# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:32:39 2021
#   Inital geometry file: a 79 line input string
#   Ligand name: ~{N}4-cyclopropyl-6-morpholin-4-yl-pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CC2)cc(n1)N3CCOCC3
#
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
 CJF  CJF  ~{N}4-cyclopropyl-6-morpholin-4-yl-pyrimidine-2,4-diamine  ligand  34  17  .  2022-07-24  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_CJF
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
 CJF  N01  N  NH2   0  -0.824  26.7933  10.4188  -13.9897
 CJF  C02  C  CR6   0   0.521  27.4000   9.5626  -14.8504
 CJF  N03  N  N     0  -0.546  28.7126   9.4083  -14.7032
 CJF  C04  C  CR6   0   0.582  29.3322   8.6029  -15.5724
 CJF  C05  C  CR16  0  -0.555  28.6207   7.9427  -16.5823
 CJF  C06  C  CR6   0   0.519  27.2484   8.1904  -16.6385
 CJF  N07  N  NH1   0  -0.658  26.4572   7.6308  -17.5834
 CJF  C08  C  CH1   0  -0.100  26.9048   6.6614  -18.5201
 CJF  C09  C  CH2   0  -0.482  27.7073   7.1170  -19.7027
 CJF  C10  C  CH2   0  -0.511  26.2862   6.6823  -19.8795
 CJF  N11  N  N     0  -0.536  26.6259   8.9954  -15.7692
 CJF  N12  N  NT    0  -0.515  30.6814   8.4793  -15.4275
 CJF  C13  C  CH2   0  -0.316  31.4533   7.5030  -16.1697
 CJF  C14  C  CH2   0  -0.182  32.8646   8.0163  -16.3945
 CJF  O15  O  O2    0  -0.483  33.4946   8.3736  -15.1872
 CJF  C16  C  CH2   0  -0.191  32.7579   9.3811  -14.5305
 CJF  C17  C  CH2   0  -0.315  31.3438   8.9330  -14.2163
 CJF  H1   H  HNH2  0   0.384  25.7925  10.3682  -13.9091
 CJF  H2   H  HNH2  0   0.384  27.2907  10.6689  -13.1527
 CJF  H3   H  HCR6  0   0.266  29.0823   7.2695  -17.2843
 CJF  H4   H  HNH1  0   0.381  25.4648   7.7425  -17.4488
 CJF  H5   H  HCH1  0   0.262  27.1564   5.6844  -18.1123
 CJF  H6   H  HCH2  0   0.255  28.4962   6.4673  -20.0587
 CJF  H7   H  HCH2  0   0.257  27.9244   8.1748  -19.7758
 CJF  H8   H  HCH2  0   0.257  25.5452   7.4467  -20.0776
 CJF  H9   H  HCH2  0   0.258  26.0893   5.7310  -20.3556
 CJF  H10  H  HCH2  0   0.260  31.0119   7.3185  -17.1466
 CJF  H11  H  HCH2  0   0.233  31.4816   6.5443  -15.6353
 CJF  H12  H  HCH2  0   0.244  33.4654   7.2368  -16.8647
 CJF  H13  H  HCH2  0   0.206  32.8280   8.8766  -17.0774
 CJF  H14  H  HCH2  0   0.242  33.2800   9.6206  -13.6030
 CJF  H15  H  HCH2  0   0.205  32.7239  10.2923  -15.1451
 CJF  H16  H  HCH2  0   0.269  30.7898   9.7624  -13.7861
 CJF  H17  H  HCH2  0   0.227  31.3649   8.1262  -13.4716

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
 CJF  C10  C09  single    1.497  0.020  1.497
 CJF  C10  C08  single    1.494  0.020  1.494
 CJF  C09  C08  single    1.500  0.020  1.500
 CJF  C08  N07  single    1.420  0.020  1.420
 CJF  N07  C06  single    1.354  0.020  1.354
 CJF  C05  C06  aromatic  1.396  0.020  1.396
