# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:48:12 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: 4-(3-carboxyphenyl)pyridine-2,5-dicarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(c1)c2cc(ncc2C(O)=O)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
 7L9  7L9  '4-(3-carboxyphenyl)pyridine-2,5-dicarboxylic acid'  ligand  27  21  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7L9
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
 7L9  OAH  O  O      0  -0.591   3.9355   0.6904   1.7314
 7L9  CAG  C  C      0   0.396   4.1604  -0.2278   0.9198
 7L9  OAI  O  OC    -1  -0.596   5.2503  -0.7992   0.7235
 7L9  CAE  C  C      0  -0.089   2.9803  -0.7016   0.0792
 7L9  CAD  C  C1     0  -0.340   1.7267  -0.1225   0.2349
 7L9  CAF  C  C1     0  -0.304   3.1340  -1.7230  -0.8568
 7L9  CAA  C  C1     0  -0.235   2.0523  -2.1546  -1.6098
 7L9  CAB  C  C1     0  -0.320   0.8026  -1.5760  -1.4333
 7L9  CAC  C  C      0   0.121   0.6287  -0.5474  -0.5099
 7L9  CAJ  C  CR6    0   0.173  -0.7114   0.0302  -0.2768
 7L9  CAK  C  CR16   0  -0.374  -1.7971  -0.8244  -0.1010
 7L9  CAL  C  CR6    0   0.038  -3.0627  -0.3178   0.1655
 7L9  CAS  C  C      0   0.384  -4.2539  -1.2612   0.3385
 7L9  OAU  O  OC    -1  -0.591  -5.3646  -0.7333   0.5087
 7L9  OAT  O  O      0  -0.592  -3.9961  -2.4804   0.2886
 7L9  NAM  N  N      0  -0.410  -3.2742   0.9902   0.2899
 7L9  CAN  C  CR16   0  -0.122  -2.2392   1.8046   0.1452
 7L9  CAO  C  CR6    0  -0.175  -0.9408   1.4042  -0.1604
 7L9  CAP  C  C      0   0.343   0.1057   2.4765  -0.4190
 7L9  OAR  O  OC    -1  -0.599   0.1562   3.4003   0.4152
 7L9  OAQ  O  O      0  -0.583   0.7781   2.3483  -1.4554
 7L9  H2   H  H      0   0.237   1.6050   0.6636   0.9691
 7L9  H3   H  H      0   0.241   4.1049  -2.1812  -0.9908
 7L9  H4   H  H      0   0.247   2.1770  -2.9466  -2.3375
 7L9  H5   H  H      0   0.248  -0.0369  -1.9169  -2.0273
 7L9  H6   H  HCR6   0   0.248  -1.6596  -1.8957  -0.1554
 7L9  H8   H  HCR6   0   0.246  -2.4482   2.8638   0.2613

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
 7L9  OAT  CAS  deloc     1.247  0.020  1.247
 7L9  OAU  CAS  deloc     1.241  0.020  1.241
 7L9  CAS  CAL  single    1.529  0.020  1.529
 7L9  CAL  NAM  aromatic  1.331  0.020  1.331
 7L9  CAL  CAK  aromatic  1.389  0.020  1.389
 7L9  NAM  CAN  aromatic  1.325  0.020  1.325
 7L9  CAK  CAJ  aromatic  1.393  0.020  1.393
 7L9  CAN  CAO  aromatic  1.393  0.020  1.393
 7L9  CAJ  CAO  aromatic  1.398  0.020  1.398
