# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 00:48:11 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-[(4-methoxypyrimidin-2-yl)amino]-2-[(3-methylbut-2-en-1-yl)oxy]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccnc(Nc2ccc(C#N)c(OCC=C(C)C)c2)n1
#
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
 JLJ  JLJ  4-[(4-methoxypyrimidin-2-yl)amino]-2-[(3-methylbut-2-en-1-yl)oxy]benzonitrile  ligand  41  23  .  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_JLJ
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
 JLJ  C11  C  CR6   0   0.618  -3.0481   0.1577  -0.0432
 JLJ  N12  N  N     0  -0.519  -3.8359  -0.9158   0.0833
 JLJ  C13  C  CR6   0   0.569  -5.1316  -0.7166   0.0186
 JLJ  C14  C  CR16  0  -0.442  -5.6831   0.5597  -0.1762
 JLJ  C15  C  CR16  0   0.009  -4.7729   1.5780  -0.2938
 JLJ  N16  N  N     0  -0.484  -3.4499   1.4000  -0.2308
 JLJ  O17  O  O2    0  -0.456  -5.9617  -1.7369   0.1409
 JLJ  C18  C  CH3   0  -0.422  -5.4170  -3.0367   0.3565
 JLJ  N19  N  NH1   0  -0.771  -1.7145  -0.1399   0.0403
 JLJ  C20  C  CR6   0  -0.131   1.8080   2.0853  -0.0243
 JLJ  C21  C  CR6   0   0.446   1.8282   0.6887   0.1456
 JLJ  C22  C  CR16  0  -0.519   0.6334  -0.0092   0.1559
 JLJ  C23  C  CR6   0   0.430  -0.5921   0.6581   0.0042
 JLJ  C24  C  CR16  0  -0.340  -0.6082   2.0480  -0.1686
 JLJ  C25  C  CR16  0  -0.218   0.5869   2.7366  -0.1797
 JLJ  N27  N  NS    0  -0.267   4.0113   3.4122  -0.0479
 JLJ  C28  C  CSP   0   0.054   3.0271   2.8097  -0.0359
 JLJ  C41  C  CH2   0  -0.267   3.1437  -1.2780   0.4783
 JLJ  C42  C  C1    0  -0.299   4.5781  -1.5848   0.7366
 JLJ  C43  C  C     0   0.110   5.4213  -2.2116  -0.0886
 JLJ  C44  C  CH3   0  -0.721   5.0794  -2.7060  -1.4610
 JLJ  C45  C  CH3   0  -0.704   6.8387  -2.4724   0.3269
 JLJ  H1   H  HCR6  0   0.282  -6.7486   0.7259  -0.2285
 JLJ  H2   H  HCR6  0   0.278  -5.1095   2.5967  -0.4464
 JLJ  H3   H  HCH3  0   0.238  -4.8007  -3.3571  -0.4835
 JLJ  H4   H  HCH3  0   0.237  -4.8213  -3.0746   1.2688
 JLJ  H5   H  HCH3  0   0.253  -6.2707  -3.7007   0.4538
 JLJ  H6   H  HNH1  0   0.417  -1.5443  -1.1246   0.1809
 JLJ  H7   H  HCR6  0   0.306   0.6285  -1.0840   0.2814
 JLJ  H8   H  HCR6  0   0.296  -1.5370   2.5780  -0.2925
 JLJ  H9   H  HCR6  0   0.281   0.5751   3.8103  -0.3101
 JLJ  H10  H  HCH2  0   0.247   2.5397  -1.5743   1.3422
 JLJ  H11  H  HCH2  0   0.247   2.7515  -1.8019  -0.3967
 JLJ  H12  H  H     0   0.243   4.9497  -1.2624   1.7047
 JLJ  H13  H  HCH3  0   0.244   5.7452  -2.2499  -2.1969
 JLJ  H14  H  HCH3  0   0.244   5.2383  -3.7845  -1.5289
 JLJ  H15  H  HCH3  0   0.244   4.0574  -2.4982  -1.7680
 JLJ  H16  H  HCH3  0   0.242   7.0525  -2.0941   1.3254
 JLJ  H17  H  HCH3  0   0.239   7.0537  -3.5438   0.3148
 JLJ  H18  H  HCH3  0   0.239   7.5377  -2.0074  -0.3722
 JLJ  O26  O  O2    0  -0.454   3.0337   0.1382   0.2853

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
 JLJ  N16  C15  aromatic  1.336  0.020  1.336
 JLJ  N16  C11  aromatic  1.319  0.020  1.319
 JLJ  C24  C25  aromatic  1.379  0.020  1.379
 JLJ  C24  C23  aromatic  1.401  0.020  1.401
 JLJ  N19  C11  single    1.369  0.020  1.369
 JLJ  N19  C23  single    1.378  0.020  1.378
 JLJ  C15  C14  aromatic  1.371  0.020  1.371
 JLJ  C25  C20  aromatic  1.393  0.020  1.393