 CJF  C05  C04  aromatic  1.401  0.020  1.401
 CJF  C06  N11  aromatic  1.338  0.020  1.338
 CJF  C14  C13  single    1.519  0.020  1.519
 CJF  C14  O15  single    1.408  0.020  1.408
 CJF  C13  N12  single    1.449  0.020  1.449
 CJF  N11  C02  aromatic  1.329  0.020  1.329
 CJF  C04  N12  single    1.363  0.020  1.363
 CJF  C04  N03  aromatic  1.337  0.020  1.337
 CJF  N12  C17  single    1.453  0.020  1.453
 CJF  O15  C16  single    1.410  0.020  1.410
 CJF  C02  N03  aromatic  1.330  0.020  1.330
 CJF  C02  N01  single    1.357  0.020  1.357
 CJF  C16  C17  single    1.516  0.020  1.516
 CJF  N01  H1   single    0.890  0.020  1.040
 CJF  N01  H2   single    0.890  0.020  1.040
 CJF  C05  H3   single    0.930  0.020  1.080
 CJF  N07  H4   single    0.860  0.020  1.020
 CJF  C08  H5   single    0.970  0.020  1.090
 CJF  C09  H6   single    0.970  0.020  1.090
 CJF  C09  H7   single    0.970  0.020  1.090
 CJF  C10  H8   single    0.970  0.020  1.090
 CJF  C10  H9   single    0.970  0.020  1.090
 CJF  C13  H10  single    0.970  0.020  1.090
 CJF  C13  H11  single    0.970  0.020  1.090
 CJF  C14  H12  single    0.970  0.020  1.090
 CJF  C14  H13  single    0.970  0.020  1.090
 CJF  C16  H14  single    0.970  0.020  1.090
 CJF  C16  H15  single    0.970  0.020  1.090
 CJF  C17  H16  single    0.970  0.020  1.090
 CJF  C17  H17  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
 CJF  H2   N01  H1   116.00  3.000
 CJF  H2   N01  C02  117.64  3.000
 CJF  H1   N01  C02  117.65  3.000
 CJF  N11  C02  N03  127.02  3.000
 CJF  N03  C02  N01  116.37  3.000
 CJF  N11  C02  N01  116.58  3.000
 CJF  C04  N03  C02  117.09  3.000
 CJF  N12  C04  C05  122.47  3.000
 CJF  N12  C04  N03  116.38  3.000
 CJF  C05  C04  N03  121.14  3.000
 CJF  H3   C05  C06  120.42  3.000
 CJF  H3   C05  C04  123.16  3.000
 CJF  C06  C05  C04  116.42  3.000
 CJF  N11  C06  N07  115.48  3.000
 CJF  N11  C06  C05  122.55  3.000
 CJF  N07  C06  C05  121.97  3.000
 CJF  H4   N07  C08  118.30  3.000
 CJF  H4   N07  C06  115.88  3.000
 CJF  C08  N07  C06  123.94  3.000
 CJF  H5   C08  C10  116.70  3.000
 CJF  H5   C08  C09  116.39  3.000
 CJF  C10  C08  C09   59.98  3.000
 CJF  H5   C08  N07  116.01  3.000
 CJF  C09  C08  N07  118.76  3.000
 CJF  C10  C08  N07  117.39  3.000
 CJF  H7   C09  H6   114.73  3.000
 CJF  H7   C09  C10  117.80  3.000
 CJF  H6   C09  C10  118.62  3.000
 CJF  H7   C09  C08  117.22  3.000
 CJF  H6   C09  C08  117.83  3.000
 CJF  C10  C09  C08   59.80  3.000
 CJF  H9   C10  H8   114.55  3.000
 CJF  H9   C10  C09  118.70  3.000
 CJF  H8   C10  C09  117.80  3.000
 CJF  H9   C10  C08  117.62  3.000
 CJF  H8   C10  C08  117.37  3.000
 CJF  C09  C10  C08   60.22  3.000
 CJF  C06  N11  C02  115.78  3.000
 CJF  C17  N12  C13  113.23  3.000
 CJF  C17  N12  C04  120.77  3.000
 CJF  C13  N12  C04  122.28  3.000
