# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 17:42:25 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-(carboxymethyl)pyridine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1cccnc1C(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
 QM1  QM1  '3-(carboxymethyl)pyridine-2-carboxylic acid'  ligand  20  13  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_QM1
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
 QM1  C   C  CR16  0  -0.297   2.3667   1.8513  -0.1072
 QM1  O   O  O     0  -0.432  -1.0395  -1.8319  -0.2347
 QM1  N   N  N     0  -0.400   2.1725  -0.4891   0.2439
 QM1  C1  C  CR16  0  -0.192   1.0362   1.9099  -0.4746
 QM1  C2  C  CR6   0   0.125   0.2538   0.7586  -0.4804
 QM1  C3  C  CR6   0   0.065   0.8911  -0.4291  -0.1038
 QM1  C4  C  CR16  0  -0.079   2.8932   0.6168   0.2457
 QM1  C5  C  C     0   0.525   0.1518  -1.7280  -0.0609
 QM1  C6  C  CH2   0  -0.687  -1.1826   0.8635  -0.8973
 QM1  C7  C  C     0   0.563  -2.1369   0.6442   0.2486
 QM1  O1  O  OH1   0  -0.577   0.9395  -2.7579   0.1877
 QM1  O2  O  O     0  -0.440  -1.8383   0.7231   1.4126
 QM1  O3  O  OH1   0  -0.592  -3.3712   0.4169  -0.1802
 QM1  H1  H  HCR6  0   0.282   2.9851   2.7378  -0.0939
 QM1  H2  H  HCR6  0   0.281   0.5944   2.8566  -0.7587
 QM1  H3  H  HCR6  0   0.274   3.9321   0.5219   0.5396
 QM1  H4  H  HCH2  0   0.312  -1.3673   1.8739  -1.2755
 QM1  H5  H  HCH2  0   0.302  -1.4215   0.1878  -1.7184
 QM1  H6  H  HOH1  0   0.488   0.4103  -3.5694   0.2064
 QM1  H7  H  HOH1  0   0.480  -3.9722   0.3262   0.5744

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
 QM1  O2  C7  double    1.204  0.020  1.204
 QM1  O   C5  double    1.208  0.020  1.208
 QM1  C6  C7  single    1.507  0.020  1.507
 QM1  C6  C2  single    1.499  0.020  1.499
 QM1  C7  O3  single    1.326  0.020  1.326
 QM1  C5  O1  single    1.320  0.020  1.320
 QM1  C5  C3  single    1.495  0.020  1.495
 QM1  C2  C3  aromatic  1.400  0.020  1.400
 QM1  C2  C1  aromatic  1.392  0.020  1.392
 QM1  C3  N   aromatic  1.329  0.020  1.329
 QM1  C1  C   aromatic  1.382  0.020  1.382
 QM1  N   C4  aromatic  1.320  0.020  1.320
 QM1  C   C4  aromatic  1.388  0.020  1.388
 QM1  C   H1  single    0.930  0.020  1.080
 QM1  C1  H2  single    0.930  0.020  1.080
 QM1  C4  H3  single    0.930  0.020  1.080
 QM1  C6  H4  single    0.970  0.020  1.090
 QM1  C6  H5  single    0.970  0.020  1.090
 QM1  O1  H6  single    0.850  0.020  0.980
 QM1  O3  H7  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
 QM1  H1  C   C4  120.62  3.000
 QM1  H1  C   C1  121.30  3.000
 QM1  C4  C   C1  118.08  3.000
 QM1  C4  N   C3  119.27  3.000
 QM1  H2  C1  C2  119.52  3.000
 QM1  H2  C1  C   119.99  3.000
 QM1  C2  C1  C   120.49  3.000
 QM1  C6  C2  C3  124.78  3.000
 QM1  C3  C2  C1  116.41  3.000
 QM1  C6  C2  C1  118.80  3.000
 QM1  C5  C3  C2  121.32  3.000
 QM1  C2  C3  N   123.22  3.000
 QM1  C5  C3  N   115.47  3.000
 QM1  H3  C4  N   116.77  3.000
 QM1  H3  C4  C   120.70  3.000
 QM1  N   C4  C   122.54  3.000
 QM1  O1  C5  C3  112.83  3.000
 QM1  C3  C5  O   123.92  3.000
 QM1  O1  C5  O   123.25  3.000
 QM1  H5  C6  H4  105.97  3.000
 QM1  H5  C6  C7  110.11  3.000
 QM1  H4  C6  C7  106.87  3.000
 QM1  H5  C6  C2  112.09  3.000
 QM1  H4  C6  C2  108.80  3.000
 QM1  C7  C6  C2  112.64  3.000
 QM1  O3  C7  O2  123.67  3.000
 QM1  O3  C7  C6  111.62  3.000
 QM1  O2  C7  C6  124.63  3.000
 QM1  H6  O1  C5  109.33  3.000
 QM1  H7  O3  C7  109.97  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
 QM1  CONST_01  C3  C2  C1  C      0.00   0.0  0
 QM1  CONST_02  C3  N   C4  C      0.00   0.0  0
 QM1  CONST_03  C1  C2  C3  N      0.00   0.0  0
 QM1  CONST_04  C1  C   C4  N      0.00   0.0  0
 QM1  CONST_05  C4  N   C3  C2     0.00   0.0  0
 QM1  CONST_06  C4  C   C1  C2     0.00   0.0  0
 QM1  CONST_07  C6  C2  C1  C    180.00   0.0  0
 QM1  CONST_08  C6  C2  C3  N    180.00   0.0  0
 QM1  CONST_09  C5  C3  C2  C1   180.00   0.0  0
 QM1  CONST_10  C5  C3  N   C4   180.00   0.0  0
 QM1  CONST_11  H1  C   C4  N    180.00   0.0  0
 QM1  CONST_12  H3  C4  C   C1   180.00   0.0  0
 QM1  CONST_13  H2  C1  C2  C3   180.00   0.0  0
 QM1  CONST_14  H6  O1  C5  C3   180.00   0.0  0
 QM1  CONST_15  H7  O3  C7  C6   180.00   0.0  0
 QM1  Var_01    C2  C3  C5  O     -6.21  30.0  2
 QM1  Var_02    C7  C6  C2  C1  -110.83  30.0  2
 QM1  Var_03    O2  C7  C6  C2    18.42  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
 QM1  plan-1  C   0.020
 QM1  plan-1  N   0.020
 QM1  plan-1  C1  0.020
 QM1  plan-1  C2  0.020
 QM1  plan-1  C3  0.020
 QM1  plan-1  C4  0.020
 QM1  plan-1  C5  0.020
 QM1  plan-1  C6  0.020
 QM1  plan-1  H1  0.020
 QM1  plan-1  H2  0.020
 QM1  plan-1  H3  0.020
 QM1  plan-2  O   0.020
 QM1  plan-2  C3  0.020
 QM1  plan-2  C5  0.020
 QM1  plan-2  O1  0.020
 QM1  plan-2  H6  0.020
 QM1  plan-3  C6  0.020
 QM1  plan-3  C7  0.020
 QM1  plan-3  O2  0.020
 QM1  plan-3  O3  0.020
 QM1  plan-3  H7  0.020

