# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 00:45:00 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  29  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   0.107  -0.1746   0.8529  -0.0028
 1E5  C2   C  CR16   0  -0.559   0.1816   2.2064   0.0052
 1E5  C3   C  CR6    0   0.606   1.5189   2.5263   0.0093
 1E5  C4   C  CR16   0  -0.563   2.5351   1.5883   0.0065
 1E5  C5   C  CR6    0   0.444   2.1733   0.2424  -0.0012
 1E5  C6   C  CR16   0  -0.417   0.8226  -0.1135  -0.0067
 1E5  O7   O  O2     0  -0.459   3.0508  -0.7680  -0.0033
 1E5  C8   C  CH2    0  -0.336   4.4356  -0.4715   0.0086
 1E5  C9   C  C      0   0.386   5.2703  -1.7633   0.0189
 1E5  O12  O  O      0  -0.591   4.6761  -2.8503   0.0142
 1E5  O13  O  OC    -1  -0.621   6.4991  -1.5567   0.0320
 1E5  C17  C  CR6    0   0.238  -1.5980   0.4334  -0.0068
 1E5  N18  N  N      0  -0.435  -1.8339  -0.8785  -0.0246
 1E5  C19  C  CR16   0  -0.091  -3.0843  -1.3129  -0.0287
 1E5  C20  C  CR6    0  -0.190  -4.2008  -0.4821  -0.0158
 1E5  C21  C  CR16   0  -0.169  -3.9512   0.8834   0.0026
 1E5  C22  C  CR16   0  -0.328  -2.6484   1.3498   0.0078
 1E5  C23  C  C      0   0.400  -5.6151  -1.0405  -0.0215
 1E5  O24  O  OC    -1  -0.590  -5.7205  -2.2809  -0.0198
 1E5  O25  O  O      0  -0.588  -6.5365  -0.2036  -0.0271
 1E5  F31  F  F      0  -0.319   1.8687   3.8233   0.0168
 1E5  H1   H  HCR6   0   0.271  -0.5499   3.0012   0.0075
 1E5  H2   H  HCR6   0   0.299   3.5644   1.9196   0.0097
 1E5  H3   H  HCR6   0   0.259   0.5546  -1.1611  -0.0128
 1E5  H4   H  HCH2   0   0.232   4.7089   0.1229  -0.8720
 1E5  H5   H  HCH2   0   0.231   4.6933   0.1251   0.8923
 1E5  H7   H  HCR6   0   0.253  -3.2150  -2.3889  -0.0434
 1E5  H8   H  HCR6   0   0.261  -4.7751   1.5843   0.0127
 1E5  H9   H  HCR6   0   0.267  -2.4719   2.4156   0.0226

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   deloc     1.239  0.020  1.239
 1E5  C8   C9   single    1.538  0.020  1.538
 1E5  C8   O7   single    1.416  0.020  1.416
 1E5  C9   O13  deloc     1.246  0.020  1.246
 1E5  O7   C5   single    1.338  0.020  1.338
 1E5  C4   C5   aromatic  1.394  0.020  1.394
 1E5  C4   C3   aromatic  1.383  0.020  1.383
 1E5  C5   C6   aromatic  1.397  0.020  1.397
 1E5  F31  C3   single    1.343  0.020  1.343
 1E5  C3   C2   aromatic  1.375  0.020  1.375
 1E5  C6   C1   aromatic  1.389  0.020  1.389
 1E5  C2   C1   aromatic  1.400  0.020  1.400
 1E5  C1   C17  single    1.484  0.020  1.484
 1E5  C17  N18  aromatic  1.333  0.020  1.333
 1E5  C17  C22  aromatic  1.394  0.020  1.394
 1E5  N18  C19  aromatic  1.324  0.020  1.324
 1E5  C22  C21  aromatic  1.384  0.020  1.384
 1E5  C19  C20  aromatic  1.392  0.020  1.392
 1E5  C21  C20  aromatic  1.388  0.020  1.388
 1E5  C20  C23  single    1.521  0.020  1.521
 1E5  C23  O25  deloc     1.245  0.020  1.245
 1E5  C23  O24  deloc     1.245  0.020  1.245
 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  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

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   119.48  3.000
 1E5  C17  C1   C2   121.17  3.000
 1E5  C6   C1   C2   119.35  3.000
 1E5  H1   C2   C3   119.17  3.000
 1E5  H1   C2   C1   122.63  3.000
 1E5  C3   C2   C1   118.20  3.000
 1E5  F31  C3   C4   117.62  3.000
 1E5  F31  C3   C2   118.55  3.000
 1E5  C4   C3   C2   123.84  3.000
 1E5  H2   C4   C5   122.89  3.000
 1E5  H2   C4   C3   119.45  3.000
 1E5  C5   C4   C3   117.66  3.000
 1E5  O7   C5   C6   116.22  3.000
 1E5  C6   C5   C4   119.81  3.000
 1E5  O7   C5   C4   123.97  3.000
 1E5  H3   C6   C5   119.11  3.000
 1E5  H3   C6   C1   119.75  3.000
 1E5  C5   C6   C1   121.14  3.000
 1E5  C8   O7   C5   118.89  3.000
 1E5  H5   C8   H4   107.06  3.000
 1E5  H5   C8   C9   108.90  3.000
 1E5  H4   C8   C9   108.98  3.000
 1E5  H5   C8   O7   110.51  3.000
 1E5  H4   C8   O7   110.51  3.000
 1E5  C9   C8   O7   110.79  3.000
 1E5  O13  C9   O12  128.21  3.000
 1E5  O13  C9   C8   113.32  3.000
 1E5  O12  C9   C8   118.46  3.000
 1E5  C22  C17  N18  120.92  3.000
 1E5  C22  C17  C1   122.47  3.000
 1E5  N18  C17  C1   116.62  3.000
 1E5  C19  N18  C17  119.35  3.000
 1E5  H7   C19  C20  119.73  3.000
 1E5  H7   C19  N18  116.08  3.000
 1E5  C20  C19  N18  124.19  3.000
 1E5  C23  C20  C21  121.90  3.000
 1E5  C23  C20  C19  121.79  3.000
 1E5  C21  C20  C19  116.30  3.000
 1E5  H8   C21  C22  119.91  3.000
 1E5  H8   C21  C20  120.03  3.000
 1E5  C22  C21  C20  120.06  3.000
 1E5  H9   C22  C21  119.10  3.000
 1E5  H9   C22  C17  121.71  3.000
 1E5  C21  C22  C17  119.19  3.000
 1E5  O25  C23  O24  127.39  3.000
 1E5  O24  C23  C20  116.40  3.000
 1E5  O25  C23  C20  116.20  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  Var_01    O25  C23  C20  C19  -179.06  30.0  2
 1E5  Var_02    C9   C8   O7   C5    179.40  30.0  1
 1E5  Var_03    O12  C9   C8   O7      0.09  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-4  C20  0.020
 1E5  plan-4  C23  0.020
 1E5  plan-4  O24  0.020
 1E5  plan-4  O25  0.020

