# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 02:33:05 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 6-[3-(carboxymethoxy)-5-fluorophenyl]pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)COc1cc(F)cc(c1)c2ccc(cn2)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
 1E5  1E5  '6-[3-(carboxymethoxy)-5-fluorophenyl]pyridine-3-carboxylic acid'  ligand  31  21  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1E5
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
 1E5  C1   C  CR6   0   0.102  -0.1440   0.8625   0.0041
 1E5  C2   C  CR16  0  -0.546   0.2116   2.2146   0.0356
 1E5  C3   C  CR6   0   0.611   1.5486   2.5356   0.0475
 1E5  C4   C  CR16  0  -0.553   2.5626   1.5946   0.0296
 1E5  C5   C  CR6   0   0.445   2.1955   0.2533  -0.0012
 1E5  C6   C  CR16  0  -0.401   0.8498  -0.1078  -0.0126
 1E5  O7   O  O2    0  -0.461   3.0763  -0.7634  -0.0213
 1E5  C8   C  CH2   0  -0.299   4.4449  -0.4619  -0.0126
 1E5  C9   C  C     0   0.514   5.2010  -1.7683  -0.0326
 1E5  O12  O  O     0  -0.422   4.6961  -2.8572  -0.0408
 1E5  O13  O  OH1   0  -0.590   6.5041  -1.5363  -0.0377
 1E5  C17  C  CR6   0   0.266  -1.5656   0.4448  -0.0122
 1E5  N18  N  N     0  -0.433  -1.8004  -0.8661   0.0420
 1E5  C19  C  CR16  0  -0.047  -3.0439  -1.3085   0.0290
 1E5  C20  C  CR6   0  -0.176  -4.1522  -0.4672  -0.0389
 1E5  C21  C  CR16  0  -0.132  -3.9131   0.9007  -0.0976
 1E5  C22  C  CR16  0  -0.323  -2.6132   1.3636  -0.0847
 1E5  C23  C  C     0   0.534  -5.5471  -0.9639  -0.0528
 1E5  O24  O  OH1   0  -0.592  -5.6237  -2.2835   0.0175
 1E5  O25  O  O     0  -0.433  -6.5093  -0.2386  -0.1208
 1E5  F31  F  F     0  -0.313   1.8999   3.8289   0.0794
 1E5  H1   H  HCR6  0   0.278  -0.5200   3.0093   0.0552
 1E5  H2   H  HCR6  0   0.309   3.5922   1.9260   0.0402
 1E5  H3   H  HCR6  0   0.271   0.5832  -1.1553  -0.0361
 1E5  H4   H  HCH2  0   0.280   4.7398   0.1338  -0.8850
 1E5  H5   H  HCH2  0   0.281   4.7360   0.1011   0.8825
 1E5  H6   H  HOH1  0   0.492   6.9979  -2.3703  -0.0469
 1E5  H7   H  HCR6  0   0.279  -3.1617  -2.3844   0.0751
 1E5  H8   H  HCR6  0   0.285  -4.7345   1.6020  -0.1535
 1E5  H9   H  HCR6  0   0.283  -2.4359   2.4273  -0.1348
 1E5  H10  H  HOH1  0   0.492  -6.5506  -2.5662   0.0055

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
 1E5  O12  C9   double    1.200  0.020  1.200
 1E5  C8   C9   single    1.510  0.020  1.510
 1E5  C8   O7   single    1.401  0.020  1.401
 1E5  C9   O13  single    1.324  0.020  1.324
 1E5  O7   C5   single    1.345  0.020  1.345
 1E5  C4   C5   aromatic  1.391  0.020  1.391
 1E5  C4   C3   aromatic  1.384  0.020  1.384
 1E5  C5   C6   aromatic  1.393  0.020  1.393
 1E5  F31  C3   single    1.341  0.020  1.341
 1E5  C3   C2   aromatic  1.375  0.020  1.375
 1E5  C6   C1   aromatic  1.389  0.020  1.389