 7L9  CAJ  CAC  single    1.478  0.020  1.478
 7L9  CAO  CAP  single    1.520  0.020  1.520
 7L9  CAC  CAB  aromatic  1.393  0.020  1.393
 7L9  CAC  CAD  aromatic  1.393  0.020  1.393
 7L9  CAB  CAA  aromatic  1.388  0.020  1.388
 7L9  CAD  CAE  aromatic  1.390  0.020  1.390
 7L9  CAP  OAQ  deloc     1.242  0.020  1.242
 7L9  CAP  OAR  deloc     1.246  0.020  1.246
 7L9  CAA  CAF  aromatic  1.387  0.020  1.387
 7L9  CAE  CAF  aromatic  1.394  0.020  1.394
 7L9  CAE  CAG  single    1.524  0.020  1.524
 7L9  OAH  CAG  deloc     1.246  0.020  1.246
 7L9  CAG  OAI  deloc     1.246  0.020  1.246
 7L9  CAD  H2   single    0.930  0.020  1.080
 7L9  CAF  H3   single    0.930  0.020  1.080
 7L9  CAA  H4   single    0.930  0.020  1.080
 7L9  CAB  H5   single    0.930  0.020  1.080
 7L9  CAK  H6   single    0.930  0.020  1.080
 7L9  CAN  H8   single    0.930  0.020  1.080

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
 7L9  CAE  CAG  OAI  116.59  3.000
 7L9  OAI  CAG  OAH  126.76  3.000
 7L9  CAE  CAG  OAH  116.65  3.000
 7L9  CAF  CAE  CAD  118.69  3.000
 7L9  CAF  CAE  CAG  120.84  3.000
 7L9  CAD  CAE  CAG  120.47  3.000
 7L9  H2   CAD  CAC  119.70  3.000
 7L9  H2   CAD  CAE  118.69  3.000
 7L9  CAC  CAD  CAE  121.60  3.000
 7L9  H3   CAF  CAA  120.06  3.000
 7L9  H3   CAF  CAE  119.50  3.000
 7L9  CAA  CAF  CAE  120.44  3.000
 7L9  H4   CAA  CAB  119.60  3.000
 7L9  H4   CAA  CAF  120.18  3.000
 7L9  CAB  CAA  CAF  120.21  3.000
 7L9  H5   CAB  CAC  119.93  3.000
 7L9  H5   CAB  CAA  119.77  3.000
 7L9  CAC  CAB  CAA  120.29  3.000
 7L9  CAJ  CAC  CAB  120.42  3.000
 7L9  CAB  CAC  CAD  118.76  3.000
 7L9  CAJ  CAC  CAD  120.74  3.000
 7L9  CAO  CAJ  CAK  117.69  3.000
 7L9  CAO  CAJ  CAC  123.10  3.000
 7L9  CAK  CAJ  CAC  119.14  3.000
 7L9  H6   CAK  CAL  119.13  3.000
 7L9  H6   CAK  CAJ  120.16  3.000
 7L9  CAL  CAK  CAJ  120.71  3.000
 7L9  NAM  CAL  CAS  118.16  3.000
 7L9  NAM  CAL  CAK  121.41  3.000
 7L9  CAS  CAL  CAK  120.43  3.000
 7L9  OAT  CAS  OAU  127.31  3.000
 7L9  OAU  CAS  CAL  116.74  3.000
 7L9  OAT  CAS  CAL  115.94  3.000
 7L9  CAN  NAM  CAL  118.03  3.000
 7L9  H8   CAN  CAO  118.91  3.000
 7L9  H8   CAN  NAM  115.95  3.000
 7L9  CAO  CAN  NAM  125.13  3.000
 7L9  CAP  CAO  CAN  118.44  3.000
 7L9  CAP  CAO  CAJ  124.48  3.000
 7L9  CAN  CAO  CAJ  116.99  3.000
 7L9  OAQ  CAP  OAR  127.83  3.000
 7L9  OAR  CAP  CAO  115.91  3.000
 7L9  OAQ  CAP  CAO  116.21  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
 7L9  CONST_01  CAJ  CAC  CAD  CAE  180.00   0.0  0
