  H7   single  0.970  0.020  1.090
 W3V  C2  H8   single  0.970  0.020  1.090
 W3V  C1  H9   single  0.970  0.020  1.090
 W3V  C1  H10  single  0.970  0.020  1.090
 W3V  N   H11  single  0.890  0.020  1.040
 W3V  N   H12  single  0.890  0.020  1.040

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
 W3V  C    N1  C1   120.19  3.000
 W3V  C1   N1  C5   113.54  3.000
 W3V  C    N1  C5   125.72  3.000
 W3V  H2   C4  H1   107.48  3.000
 W3V  H2   C4  C3   111.07  3.000
 W3V  H1   C4  C3   110.65  3.000
 W3V  H2   C4  C5   108.75  3.000
 W3V  H1   C4  C5   108.75  3.000
 W3V  C3   C4  C5   110.06  3.000
 W3V  H4   C5  H3   105.93  3.000
 W3V  H4   C5  C4   109.48  3.000
 W3V  H3   C5  C4   109.72  3.000
 W3V  H4   C5  N1   111.60  3.000
 W3V  H3   C5  N1   109.01  3.000
 W3V  C4   C5  N1   110.96  3.000
 W3V  C3   C6  O1   123.41  3.000
 W3V  O1   C6  O2   122.86  3.000
 W3V  C3   C6  O2   113.70  3.000
 W3V  H5   O2  C6   109.85  3.000
 W3V  H6   C3  C2   107.37  3.000
 W3V  H6   C3  C6   105.75  3.000
 W3V  C2   C3  C6   109.26  3.000
 W3V  H6   C3  C4   108.57  3.000
 W3V  C6   C3  C4   115.43  3.000
 W3V  C2   C3  C4   110.10  3.000
 W3V  H8   C2  H7   107.38  3.000
 W3V  H8   C2  C1   108.79  3.000
 W3V  H7   C2  C1   109.50  3.000
 W3V  H8   C2  C3   110.30  3.000
 W3V  H7   C2  C3   110.14  3.000
 W3V  C1   C2  C3   110.66  3.000
 W3V  H10  C1  H9   107.22  3.000
 W3V  H10  C1  C2   109.43  3.000
 W3V  H9   C1  C2   110.00  3.000
 W3V  H10  C1  N1   109.79  3.000
 W3V  H9   C1  N1   109.45  3.000
 W3V  C2   C1  N1   110.87  3.000
 W3V  N    C   O    120.83  3.000
 W3V  N    C   N1   116.90  3.000
 W3V  O    C   N1   122.25  3.000
 W3V  H12  N   H11  113.14  3.000
 W3V  H12  N   C    120.42  3.000
 W3V  H11  N   C    114.22  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
 W3V  CONST_01  O    C   N1  C5  180.00   0.0  0
 W3V  CONST_02  O    C   N1  C1    0.00   0.0  0
 W3V  CONST_03  N    C   N1  C5    0.00   0.0  0
 W3V  CONST_04  N    C   N1  C1  180.00   0.0  0
 W3V  CONST_05  H11  N   C   N1  180.00   0.0  0
 W3V  CONST_07  H5   O2  C6  C3  180.00   0.0  0
 W3V  Var_01    C3   C4  C5  N1   56.23  30.0  1
 W3V  Var_02    C3   C2  C1  N1  -54.73  30.0  1
 W3V  Var_03    C1   N1  C5  C4  -58.44  30.0  1
 W3V  Var_04    C2   C1  N1  C5   57.55  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
 W3V  chir_01  C3  C4  C2  C6  positiv

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
 W3V  plan-1  N1   0.020
 W3V  plan-1  C5   0.020
 W3V  plan-1  C1   0.020
 W3V  plan-1  C    0.020
 W3V  plan-1  O    0.020
 W3V  plan-1  N    0.020
 W3V  plan-1  H11  0.020
 W3V  plan-1  H12  0.020
 W3V  plan-2  C6   0.020
 W3V  plan-2  O2   0.020
 W3V  plan-2  O1   0.020
 W3V  plan-2  C3   0.020
 W3V  plan-2  H5   0.020

