# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 19:44:28 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  18  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 PERFECT
;

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  -0.253   2.3291   1.9100  -0.0785
 QM1  O   O  O      0  -0.558  -0.3930  -2.1105  -1.1042
 QM1  N   N  N      0  -0.387   2.1906  -0.4338   0.3050
 QM1  C1  C  CR16   0  -0.184   0.9986   1.9137  -0.4732
 QM1  C2  C  CR6    0   0.026   0.2593   0.7378  -0.4949
 QM1  C3  C  CR6    0   0.017   0.9184  -0.4346  -0.0888
 QM1  C4  C  CR16   0  -0.133   2.8794   0.7002   0.3023
 QM1  C5  C  C      0   0.372   0.2560  -1.8078  -0.0812
 QM1  C6  C  CH2    0  -0.618  -1.1877   0.7940  -0.8712
 QM1  C7  C  C      0   0.438  -2.1476   0.7335   0.3365
 QM1  O1  O  OC    -1  -0.587   0.4745  -2.5266   0.9069
 QM1  O2  O  O      0  -0.584  -1.7250   0.1784   1.3675
 QM1  O3  O  OC    -1  -0.740  -3.2851   1.2147   0.1574
 QM1  H1  H  HCR6   0   0.227   2.9193   2.8163  -0.0621
 QM1  H2  H  HCR6   0   0.234   0.5353   2.8486  -0.7682
 QM1  H3  H  HCR6   0   0.224   3.9141   0.6366   0.6246
 QM1  H4  H  HCH2   0   0.226  -1.3834   1.6930  -1.4599
 QM1  H5  H  HCH2   0   0.280  -1.4262  -0.0608  -1.5069

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  deloc     1.245  0.020  1.245
 QM1  O   C5  deloc     1.249  0.020  1.249
 QM1  C6  C7  single    1.544  0.020  1.544
 QM1  C6  C2  single    1.496  0.020  1.496
 QM1  C7  O3  deloc     1.248  0.020  1.248
 QM1  C5  O1  deloc     1.241  0.020  1.241
 QM1  C5  C3  single    1.525  0.020  1.525
 QM1  C2  C3  aromatic  1.405  0.020  1.405
 QM1  C2  C1  aromatic  1.389  0.020  1.389
 QM1  C3  N   aromatic  1.332  0.020  1.332
 QM1  C1  C   aromatic  1.388  0.020  1.388
 QM1  N   C4  aromatic  1.327  0.020  1.327
 QM1  C   C4  aromatic  1.383  0.020  1.383
 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

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  120.78  3.000
 QM1  H1  C   C1  121.69  3.000
 QM1  C4  C   C1  117.53  3.000
 QM1  C4  N   C3  119.73  3.000
 QM1  H2  C1  C2  119.89  3.000
 QM1  H2  C1  C   119.29  3.000
 QM1  C2  C1  C   120.82  3.000
 QM1  C6  C2  C3  123.90  3.000
 QM1  C3  C2  C1  116.89  3.000
 QM1  C6  C2  C1  119.13  3.000
 QM1  C5  C3  C2  123.32  3.000
 QM1  C2  C3  N   122.21  3.000
 QM1  C5  C3  N   114.46  3.000
 QM1  H3  C4  N   116.36  3.000
 QM1  H3  C4  C   120.83  3.000
 QM1  N   C4  C   122.81  3.000
 QM1  O1  C5  C3  116.68  3.000
 QM1  C3  C5  O   116.10  3.000
 QM1  O1  C5  O   127.10  3.000
 QM1  H5  C6  H4  106.95  3.000
 QM1  H5  C6  C7  106.80  3.000
 QM1  H4  C6  C7  110.03  3.000
 QM1  H5  C6  C2  109.17  3.000
 QM1  H4  C6  C2  109.86  3.000
 QM1  C7  C6  C2  113.77  3.000
 QM1  O3  C7  O2  126.88  3.000
 QM1  O3  C7  C6  116.06  3.000
 QM1  O2  C7  C6  117.02  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  Var_01    C2  C3  C5  O     46.13  30.0  2
 QM1  Var_02    C7  C6  C2  C1  -101.22  30.0  3
 QM1  Var_03    O2  C7  C6  C2   -25.40  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-3  C6  0.020
 QM1  plan-3  C7  0.020
 QM1  plan-3  O2  0.020
 QM1  plan-3  O3  0.020

