# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 12:00:43 2022
#   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  23  12  .  2022-03-29  2022-03-29
;
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  -0.453  -0.8922  15.7998  -4.7712
 W3V  C4   C  CH2    0  -0.402   0.9959  14.7723  -3.5793
 W3V  C5   C  CH2    0  -0.344   0.5328  15.5232  -4.8231
 W3V  C6   C  C      0   0.430   0.5952  12.6894  -2.1237
 W3V  O2   O  OC    -1  -0.600   1.7210  12.9200  -1.6384
 W3V  O1   O  O      0  -0.607  -0.2326  11.8542  -1.7046
 W3V  C3   C  CH1    0  -0.394   0.1928  13.4871  -3.3889
 W3V  C2   C  CH2    0  -0.413  -1.3074  13.7789  -3.4470
 W3V  C1   C  CH2    0  -0.311  -1.6802  14.5817  -4.6881
 W3V  C    C  C      0   0.648  -1.4338  16.9736  -4.3371
 W3V  O    O  O      0  -0.539  -2.6444  17.1253  -4.1987
 W3V  N    N  NH2    0  -0.845  -0.5729  18.0202  -4.1365
 W3V  H1   H  HCH2   0   0.223   2.0594  14.5476  -3.6709
 W3V  H2   H  HCH2   0   0.209   0.8836  15.4217  -2.7045
 W3V  H3   H  HCH2   0   0.241   0.7135  14.9051  -5.7088
 W3V  H4   H  HCH2   0   0.249   1.1027  16.4369  -4.9837
 W3V  H6   H  HCH1   0   0.215   0.4225  12.8361  -4.2478
 W3V  H7   H  HCH2   0   0.207  -1.6169  14.3393  -2.5577
 W3V  H8   H  HCH2   0   0.223  -1.8727  12.8462  -3.4419
 W3V  H9   H  HCH2   0   0.253  -2.7385  14.8285  -4.6955
 W3V  H10  H  HCH2   0   0.225  -1.4810  13.9870  -5.5860
 W3V  H11  H  HNH2   0   0.388  -0.9932  18.8214  -3.6955
 W3V  H12  H  HNH2   0   0.396   0.3775  17.8591  -3.8500

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  1.452  0.020  1.452
 W3V  C5  C4   single  1.525  0.020  1.525
 W3V  C   N    single  1.370  0.020  1.370
 W3V  C   N1   single  1.364  0.020  1.364
 W3V  N1  C1   single  1.453  0.020  1.453
 W3V  C1  C2   single  1.524  0.020  1.524
 W3V  C3  C4   single  1.527  0.020  1.527
 W3V  C3  C2   single  1.529  0.020  1.529
 W3V  C3  C6   single  1.549  0.020  1.549
 W3V  O1  C6   deloc   1.248  0.020  1.248
 W3V  C6  O2   deloc   1.247  0.020  1.247
 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  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   119.21  3.000
 W3V  C1   N1  C5   111.99  3.000
 W3V  C    N1  C5   124.40  3.000
 W3V  H2   C4  H1   106.81  3.000
 W3V  H2   C4  C3   110.20  3.000
 W3V  H1   C4  C3   110.47  3.000
 W3V  H2   C4  C5   109.17  3.000
 W3V  H1   C4  C5   109.21  3.000
 W3V  C3   C4  C5   110.87  3.000
 W3V  H4   C5  H3   105.54  3.000
 W3V  H4   C5  C4   112.00  3.000
 W3V  H3   C5  C4   109.37  3.000
 W3V  H4   C5  N1   111.04  3.000
 W3V  H3   C5  N1   107.36  3.000
 W3V  C4   C5  N1   111.26  3.000
 W3V  C3   C6  O1   116.52  3.000
 W3V  O1   C6  O2   126.26  3.000
 W3V  C3   C6  O2   117.20  3.000
 W3V  H6   C3  C2   106.71  3.000
 W3V  H6   C3  C6   106.16  3.000
 W3V  C2   C3  C6   112.59  3.000
 W3V  H6   C3  C4   106.88  3.000
 W3V  C6   C3  C4   113.49  3.000
 W3V  C2   C3  C4   110.52  3.000
 W3V  H8   C2  H7   106.68  3.000
 W3V  H8   C2  C1   109.11  3.000
 W3V  H7   C2  C1   108.81  3.000
 W3V  H8   C2  C3   110.18  3.000
 W3V  H7   C2  C3   110.11  3.000
 W3V  C1   C2  C3   111.80  3.000
 W3V  H10  C1  H9   107.15  3.000
 W3V  H10  C1  C2   109.70  3.000
 W3V  H9   C1  C2   111.30  3.000
 W3V  H10  C1  N1   108.04  3.000
 W3V  H9   C1  N1   109.71  3.000
 W3V  C2   C1  N1   110.81  3.000
 W3V  N    C   O    120.58  3.000
 W3V  N    C   N1   117.04  3.000
 W3V  O    C   N1   122.27  3.000
 W3V  H12  N   H11  113.41  3.000
 W3V  H12  N   C    120.88  3.000
 W3V  H11  N   C    114.20  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_03  N    C   N1  C5    0.00   0.0  0
 W3V  CONST_05  H11  N   C   N1  180.00   0.0  0
 W3V  Var_01    C3   C4  C5  N1   55.82  30.0  1
 W3V  Var_02    C3   C2  C1  N1  -54.68  30.0  1
 W3V  Var_03    C1   N1  C5  C4  -60.13  30.0  1
 W3V  Var_04    C2   C1  N1  C5   59.17  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