 1E5  C2   C1   aromatic  1.398  0.020  1.398
 1E5  C1   C17  single    1.482  0.020  1.482
 1E5  C17  N18  aromatic  1.333  0.020  1.333
 1E5  C17  C22  aromatic  1.395  0.020  1.395
 1E5  N18  C19  aromatic  1.320  0.020  1.320
 1E5  C22  C21  aromatic  1.380  0.020  1.380
 1E5  C19  C20  aromatic  1.393  0.020  1.393
 1E5  C21  C20  aromatic  1.390  0.020  1.390
 1E5  C20  C23  single    1.481  0.020  1.481
 1E5  C23  O25  double    1.207  0.020  1.207
 1E5  C23  O24  single    1.324  0.020  1.324
 1E5  C2   H1   single    0.930  0.020  1.080
 1E5  C4   H2   single    0.930  0.020  1.080
 1E5  C6   H3   single    0.930  0.020  1.080
 1E5  C8   H4   single    0.970  0.020  1.090
 1E5  C8   H5   single    0.970  0.020  1.090
 1E5  O13  H6   single    0.850  0.020  0.980
 1E5  C19  H7   single    0.930  0.020  1.080
 1E5  C21  H8   single    0.930  0.020  1.080
 1E5  C22  H9   single    0.930  0.020  1.080
 1E5  O24  H10  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
 1E5  C17  C1   C6   119.30  3.000
 1E5  C17  C1   C2   121.11  3.000
 1E5  C6   C1   C2   119.59  3.000
 1E5  H1   C2   C3   119.11  3.000
 1E5  H1   C2   C1   122.65  3.000
 1E5  C3   C2   C1   118.24  3.000
 1E5  F31  C3   C4   117.67  3.000
 1E5  F31  C3   C2   118.70  3.000
 1E5  C4   C3   C2   123.63  3.000
 1E5  H2   C4   C5   123.16  3.000
 1E5  H2   C4   C3   119.28  3.000
 1E5  C5   C4   C3   117.57  3.000
 1E5  O7   C5   C6   115.87  3.000
 1E5  C6   C5   C4   120.33  3.000
 1E5  O7   C5   C4   123.80  3.000
 1E5  H3   C6   C5   119.30  3.000
 1E5  H3   C6   C1   120.04  3.000
 1E5  C5   C6   C1   120.66  3.000
 1E5  C8   O7   C5   118.47  3.000
 1E5  H5   C8   H4   107.40  3.000
 1E5  H5   C8   C9   108.79  3.000
 1E5  H4   C8   C9   108.96  3.000
 1E5  H5   C8   O7   112.00  3.000
 1E5  H4   C8   O7   111.99  3.000
 1E5  C9   C8   O7   107.63  3.000
 1E5  O13  C9   O12  124.97  3.000
 1E5  O13  C9   C8   109.97  3.000
 1E5  O12  C9   C8   125.06  3.000
 1E5  H6   O13  C9   110.54  3.000
 1E5  C22  C17  N18  121.16  3.000
 1E5  C22  C17  C1   122.36  3.000
 1E5  N18  C17  C1   116.48  3.000
 1E5  C19  N18  C17  119.69  3.000
 1E5  H7   C19  C20  121.02  3.000
 1E5  H7   C19  N18  115.78  3.000
 1E5  C20  C19  N18  123.20  3.000
 1E5  C23  C20  C21  119.46  3.000
 1E5  C23  C20  C19  123.18  3.000
 1E5  C21  C20  C19  117.36  3.000
 1E5  H8   C21  C22  119.90  3.000
 1E5  H8   C21  C20  120.65  3.000
 1E5  C22  C21  C20  119.46  3.000
 1E5  H9   C22  C21  119.00  3.000
 1E5  H9   C22  C17  121.86  3.000
 1E5  C21  C22  C17  119.14  3.000
 1E5  O25  C23  O24  123.77  3.000
 1E5  O24  C23  C20  112.86  3.000
 1E5  O25  C23  C20  123.37  3.000
 1E5  H10  O24  C23  110.22  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