 JLJ  C11  N12  aromatic  1.338  0.020  1.338
 JLJ  C23  C22  aromatic  1.404  0.020  1.404
 JLJ  C14  C13  aromatic  1.404  0.020  1.404
 JLJ  C20  C28  single    1.418  0.020  1.418
 JLJ  C20  C21  aromatic  1.407  0.020  1.407
 JLJ  N12  C13  aromatic  1.313  0.020  1.313
 JLJ  C22  C21  aromatic  1.384  0.020  1.384
 JLJ  C28  N27  triple    1.154  0.020  1.154
 JLJ  C13  O17  single    1.321  0.020  1.321
 JLJ  C21  O26  single    1.333  0.020  1.333
 JLJ  O17  C18  single    1.426  0.020  1.426
 JLJ  O26  C41  single    1.434  0.020  1.434
 JLJ  C42  C41  single    1.489  0.020  1.489
 JLJ  C42  C43  double    1.336  0.020  1.336
 JLJ  C45  C43  single    1.500  0.020  1.500
 JLJ  C43  C44  single    1.498  0.020  1.498
 JLJ  C14  H1   single    0.930  0.020  1.080
 JLJ  C15  H2   single    0.930  0.020  1.080
 JLJ  C18  H3   single    0.970  0.020  1.090
 JLJ  C18  H4   single    0.970  0.020  1.090
 JLJ  C18  H5   single    0.970  0.020  1.090
 JLJ  N19  H6   single    0.860  0.020  1.020
 JLJ  C22  H7   single    0.930  0.020  1.080
 JLJ  C24  H8   single    0.930  0.020  1.080
 JLJ  C25  H9   single    0.930  0.020  1.080
 JLJ  C41  H10  single    0.970  0.020  1.090
 JLJ  C41  H11  single    0.970  0.020  1.090
 JLJ  C42  H12  single    0.930  0.020  1.080
 JLJ  C44  H13  single    0.970  0.020  1.090
 JLJ  C44  H14  single    0.970  0.020  1.090
 JLJ  C44  H15  single    0.970  0.020  1.090
 JLJ  C45  H16  single    0.970  0.020  1.090
 JLJ  C45  H17  single    0.970  0.020  1.090
 JLJ  C45  H18  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
 JLJ  N19  C11  N16  120.68  3.000
 JLJ  N19  C11  N12  113.17  3.000
 JLJ  N16  C11  N12  126.15  3.000
 JLJ  C13  N12  C11  117.06  3.000
 JLJ  O17  C13  C14  117.91  3.000
 JLJ  O17  C13  N12  119.90  3.000
 JLJ  C14  C13  N12  122.18  3.000
 JLJ  H1   C14  C15  122.46  3.000
 JLJ  H1   C14  C13  122.30  3.000
 JLJ  C15  C14  C13  115.24  3.000
 JLJ  H2   C15  N16  116.06  3.000
 JLJ  H2   C15  C14  120.28  3.000
 JLJ  N16  C15  C14  123.66  3.000
 JLJ  C15  N16  C11  115.70  3.000
 JLJ  C18  O17  C13  118.56  3.000
 JLJ  H5   C18  H4   109.47  3.000
 JLJ  H5   C18  H3   109.50  3.000
 JLJ  H4   C18  H3   109.01  3.000
 JLJ  H5   C18  O17  105.71  3.000
 JLJ  H4   C18  O17  111.53  3.000
 JLJ  H3   C18  O17  111.56  3.000
 JLJ  H6   N19  C23  115.56  3.000
 JLJ  H6   N19  C11  112.64  3.000
 JLJ  C23  N19  C11  131.77  3.000
 JLJ  C28  C20  C25  120.93  3.000
 JLJ  C28  C20  C21  119.71  3.000
 JLJ  C25  C20  C21  119.36  3.000
 JLJ  O26  C21  C22  124.89  3.000
 JLJ  O26  C21  C20  115.83  3.000
 JLJ  C22  C21  C20  119.28  3.000
 JLJ  H7   C22  C23  118.74  3.000
 JLJ  H7   C22  C21  120.37  3.000
 JLJ  C23  C22  C21  120.89  3.000
 JLJ  C24  C23  C22  119.68  3.000
 JLJ  C22  C23  N19  115.67  3.000
 JLJ  C24  C23  N19  124.65  3.000
 JLJ  H8   C24  C25  120.05  3.000
 JLJ  H8   C24  C23  120.84  3.000
 JLJ  C25  C24  C23  119.10  3.000
 JLJ  H9   C25  C24  119.15  3.000
 JLJ  H9   C25  C20  119.16  3.000
 JLJ  C24  C25  C20  121.69  3.000
 JLJ  N27  C28  C20  180.00  3.000
 JLJ  H11  C41  H10  107.70  3.000
 JLJ  H11  C41  C42  112.69  3.000
 JLJ  H10  C41  C42  109.80  3.000
 JLJ  H11  C41  O26  109.77  3.000
 JLJ  H10  C41  O26  109.34  3.000
 JLJ  C42  C41  O26  107.50  3.000
 JLJ  H12  C42  C43  118.29  3.000
