# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 21:48:10 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 5-butylpyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCc1ccc(nc1)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
 CQV  CQV  '5-butylpyridine-2-carboxylic acid'  ligand  25  13  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CQV
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
 CQV  C9   C  C      0   0.384   3.4071   0.0382  -0.3857
 CQV  C8   C  CR16   0  -0.130  -0.0325   1.0216   0.4722
 CQV  C7   C  CR6    0   0.030   1.9316  -0.0510   0.0052
 CQV  C4   C  CR6    0   0.053  -0.7359  -0.1618   0.6866
 CQV  C5   C  CR16   0  -0.206  -0.0148  -1.3410   0.5478
 CQV  C6   C  CR16   0  -0.304   1.3272  -1.2878   0.2076
 CQV  C3   C  CH2    0  -0.509  -2.2023  -0.1462   1.0009
 CQV  C2   C  CH2    0  -0.405  -3.0580   0.0327  -0.2551
 CQV  C1   C  CH2    0  -0.422  -4.5514   0.0412   0.0430
 CQV  O    O  O      0  -0.593   4.0127  -1.0486  -0.4675
 CQV  O1   O  OC    -1  -0.592   3.8662   1.1738  -0.5877
 CQV  N    N  N      0  -0.404   1.2488   1.0840   0.1431
 CQV  C    C  CH3    0  -0.662  -5.3982   0.2456  -1.2055
 CQV  H9   H  HCR6   0   0.254  -0.4997  -2.2968   0.7109
 CQV  H10  H  HCR6   0   0.253   1.9050  -2.1942   0.0974
 CQV  H7   H  HCH2   0   0.239  -2.4806  -1.0780   1.4999
 CQV  H8   H  HCH2   0   0.240  -2.4222   0.6628   1.7036
 CQV  H6   H  HCH2   0   0.219  -2.7782   0.9693  -0.7475
 CQV  H5   H  HCH2   0   0.220  -2.8308  -0.7676  -0.9668
 CQV  H4   H  HCH2   0   0.214  -4.8298  -0.9025   0.5217
 CQV  H3   H  HCH2   0   0.214  -4.7710   0.8279   0.7712
 CQV  H2   H  HCH3   0   0.227  -6.4630   0.2440  -0.9693
 CQV  H1   H  HCH3   0   0.217  -5.1683   1.1968  -1.6889
 CQV  H    H  HCH3   0   0.217  -5.2214  -0.5463  -1.9354
 CQV  H11  H  HCR6   0   0.245  -0.5477   1.9734   0.5790

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
 CQV  O   C9   deloc     1.247  0.020  1.247
 CQV  C6  C5   aromatic  1.385  0.020  1.385
 CQV  C6  C7   aromatic  1.391  0.020  1.391
 CQV  C5  C4   aromatic  1.389  0.020  1.389
 CQV  C9  C7   single    1.529  0.020  1.529
 CQV  C9  O1   deloc     1.241  0.020  1.241
 CQV  C7  N    aromatic  1.332  0.020  1.332
 CQV  C2  C1   single    1.523  0.020  1.523
 CQV  C2  C3   single    1.530  0.020  1.530
 CQV  C1  C    single    1.522  0.020  1.522
 CQV  C4  C3   single    1.500  0.020  1.500
 CQV  C4  C8   aromatic  1.393  0.020  1.393
 CQV  N   C8   aromatic  1.324  0.020  1.324
 CQV  C8  H11  single    0.930  0.020  1.080
 CQV  C5  H9   single    0.930  0.020  1.080
 CQV  C6  H10  single    0.930  0.020  1.080
 CQV  C3  H7   single    0.970  0.020  1.090
 CQV  C3  H8   single    0.970  0.020  1.090
 CQV  C2  H6   single    0.970  0.020  1.090
 CQV  C2  H5   single    0.970  0.020  1.090
 CQV  C1  H4   single    0.970  0.020  1.090
 CQV  C1  H3   single    0.970  0.020  1.090