 1E5  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 1E5  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 1E5  CONST_03  C19  N18  C17  C1    180.00   0.0  0
 1E5  CONST_04  C21  C22  C17  C1    180.00   0.0  0
 1E5  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 1E5  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 1E5  CONST_07  N18  C17  C1   C2    180.00   0.0  0
 1E5  CONST_08  C22  C17  C1   C2      0.00   0.0  0
 1E5  CONST_09  C6   C5   C4   C3      0.00   0.0  0
 1E5  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 1E5  CONST_11  C17  C1   C2   C3    180.00   0.0  0
 1E5  CONST_12  C17  C1   C6   C5    180.00   0.0  0
 1E5  CONST_13  N18  C17  C1   C6      0.00   0.0  0
 1E5  CONST_14  C22  C17  C1   C6    180.00   0.0  0
 1E5  CONST_15  C20  C19  N18  C17     0.00   0.0  0
 1E5  CONST_16  C20  C21  C22  C17     0.00   0.0  0
 1E5  CONST_17  C21  C22  C17  N18     0.00   0.0  0
 1E5  CONST_18  C21  C20  C19  N18     0.00   0.0  0
 1E5  CONST_19  C22  C17  N18  C19     0.00   0.0  0
 1E5  CONST_20  C22  C21  C20  C19     0.00   0.0  0
 1E5  CONST_21  O7   C5   C6   C1    180.00   0.0  0
 1E5  CONST_22  F31  C3   C2   C1    180.00   0.0  0
 1E5  CONST_23  O7   C5   C4   C3    180.00   0.0  0
 1E5  CONST_24  F31  C3   C4   C5    180.00   0.0  0
 1E5  CONST_25  C23  C20  C19  N18   180.00   0.0  0
 1E5  CONST_26  C23  C20  C21  C22   180.00   0.0  0
 1E5  CONST_27  H9   C22  C17  C1      0.00   0.0  0
 1E5  CONST_28  H2   C4   C3   C2    180.00   0.0  0
 1E5  CONST_29  H3   C6   C1   C2    180.00   0.0  0
 1E5  CONST_30  H1   C2   C3   C4    180.00   0.0  0
 1E5  CONST_31  H7   C19  N18  C17   180.00   0.0  0
 1E5  CONST_32  H8   C21  C22  C17   180.00   0.0  0
 1E5  CONST_33  H10  O24  C23  C20   180.00   0.0  0
 1E5  CONST_34  H6   O13  C9   C8    180.00   0.0  0
 1E5  Var_01    O25  C23  C20  C19  -179.47  30.0  2
 1E5  Var_02    C9   C8   O7   C5    179.74  30.0  2
 1E5  Var_03    O12  C9   C8   O7     -0.66  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
 1E5  plan-1  C1   0.020
 1E5  plan-1  C2   0.020
 1E5  plan-1  C3   0.020
 1E5  plan-1  C4   0.020
 1E5  plan-1  C5   0.020
 1E5  plan-1  C6   0.020
 1E5  plan-1  O7   0.020
 1E5  plan-1  C17  0.020
 1E5  plan-1  F31  0.020
 1E5  plan-1  H1   0.020
 1E5  plan-1  H2   0.020
 1E5  plan-1  H3   0.020
 1E5  plan-2  C1   0.020
 1E5  plan-2  C17  0.020
 1E5  plan-2  N18  0.020
 1E5  plan-2  C19  0.020
 1E5  plan-2  C20  0.020
 1E5  plan-2  C21  0.020
 1E5  plan-2  C22  0.020
 1E5  plan-2  C23  0.020
 1E5  plan-2  H7   0.020
 1E5  plan-2  H8   0.020
 1E5  plan-2  H9   0.020
 1E5  plan-3  C8   0.020
 1E5  plan-3  C9   0.020
 1E5  plan-3  O12  0.020
 1E5  plan-3  O13  0.020
 1E5  plan-3  H6   0.020
 1E5  plan-4  C20  0.020
 1E5  plan-4  C23  0.020
 1E5  plan-4  O24  0.020
 1E5  plan-4  O25  0.020
 1E5  plan-4  H10  0.020