 JLJ  H12  C42  C41  115.02  3.000
 JLJ  C43  C42  C41  126.69  3.000
 JLJ  C45  C43  C44  114.33  3.000
 JLJ  C44  C43  C42  125.21  3.000
 JLJ  C45  C43  C42  120.46  3.000
 JLJ  H15  C44  H14  107.94  3.000
 JLJ  H15  C44  H13  107.63  3.000
 JLJ  H14  C44  H13  106.36  3.000
 JLJ  H15  C44  C43  114.21  3.000
 JLJ  H14  C44  C43  110.46  3.000
 JLJ  H13  C44  C43  109.90  3.000
 JLJ  H18  C45  H17  106.52  3.000
 JLJ  H18  C45  H16  108.25  3.000
 JLJ  H17  C45  H16  108.18  3.000
 JLJ  H18  C45  C43  110.69  3.000
 JLJ  H17  C45  C43  110.70  3.000
 JLJ  H16  C45  C43  112.28  3.000
 JLJ  C41  O26  C21  119.45  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
 JLJ  CONST_01  C14  C15  N16  C11     0.00   0.0  0
 JLJ  CONST_02  C14  C13  N12  C11     0.00   0.0  0
 JLJ  CONST_03  C15  N16  C11  N12     0.00   0.0  0
 JLJ  CONST_04  C15  C14  C13  N12     0.00   0.0  0
 JLJ  CONST_05  N16  C15  C14  C13     0.00   0.0  0
 JLJ  CONST_06  N16  C11  N12  C13     0.00   0.0  0
 JLJ  CONST_07  C23  C24  C25  C20     0.00   0.0  0
 JLJ  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 JLJ  CONST_09  C24  C25  C20  C21     0.00   0.0  0
 JLJ  CONST_10  C24  C23  C22  C21     0.00   0.0  0
 JLJ  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 JLJ  CONST_12  C25  C20  C21  C22     0.00   0.0  0
 JLJ  CONST_13  O17  C13  N12  C11   180.00   0.0  0
 JLJ  CONST_14  N19  C11  N12  C13   180.00   0.0  0
 JLJ  CONST_15  N19  C11  N16  C15   180.00   0.0  0
 JLJ  CONST_16  O17  C13  C14  C15   180.00   0.0  0
 JLJ  CONST_17  C25  C24  C23  N19   180.00   0.0  0
 JLJ  CONST_18  C21  C22  C23  N19   180.00   0.0  0
 JLJ  CONST_19  C28  C20  C21  C22   180.00   0.0  0
 JLJ  CONST_20  O26  C21  C22  C23   180.00   0.0  0
 JLJ  CONST_21  C28  C20  C25  C24   180.00   0.0  0
 JLJ  CONST_22  O26  C21  C20  C25   180.00   0.0  0
 JLJ  CONST_23  H2   C15  N16  C11   180.00   0.0  0
 JLJ  CONST_24  H1   C14  C13  N12   180.00   0.0  0
 JLJ  CONST_25  H8   C24  C25  C20   180.00   0.0  0
 JLJ  CONST_26  H7   C22  C21  C20   180.00   0.0  0
 JLJ  CONST_27  H9   C25  C20  C21   180.00   0.0  0
 JLJ  Var_01    C24  C23  N19  C11    -1.54  30.0  2
 JLJ  Var_02    C23  N19  C11  N12  -177.72  30.0  2
 JLJ  Var_03    C42  C41  O26  C21  -174.48  30.0  3
 JLJ  Var_04    H3   C18  O17  C13   -62.65  30.0  3
 JLJ  Var_05    C45  C43  C42  C41  -178.80   0.0  2
 JLJ  Var_06    C43  C42  C41  O26  -109.01  30.0  1
 JLJ  Var_07    H16  C45  C43  C42    -0.30  30.0  3
 JLJ  Var_08    H13  C44  C43  C42   122.15  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
 JLJ  plan-1  C11  0.020
 JLJ  plan-1  N12  0.020
 JLJ  plan-1  C13  0.020
 JLJ  plan-1  C14  0.020
 JLJ  plan-1  C15  0.020
 JLJ  plan-1  N16  0.020
 JLJ  plan-1  O17  0.020
 JLJ  plan-1  N19  0.020
 JLJ  plan-1  H1   0.020
 JLJ  plan-1  H2   0.020
 JLJ  plan-2  N19  0.020
 JLJ  plan-2  C20  0.020
 JLJ  plan-2  C21  0.020
 JLJ  plan-2  C22  0.020
 JLJ  plan-2  C23  0.020
 JLJ  plan-2  C24  0.020
 JLJ  plan-2  C25  0.020
 JLJ  plan-2  N27  0.020
 JLJ  plan-2  C28  0.020
 JLJ  plan-2  H7   0.020
 JLJ  plan-2  H8   0.020
 JLJ  plan-2  H9   0.020
 JLJ  plan-2  O26  0.020
 JLJ  plan-3  C41  0.020
 JLJ  plan-3  C42  0.020
 JLJ  plan-3  C43  0.020
 JLJ  plan-3  C44  0.020
 JLJ  plan-3  C45  0.020
 JLJ  plan-3  H12  0.020