 7L9  CONST_02  CAB  CAC  CAD  CAE    0.00   0.0  0
 7L9  CONST_03  CAB  CAA  CAF  CAE    0.00   0.0  0
 7L9  CONST_06  CAA  CAB  CAC  CAD    0.00   0.0  0
 7L9  CONST_07  CAA  CAF  CAE  CAD    0.00   0.0  0
 7L9  CONST_08  CAC  CAB  CAA  CAF    0.00   0.0  0
 7L9  CONST_09  CAC  CAD  CAE  CAF    0.00   0.0  0
 7L9  CONST_10  CAJ  CAC  CAB  CAA  180.00   0.0  0
 7L9  CONST_13  CAL  CAK  CAJ  CAC  180.00   0.0  0
 7L9  CONST_14  CAN  CAO  CAJ  CAC  180.00   0.0  0
 7L9  CONST_15  NAM  CAL  CAK  CAJ    0.00   0.0  0
 7L9  CONST_16  NAM  CAN  CAO  CAJ    0.00   0.0  0
 7L9  CONST_17  CAN  NAM  CAL  CAK    0.00   0.0  0
 7L9  CONST_18  CAN  CAO  CAJ  CAK    0.00   0.0  0
 7L9  CONST_19  CAO  CAN  NAM  CAL    0.00   0.0  0
 7L9  CONST_20  CAO  CAJ  CAK  CAL    0.00   0.0  0
 7L9  CONST_21  CAC  CAD  CAE  CAG  180.00   0.0  0
 7L9  CONST_22  CAA  CAF  CAE  CAG  180.00   0.0  0
 7L9  CONST_23  CAP  CAO  CAJ  CAC    0.00   0.0  0
 7L9  CONST_24  CAS  CAL  CAK  CAJ  180.00   0.0  0
 7L9  CONST_25  CAP  CAO  CAJ  CAK  180.00   0.0  0
 7L9  CONST_26  CAN  NAM  CAL  CAS  180.00   0.0  0
 7L9  CONST_27  CAP  CAO  CAN  NAM  180.00   0.0  0
 7L9  CONST_28  H4   CAA  CAF  CAE  180.00   0.0  0
 7L9  CONST_29  H5   CAB  CAC  CAD  180.00   0.0  0
 7L9  CONST_30  H3   CAF  CAE  CAD  180.00   0.0  0
 7L9  CONST_31  H2   CAD  CAE  CAF  180.00   0.0  0
 7L9  CONST_32  H6   CAK  CAJ  CAC    0.00   0.0  0
 7L9  CONST_33  H8   CAN  CAO  CAJ  180.00   0.0  0
 7L9  Var_01    CAD  CAE  CAG  OAH   -0.19  30.0  2
 7L9  Var_02    OAQ  CAP  CAO  CAJ   46.42  30.0  2
 7L9  Var_03    OAT  CAS  CAL  CAK    3.28  30.0  2

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
 7L9  plan-1  CAG  0.020
 7L9  plan-1  CAE  0.020
 7L9  plan-1  CAD  0.020
 7L9  plan-1  CAF  0.020
 7L9  plan-1  CAA  0.020
 7L9  plan-1  CAB  0.020
 7L9  plan-1  CAC  0.020
 7L9  plan-1  CAJ  0.020
 7L9  plan-1  H2   0.020
 7L9  plan-1  H3   0.020
 7L9  plan-1  H4   0.020
 7L9  plan-1  H5   0.020
 7L9  plan-2  CAC  0.020
 7L9  plan-2  CAJ  0.020
 7L9  plan-2  CAK  0.020
 7L9  plan-2  CAL  0.020
 7L9  plan-2  CAS  0.020
 7L9  plan-2  NAM  0.020
 7L9  plan-2  CAN  0.020
 7L9  plan-2  CAO  0.020
 7L9  plan-2  CAP  0.020
 7L9  plan-2  H6   0.020
 7L9  plan-2  H8   0.020
 7L9  plan-3  OAH  0.020
 7L9  plan-3  CAG  0.020
 7L9  plan-3  OAI  0.020
 7L9  plan-3  CAE  0.020
 7L9  plan-4  CAL  0.020
 7L9  plan-4  CAS  0.020
 7L9  plan-4  OAU  0.020
 7L9  plan-4  OAT  0.020
 7L9  plan-5  CAO  0.020
 7L9  plan-5  CAP  0.020
 7L9  plan-5  OAR  0.020
 7L9  plan-5  OAQ  0.020

