# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 13:34:24 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 5-ethyl-4-fluoro-2-[(2-fluoropyridin-3-yl)oxy]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cc(O)c(Oc2cccnc2F)cc1F
#
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
 JA3  JA3  5-ethyl-4-fluoro-2-[(2-fluoropyridin-3-yl)oxy]phenol  ligand  29  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JA3
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
 JA3  F1    F  F     0  -0.315   2.0422  -2.3162  -0.7994
 JA3  C8    C  CR6   0   0.512   1.8049  -1.0065  -0.6011
 JA3  C9    C  CR6   0  -0.077   2.8681  -0.1587  -0.3622
 JA3  C10   C  CH2   0  -0.485   4.2846  -0.6523  -0.2771
 JA3  C11   C  CH3   0  -0.634   4.6353  -1.1834   1.1106
 JA3  C12   C  CR16  0  -0.389   2.5572   1.1859  -0.1589
 JA3  C     C  CR6   0   0.300   1.2572   1.6610  -0.1905
 JA3  O     O  OH1   0  -0.608   0.9223   2.9537   0.0034
 JA3  C7    C  CR16  0  -0.479   0.4910  -0.5754  -0.6542
 JA3  C1    C  CR6   0   0.314   0.2169   0.7631  -0.4439
 JA3  O1    O  O2    0  -0.486  -1.0350   1.3036  -0.5014
 JA3  C2    C  CR6   0   0.091  -2.1121   0.4794  -0.4211
 JA3  C6    C  CR6   0   0.550  -2.4664  -0.1444   0.7730
 JA3  F     F  F     0  -0.289  -1.6822   0.0334   1.8349
 JA3  N     N  N     0  -0.410  -3.5119  -0.8951   0.9319
 JA3  C5    C  CR16  0  -0.040  -4.3101  -1.0869  -0.1181
 JA3  C4    C  CR16  0  -0.284  -4.0671  -0.5216  -1.3543
 JA3  C3    C  CR16  0  -0.176  -2.9390   0.2749  -1.5072
 JA3  H7    H  HCR6  0   0.286  -0.2937  -1.2903  -0.8680
 JA3  H101  H  HCH2  0   0.241   4.4614  -1.4292  -1.0223
 JA3  H102  H  HCH2  0   0.233   4.9604   0.1663  -0.5310
 JA3  H12   H  HCR6  0   0.235   3.3693   1.8801   0.0300
 JA3  H111  H  HCH3  0   0.227   5.6699  -1.5248   1.1416
 JA3  H112  H  HCH3  0   0.219   4.5146  -0.4098   1.8690
 JA3  H113  H  HCH3  0   0.224   3.9998  -2.0238   1.3891
 JA3  H     H  HOH1  0   0.449   1.7099   3.4762   0.1747
 JA3  H3    H  HCR6  0   0.269  -2.7068   0.7420  -2.4548
 JA3  H5    H  HCR6  0   0.258  -5.1773  -1.7135   0.0428
 JA3  H4    H  HCR6  0   0.265  -4.7344  -0.7047  -2.1823

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
 JA3  F1   C8    single    1.346  0.020  1.346
 JA3  C8   C9    aromatic  1.381  0.020  1.381
 JA3  C8   C7    aromatic  1.384  0.020  1.384
 JA3  C9   C10   single    1.502  0.020  1.502
 JA3  C9   C12   aromatic  1.395  0.020  1.395
 JA3  C10  C11   single    1.527  0.020  1.527
 JA3  C12  C     aromatic  1.384  0.020  1.384
 JA3  C    O     single    1.349  0.020  1.349
 JA3  C    C1    aromatic  1.397  0.020  1.397
 JA3  C7   C1    aromatic  1.382  0.020  1.382
 JA3  C1   O1    single    1.365  0.020  1.365
 JA3  O1   C2    single    1.359  0.020  1.359
 JA3  C2   C6    aromatic  1.393  0.020  1.393
 JA3  C2   C3    aromatic  1.380  0.020  1.380
 JA3  C6   F     single    1.332  0.020  1.332
 JA3  C6   N     aromatic  1.297  0.020  1.297
 JA3  N    C5    aromatic  1.333  0.020  1.333
 JA3  C5   C4    aromatic  1.381  0.020  1.381
 JA3  C4   C3    aromatic  1.389  0.020  1.389
 JA3  C7   H7    single    0.930  0.020  1.080
 JA3  C10  H101  single    0.970  0.020  1.090
 JA3  C10  H102  single    0.970  0.020  1.090
 JA3  C12  H12   single    0.930  0.020  1.080
 JA3  C11  H111  single    0.970  0.020  1.090
 JA3  C11  H112  single    0.970  0.020  1.090
 JA3  C11  H113  single    0.970  0.020  1.090
 JA3  O    H     single    0.850  0.020  0.980
 JA3  C3   H3    single    0.930  0.020  1.080
 JA3  C5   H5    single    0.930  0.020  1.080
 JA3  C4   H4    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
 JA3  C7    C8   C9    123.13  3.000
 JA3  C7    C8   F1    117.70  3.000
 JA3  C9    C8   F1    119.17  3.000
 JA3  C12   C9   C10   121.24  3.000
 JA3  C12   C9   C8    116.45  3.000
 JA3  C10   C9   C8    122.28  3.000
 JA3  H102  C10  H101  105.96  3.000
