# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 21:56:01 2021
#   Inital geometry file: a 71 line input string
#   Ligand name: ~{N}4-methyl-6-morpholin-4-yl-pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(nc(N)n1)N2CCOCC2
#
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
 CJ0  CJ0  ~{N}4-methyl-6-morpholin-4-yl-pyrimidine-2,4-diamine  ligand  30  15  .  2022-03-15  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CJ0
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
 CJ0  N1   N  N     0  -0.546  28.3914   9.6781  -14.9870
 CJ0  N3   N  N     0  -0.534  26.2359   9.3240  -15.9306
 CJ0  C2   C  CR6   0   0.519  27.0801   9.8829  -15.0716
 CJ0  C4   C  CR6   0   0.523  26.7794   8.4828  -16.8206
 CJ0  C5   C  CR16  0  -0.565  28.1489   8.1967  -16.8396
 CJ0  C6   C  CR6   0   0.580  28.9298   8.8230  -15.8626
 CJ0  CAA  C  CH2   0  -0.185  32.2570   7.2322  -16.1265
 CJ0  CAC  C  CH2   0  -0.194  32.3493   8.8537  -14.4860
 CJ0  CAD  C  CH2   0  -0.316  30.9930   7.8206  -16.7282
 CJ0  CAF  C  CH2   0  -0.312  31.0995   9.5333  -15.0058
 CJ0  CAO  C  CH3   0  -0.529  26.3274   7.0693  -18.7843
 CJ0  NAE  N  NT    0  -0.512  30.2688   8.5874  -15.7341
 CJ0  NAM  N  NH2   0  -0.824  26.5561  10.7924  -14.2087
 CJ0  NAN  N  NH1   0  -0.647  25.9285   7.9253  -17.7014
 CJ0  OAB  O  O2    0  -0.482  33.0638   8.2117  -15.5180
 CJ0  H1   H  HCR6  0   0.265  28.5635   7.5358  -17.5826
 CJ0  H2   H  HCH2  0   0.206  31.9838   6.4552  -15.3982
 CJ0  H3   H  HCH2  0   0.245  32.8441   6.7594  -16.9146
 CJ0  H4   H  HCH2  0   0.205  32.0792   8.1322  -13.7019
 CJ0  H5   H  HCH2  0   0.242  33.0091   9.6000  -14.0414
 CJ0  H6   H  HCH2  0   0.231  31.2425   8.4416  -17.5990
 CJ0  H7   H  HCH2  0   0.259  30.3905   6.9856  -17.0821
 CJ0  H8   H  HCH2  0   0.224  31.3793  10.3740  -15.6554
 CJ0  H9   H  HCH2  0   0.267  30.5397   9.9397  -14.1684
 CJ0  H10  H  HCH3  0   0.263  25.4429   6.7997  -19.3548
 CJ0  H11  H  HCH3  0   0.231  27.0314   7.5585  -19.4629
 CJ0  H12  H  HCH3  0   0.233  26.7897   6.1455  -18.4285
 CJ0  H13  H  HNH2  0   0.383  25.5606  10.7754  -14.0685
 CJ0  H14  H  HNH2  0   0.383  27.1059  11.0329  -13.4019
 CJ0  H15  H  HNH1  0   0.386  24.9699   8.2232  -17.6556

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
 CJ0  CAO  NAN  single    1.437  0.020  1.437
 CJ0  NAN  C4   single    1.346  0.020  1.346
 CJ0  CAD  CAA  single    1.519  0.020  1.519
 CJ0  CAD  NAE  single    1.449  0.020  1.449