 CJF  H11  C13  H10  107.43  3.000
 CJF  H11  C13  C14  110.08  3.000
 CJF  H10  C13  C14  107.55  3.000
 CJF  H11  C13  N12  110.65  3.000
 CJF  H10  C13  N12  110.98  3.000
 CJF  C14  C13  N12  110.07  3.000
 CJF  H13  C14  H12  108.06  3.000
 CJF  H13  C14  O15  110.43  3.000
 CJF  H12  C14  O15  107.74  3.000
 CJF  H13  C14  C13  109.00  3.000
 CJF  H12  C14  C13  109.52  3.000
 CJF  O15  C14  C13  112.01  3.000
 CJF  C16  O15  C14  110.30  3.000
 CJF  H15  C16  H14  107.94  3.000
 CJF  H15  C16  C17  109.38  3.000
 CJF  H14  C16  C17  109.57  3.000
 CJF  H15  C16  O15  110.36  3.000
 CJF  H14  C16  O15  107.62  3.000
 CJF  C17  C16  O15  111.87  3.000
 CJF  H17  C17  H16  107.59  3.000
 CJF  H17  C17  C16  109.86  3.000
 CJF  H16  C17  C16  109.39  3.000
 CJF  H17  C17  N12  110.16  3.000
 CJF  H16  C17  N12  109.64  3.000
 CJF  C16  C17  N12  110.16  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
 CJF  CONST_01  C05  C06  N11  C02     0.00   0.0  0
 CJF  CONST_02  C05  C04  N03  C02     0.00   0.0  0
 CJF  CONST_03  C06  C05  C04  N03     0.00   0.0  0
 CJF  CONST_04  C06  N11  C02  N03     0.00   0.0  0
 CJF  CONST_05  N11  C06  C05  C04     0.00   0.0  0
 CJF  CONST_06  N11  C02  N03  C04     0.00   0.0  0
 CJF  CONST_07  N12  C04  N03  C02   180.00   0.0  0
 CJF  CONST_08  N12  C04  C05  C06   180.00   0.0  0
 CJF  CONST_09  C06  N11  C02  N01   180.00   0.0  0
 CJF  CONST_10  C04  N03  C02  N01   180.00   0.0  0
 CJF  CONST_11  N07  C06  N11  C02   180.00   0.0  0
 CJF  CONST_12  N07  C06  C05  C04   180.00   0.0  0
 CJF  CONST_13  C08  N07  C06  C05     0.00   0.0  0
 CJF  CONST_14  N11  C06  N07  C08   180.00   0.0  0
 CJF  CONST_15  H3   C05  C04  N03   180.00   0.0  0
 CJF  CONST_18  H4   N07  C06  C05   180.00   0.0  0
 CJF  Var_01    C13  N12  C04  N03   171.09  30.0  2
 CJF  Var_02    C14  C13  N12  C04   150.42  30.0  1
 CJF  Var_03    C16  C17  N12  C04  -149.96  30.0  1
 CJF  Var_04    O15  C14  C13  N12    54.92  30.0  1
 CJF  Var_05    O15  C16  C17  N12   -54.86  30.0  1
 CJF  Var_06    C17  C16  O15  C14    59.35  30.0  1
 CJF  Var_07    C10  C08  N07  C06  -146.58  30.0  1
 CJF  Var_08    C09  C10  C08  N07   109.06  30.0  1
 CJF  Var_09    H6   C09  C10  C08   107.33  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 CJF  chir_01  C08  C10  C09  N07  both

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
 CJF  plan-1  N01  0.020
 CJF  plan-1  C02  0.020
 CJF  plan-1  N03  0.020
 CJF  plan-1  C04  0.020
 CJF  plan-1  C05  0.020
 CJF  plan-1  C06  0.020
 CJF  plan-1  N07  0.020
 CJF  plan-1  N11  0.020
 CJF  plan-1  N12  0.020
 CJF  plan-1  H3   0.020
 CJF  plan-2  N01  0.020
 CJF  plan-2  C02  0.020
 CJF  plan-2  H1   0.020
 CJF  plan-2  H2   0.020
 CJF  plan-3  C06  0.020
 CJF  plan-3  N07  0.020
 CJF  plan-3  C08  0.020
 CJF  plan-3  H4   0.020