 JA3  H102  C10  C11   109.28  3.000
 JA3  H101  C10  C11   109.63  3.000
 JA3  H102  C10  C9    108.91  3.000
 JA3  H101  C10  C9    110.37  3.000
 JA3  C11   C10  C9    112.48  3.000
 JA3  H113  C11  H112  107.75  3.000
 JA3  H113  C11  H111  107.75  3.000
 JA3  H112  C11  H111  107.92  3.000
 JA3  H113  C11  C10   111.50  3.000
 JA3  H112  C11  C10   111.10  3.000
 JA3  H111  C11  C10   110.66  3.000
 JA3  H12   C12  C     119.15  3.000
 JA3  H12   C12  C9    118.38  3.000
 JA3  C     C12  C9    122.46  3.000
 JA3  C1    C    O     117.18  3.000
 JA3  C1    C    C12   118.86  3.000
 JA3  O     C    C12   123.96  3.000
 JA3  H     O    C     110.07  3.000
 JA3  H7    C7   C1    121.71  3.000
 JA3  H7    C7   C8    119.34  3.000
 JA3  C1    C7   C8    118.95  3.000
 JA3  O1    C1   C7    123.98  3.000
 JA3  O1    C1   C     115.85  3.000
 JA3  C7    C1   C     120.14  3.000
 JA3  C2    O1   C1    118.98  3.000
 JA3  C3    C2   C6    117.12  3.000
 JA3  C3    C2   O1    121.22  3.000
 JA3  C6    C2   O1    121.60  3.000
 JA3  N     C6   F     117.01  3.000
 JA3  N     C6   C2    124.70  3.000
 JA3  F     C6   C2    118.29  3.000
 JA3  C5    N    C6    118.01  3.000
 JA3  H5    C5   C4    120.75  3.000
 JA3  H5    C5   N     116.50  3.000
 JA3  C4    C5   N     122.75  3.000
 JA3  H4    C4   C3    120.99  3.000
 JA3  H4    C4   C5    120.58  3.000
 JA3  C3    C4   C5    118.43  3.000
 JA3  H3    C3   C4    121.21  3.000
 JA3  H3    C3   C2    119.78  3.000
 JA3  C4    C3   C2    119.00  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
 JA3  CONST_01  C     C12  C9   C8      0.00   0.0  0
 JA3  CONST_02  C     C1   C7   C8      0.00   0.0  0
 JA3  CONST_03  C1    C7   C8   C9      0.00   0.0  0
 JA3  CONST_04  C1    C    C12  C9      0.00   0.0  0
 JA3  CONST_05  C7    C8   C9   C12     0.00   0.0  0
 JA3  CONST_06  C7    C1   C    C12     0.00   0.0  0
 JA3  CONST_07  C5    N    C6   C2      0.00   0.0  0
 JA3  CONST_08  C5    C4   C3   C2      0.00   0.0  0
 JA3  CONST_09  C4    C3   C2   C6      0.00   0.0  0
 JA3  CONST_10  C4    C5   N    C6      0.00   0.0  0
 JA3  CONST_11  C3    C2   C6   N       0.00   0.0  0
 JA3  CONST_12  C3    C4   C5   N       0.00   0.0  0
 JA3  CONST_13  C12   C9   C8   F1    180.00   0.0  0
 JA3  CONST_14  C1    C7   C8   F1    180.00   0.0  0
 JA3  CONST_15  O1    C1   C7   C8    180.00   0.0  0
 JA3  CONST_16  O     C    C12  C9    180.00   0.0  0
 JA3  CONST_17  C7    C8   C9   C10   180.00   0.0  0
 JA3  CONST_18  C     C12  C9   C10   180.00   0.0  0
 JA3  CONST_19  O1    C1   C    C12   180.00   0.0  0
 JA3  CONST_20  C7    C1   C    O     180.00   0.0  0
 JA3  CONST_21  N     C6   C2   O1    180.00   0.0  0
 JA3  CONST_22  C4    C3   C2   O1    180.00   0.0  0
 JA3  CONST_23  C3    C2   C6   F     180.00   0.0  0
 JA3  CONST_24  C5    N    C6   F     180.00   0.0  0
 JA3  CONST_25  H12   C12  C9   C8    180.00   0.0  0
 JA3  CONST_26  H7    C7   C8   C9    180.00   0.0  0
 JA3  CONST_27  H4    C4   C3   C2    180.00   0.0  0
 JA3  CONST_28  H3    C3   C2   C6    180.00   0.0  0
 JA3  CONST_29  H5    C5   N    C6    180.00   0.0  0
 JA3  Var_01    C6    C2   O1   C1     71.70  30.0  2
 JA3  Var_02    C11   C10  C9   C8    -83.86  30.0  2
 JA3  Var_03    H111  C11  C10  C9   -179.49  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
 JA3  plan-1  F1   0.020
 JA3  plan-1  C8   0.020
 JA3  plan-1  C9   0.020
 JA3  plan-1  C10  0.020
 JA3  plan-1  C12  0.020
 JA3  plan-1  C    0.020
 JA3  plan-1  O    0.020
 JA3  plan-1  C7   0.020
 JA3  plan-1  C1   0.020
 JA3  plan-1  O1   0.020
 JA3  plan-1  H7   0.020
 JA3  plan-1  H12  0.020
 JA3  plan-2  O1   0.020
 JA3  plan-2  C2   0.020
 JA3  plan-2  C6   0.020
 JA3  plan-2  F    0.020
 JA3  plan-2  N    0.020
 JA3  plan-2  C5   0.020
 JA3  plan-2  C4   0.020
 JA3  plan-2  C3   0.020
 JA3  plan-2  H3   0.020
 JA3  plan-2  H5   0.020
 JA3  plan-2  H4   0.020