 CJ0  C5   C4   aromatic  1.399  0.020  1.399
 CJ0  C5   C6   aromatic  1.399  0.020  1.399
 CJ0  C4   N3   aromatic  1.340  0.020  1.340
 CJ0  CAA  OAB  single    1.407  0.020  1.407
 CJ0  C6   NAE  single    1.366  0.020  1.366
 CJ0  C6   N1   aromatic  1.337  0.020  1.337
 CJ0  NAE  CAF  single    1.454  0.020  1.454
 CJ0  N3   C2   aromatic  1.328  0.020  1.328
 CJ0  OAB  CAC  single    1.410  0.020  1.410
 CJ0  N1   C2   aromatic  1.330  0.020  1.330
 CJ0  C2   NAM  single    1.359  0.020  1.359
 CJ0  CAF  CAC  single    1.515  0.020  1.515
 CJ0  C5   H1   single    0.930  0.020  1.080
 CJ0  CAA  H2   single    0.970  0.020  1.090
 CJ0  CAA  H3   single    0.970  0.020  1.090
 CJ0  CAC  H4   single    0.970  0.020  1.090
 CJ0  CAC  H5   single    0.970  0.020  1.090
 CJ0  CAD  H6   single    0.970  0.020  1.090
 CJ0  CAD  H7   single    0.970  0.020  1.090
 CJ0  CAF  H8   single    0.970  0.020  1.090
 CJ0  CAF  H9   single    0.970  0.020  1.090
 CJ0  CAO  H10  single    0.970  0.020  1.090
 CJ0  CAO  H11  single    0.970  0.020  1.090
 CJ0  CAO  H12  single    0.970  0.020  1.090
 CJ0  NAM  H13  single    0.890  0.020  1.040
 CJ0  NAM  H14  single    0.890  0.020  1.040
 CJ0  NAN  H15  single    0.860  0.020  1.020

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
 CJ0  C6   N1   C2   116.99  3.000
 CJ0  C4   N3   C2   115.85  3.000
 CJ0  NAM  C2   N3   116.58  3.000
 CJ0  NAM  C2   N1   116.29  3.000
 CJ0  N3   C2   N1   127.11  3.000
 CJ0  NAN  C4   C5   121.69  3.000
 CJ0  C5   C4   N3   122.31  3.000
 CJ0  NAN  C4   N3   116.00  3.000
 CJ0  H1   C5   C6   122.79  3.000
 CJ0  H1   C5   C4   120.76  3.000
 CJ0  C6   C5   C4   116.45  3.000
 CJ0  NAE  C6   C5   122.40  3.000
 CJ0  NAE  C6   N1   116.33  3.000
 CJ0  C5   C6   N1   121.26  3.000
 CJ0  H3   CAA  H2   107.82  3.000
 CJ0  H3   CAA  OAB  107.80  3.000
 CJ0  H2   CAA  OAB  110.36  3.000
 CJ0  H3   CAA  CAD  109.25  3.000
 CJ0  H2   CAA  CAD  109.24  3.000
 CJ0  OAB  CAA  CAD  112.27  3.000
 CJ0  H5   CAC  H4   107.87  3.000
 CJ0  H5   CAC  OAB  107.66  3.000
 CJ0  H4   CAC  OAB  110.35  3.000
 CJ0  H5   CAC  CAF  109.39  3.000
 CJ0  H4   CAC  CAF  109.66  3.000
 CJ0  OAB  CAC  CAF  111.80  3.000
 CJ0  H7   CAD  H6   107.56  3.000
 CJ0  H7   CAD  NAE  110.62  3.000
 CJ0  H6   CAD  NAE  110.99  3.000
 CJ0  H7   CAD  CAA  107.00  3.000
 CJ0  H6   CAD  CAA  110.13  3.000
 CJ0  NAE  CAD  CAA  110.43  3.000
 CJ0  H9   CAF  H8   107.51  3.000
 CJ0  H9   CAF  NAE  109.58  3.000
 CJ0  H8   CAF  NAE  110.31  3.000