 CQV  C   H2   single    0.970  0.020  1.090
 CQV  C   H1   single    0.970  0.020  1.090
 CQV  C   H    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
 CQV  O1   C9  O   127.38  3.000
 CQV  O1   C9  C7  116.86  3.000
 CQV  O    C9  C7  115.76  3.000
 CQV  H11  C8  N   116.20  3.000
 CQV  H11  C8  C4  119.28  3.000
 CQV  N    C8  C4  124.52  3.000
 CQV  N    C7  C6  121.32  3.000
 CQV  N    C7  C9  118.14  3.000
 CQV  C6   C7  C9  120.55  3.000
 CQV  C3   C4  C5  122.50  3.000
 CQV  C3   C4  C8  121.14  3.000
 CQV  C5   C4  C8  116.33  3.000
 CQV  H9   C5  C6  120.27  3.000
 CQV  H9   C5  C4  120.07  3.000
 CQV  C6   C5  C4  119.65  3.000
 CQV  H10  C6  C5  120.72  3.000
 CQV  H10  C6  C7  119.90  3.000
 CQV  C5   C6  C7  119.38  3.000
 CQV  H8   C3  H7  106.62  3.000
 CQV  H8   C3  C2  109.17  3.000
 CQV  H7   C3  C2  109.39  3.000
 CQV  H8   C3  C4  109.81  3.000
 CQV  H7   C3  C4  109.62  3.000
 CQV  C2   C3  C4  112.08  3.000
 CQV  H5   C2  H6  106.26  3.000
 CQV  H5   C2  C1  109.57  3.000
 CQV  H6   C2  C1  109.51  3.000
 CQV  H5   C2  C3  109.39  3.000
 CQV  H6   C2  C3  109.04  3.000
 CQV  C1   C2  C3  112.85  3.000
 CQV  H3   C1  H4  106.13  3.000
 CQV  H3   C1  C   109.73  3.000
 CQV  H4   C1  C   109.46  3.000
 CQV  H3   C1  C2  109.34  3.000
 CQV  H4   C1  C2  109.29  3.000
 CQV  C    C1  C2  112.69  3.000
 CQV  C7   N   C8  118.79  3.000
 CQV  H    C   H1  107.58  3.000
 CQV  H    C   H2  107.57  3.000
 CQV  H1   C   H2  107.63  3.000
 CQV  H    C   C1  111.15  3.000
 CQV  H1   C   C1  111.29  3.000
 CQV  H2   C   C1  111.42  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
 CQV  CONST_01  C6   C5  C4  C8    0.00   0.0  0
 CQV  CONST_02  C6   C7  N   C8    0.00   0.0  0
 CQV  CONST_03  C4   C5  C6  C7    0.00   0.0  0
 CQV  CONST_04  C4   C8  N   C7    0.00   0.0  0
 CQV  CONST_05  N    C7  C6  C5    0.00   0.0  0
 CQV  CONST_06  N    C8  C4  C5    0.00   0.0  0
 CQV  CONST_07  C5   C6  C7  C9  180.00   0.0  0
 CQV  CONST_08  C8   N   C7  C9  180.00   0.0  0
 CQV  CONST_09  C3   C4  C5  C6  180.00   0.0  0
 CQV  CONST_10  N    C8  C4  C3  180.00   0.0  0
 CQV  CONST_11  H9   C5  C4  C8  180.00   0.0  0
 CQV  CONST_12  H11  C8  N   C7  180.00   0.0  0
 CQV  CONST_13  H10  C6  C5  C4  180.00   0.0  0
 CQV  Var_01    C2   C3  C4  C8   80.00  30.0  2
 CQV  Var_02    O    C9  C7  C6   -1.92  30.0  2
 CQV  Var_03    C1   C2  C3  C4  179.60  30.0  1
 CQV  Var_04    C    C1  C2  C3  178.92  30.0  3
 CQV  Var_05    H2   C   C1  C2  179.76  30.0  3

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
 CQV  plan-1  C9   0.020
 CQV  plan-1  C8   0.020
 CQV  plan-1  C7   0.020
 CQV  plan-1  C4   0.020
 CQV  plan-1  C5   0.020
 CQV  plan-1  C6   0.020
 CQV  plan-1  C3   0.020
 CQV  plan-1  N    0.020
 CQV  plan-1  H9   0.020
 CQV  plan-1  H10  0.020
 CQV  plan-1  H11  0.020
 CQV  plan-2  C9   0.020
 CQV  plan-2  C7   0.020
 CQV  plan-2  O    0.020
 CQV  plan-2  O1   0.020