 CJ0  H9   CAF  CAC  109.18  3.000
 CJ0  H8   CAF  CAC  109.63  3.000
 CJ0  NAE  CAF  CAC  110.57  3.000
 CJ0  H12  CAO  H11  107.94  3.000
 CJ0  H12  CAO  H10  107.80  3.000
 CJ0  H11  CAO  H10  108.02  3.000
 CJ0  H12  CAO  NAN  112.07  3.000
 CJ0  H11  CAO  NAN  112.33  3.000
 CJ0  H10  CAO  NAN  108.51  3.000
 CJ0  CAF  NAE  CAD  113.71  3.000
 CJ0  CAF  NAE  C6   119.67  3.000
 CJ0  CAD  NAE  C6   121.11  3.000
 CJ0  H14  NAM  H13  115.69  3.000
 CJ0  H14  NAM  C2   117.31  3.000
 CJ0  H13  NAM  C2   117.32  3.000
 CJ0  H15  NAN  CAO  118.41  3.000
 CJ0  H15  NAN  C4   116.78  3.000
 CJ0  CAO  NAN  C4   124.38  3.000
 CJ0  CAC  OAB  CAA  110.05  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
 CJ0  CONST_01  C4   C5   C6   N1      0.00   0.0  0
 CJ0  CONST_02  C4   N3   C2   N1      0.00   0.0  0
 CJ0  CONST_03  C6   C5   C4   N3      0.00   0.0  0
 CJ0  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 CJ0  CONST_05  C5   C4   N3   C2      0.00   0.0  0
 CJ0  CONST_06  C5   C6   N1   C2      0.00   0.0  0
 CJ0  CONST_07  NAE  C6   N1   C2    180.00   0.0  0
 CJ0  CONST_08  NAE  C6   C5   C4    180.00   0.0  0
 CJ0  CONST_09  NAN  C4   N3   C2    180.00   0.0  0
 CJ0  CONST_10  NAM  C2   N3   C4    180.00   0.0  0
 CJ0  CONST_11  NAN  C4   C5   C6    180.00   0.0  0
 CJ0  CONST_12  NAM  C2   N1   C6    180.00   0.0  0
 CJ0  CONST_13  H1   C5   C6   N1    180.00   0.0  0
 CJ0  CONST_14  CAO  NAN  C4   N3    180.00   0.0  0
 CJ0  CONST_15  CAO  NAN  C4   C5      0.00   0.0  0
 CJ0  CONST_18  H15  NAN  C4   N3      0.00   0.0  0
 CJ0  Var_01    CAD  NAE  C6   N1   -171.82  30.0  2
 CJ0  Var_02    CAA  CAD  NAE  C6   -157.25  30.0  1
 CJ0  Var_03    CAC  CAF  NAE  C6    156.30  30.0  1
 CJ0  Var_04    CAF  CAC  OAB  CAA   -59.97  30.0  1
 CJ0  Var_05    CAD  CAA  OAB  CAC    59.74  30.0  1
 CJ0  Var_06    OAB  CAA  CAD  NAE   -53.93  30.0  1
 CJ0  Var_07    OAB  CAC  CAF  NAE    54.59  30.0  1
 CJ0  Var_08    H10  CAO  NAN  C4   -177.68  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
 CJ0  plan-1  N1   0.020
 CJ0  plan-1  N3   0.020
 CJ0  plan-1  C2   0.020
 CJ0  plan-1  C4   0.020
 CJ0  plan-1  C5   0.020
 CJ0  plan-1  C6   0.020
 CJ0  plan-1  NAE  0.020
 CJ0  plan-1  NAM  0.020
 CJ0  plan-1  NAN  0.020
 CJ0  plan-1  H1   0.020
 CJ0  plan-2  C2   0.020
 CJ0  plan-2  NAM  0.020
 CJ0  plan-2  H13  0.020
 CJ0  plan-2  H14  0.020
 CJ0  plan-3  C4   0.020
 CJ0  plan-3  CAO  0.020
 CJ0  plan-3  NAN  0.020
 CJ0  plan-3  H15  0.020

