# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 03:48:49 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: ~{N}4-cyclopropyl-6-[4-(oxetan-3-yl)piperazin-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CC2)cc(n1)N3CCN(CC3)C4COC4
#
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
 CJL  CJL  ~{N}4-cyclopropyl-6-[4-(oxetan-3-yl)piperazin-1-yl]pyrimidine-2,4-diamine  ligand  43  21  .  2023-02-02  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_CJL
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
 CJL  C10  C  CH2   0  -0.483  27.3879   6.6814  -19.3243
 CJL  C13  C  C     0  -0.328  31.3333   7.6912  -16.2305
 CJL  C18  C  C     0  -0.179  33.9613  10.1938  -17.0988
 CJL  C17  C  C     0  -0.327  31.3586   9.3956  -14.5449
 CJL  C16  C  C     0  -0.291  32.2608  10.2482  -15.4219
 CJL  C14  C  C     0  -0.284  32.2328   8.5481  -17.1081
 CJL  C19  C  C     0  -0.138  35.1112  10.8842  -16.3581
 CJL  C21  C  C     0  -0.138  35.0832   9.4261  -17.8057
 CJL  N12  N  NR6   0  -0.498  30.5324   8.5283  -15.3621
 CJL  C02  C  CR6   0   0.521  27.3643   9.9709  -14.9740
 CJL  C04  C  CR6   0   0.575  29.2086   8.7696  -15.5554
 CJL  C05  C  CR16  0  -0.551  28.4267   8.0171  -16.4442
 CJL  C06  C  CR6   0   0.517  27.0741   8.3468  -16.5157
 CJL  C08  C  CH1   0  -0.099  26.5644   6.5344  -18.0794
 CJL  C09  C  CH2   0  -0.511  25.9313   6.3519  -19.4198
 CJL  N03  N  N     0  -0.546  28.6663   9.7491  -14.8227
 CJL  N07  N  NH1   0  -0.659  26.2199   7.7014  -17.3462
 CJL  N11  N  N     0  -0.538  26.5300   9.3248  -15.7804
 CJL  N15  N  NR6   0  -0.432  33.0705   9.4060  -16.2875
 CJL  O20  O  O     0  -0.513  36.0918  10.2078  -17.1544
 CJL  H1   H  HCH2  0   0.255  28.1114   5.9070  -19.5443
 CJL  H2   H  HCH2  0   0.257  27.6977   7.6818  -19.5969
 CJL  H3   H  H     0   0.265  30.7142   7.0535  -16.8533
 CJL  H4   H  H     0   0.247  31.9493   7.0313  -15.6124
 CJL  H5   H  H     0   0.237  33.4171  10.8738  -17.7734
 CJL  H6   H  H     0   0.238  31.9725   8.7737  -13.8860
 CJL  H7   H  H     0   0.272  30.7280  10.0254  -13.9264
 CJL  H8   H  H     0   0.247  32.9173  10.8434  -14.7827
 CJL  H9   H  H     0   0.203  31.6405  10.9545  -16.0007
 CJL  H10  H  H     0   0.203  31.6073   9.1299  -17.8072
 CJL  H11  H  H     0   0.249  32.8664   7.8923  -17.7097
 CJL  H12  H  H     0   0.211  35.1814  10.6187  -15.2981
 CJL  H13  H  H     0   0.223  35.1681  11.9706  -16.4582
 CJL  H14  H  H     0   0.223  35.1203   9.5173  -18.8939
 CJL  H15  H  H     0   0.211  35.1380   8.3666  -17.5343
 CJL  H16  H  HCR6  0   0.266  28.8219   7.2115  -17.0393
 CJL  H17  H  HCH1  0   0.261  26.7337   5.6347  -17.4913
 CJL  H18  H  HCH2  0   0.257  25.2608   7.1290  -19.7646
 CJL  H19  H  HCH2  0   0.258  25.6430   5.3496  -19.7069
 CJL  H20  H  HNH2  0   0.383  25.8410  11.0206  -14.1457
 CJL  H21  H  HNH2  0   0.383  27.3711  11.3217  -13.4629
 CJL  H22  H  HNH1  0   0.380  25.2422   7.9025  -17.2072
 CJL  N01  N  NH2   0  -0.824  26.8406  10.9966  -14.2528

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
 CJL  C09  C10  single    1.496  0.020  1.496
 CJL  C09  C08  single    1.494  0.020  1.494
 CJL  C10  C08  single    1.500  0.020  1.500
 CJL  C08  N07  single    1.420  0.020  1.420
 CJL  O20  C21  single    1.433  0.020  1.433
 CJL  O20  C19  single    1.433  0.020  1.433
 CJL  C21  C18  single    1.532  0.020  1.532
 CJL  N07  C06  single    1.355  0.020  1.355
 CJL  C19  C18  single    1.532  0.020  1.532
 CJL  C18  N15  single    1.440  0.020  1.440
 CJL  C14  N15  single    1.453  0.020  1.453
 CJL  C14  C13  single    1.521  0.020  1.521
 CJL  C06  C05  aromatic  1.394  0.020  1.394
 CJL  C06  N11  aromatic  1.339  0.020  1.339
 CJL  N15  C16  single    1.454  0.020  1.454
 CJL  C05  C04  aromatic  1.403  0.020  1.403
 CJL  C13  N12  single    1.448  0.020  1.448
 CJL  N11  C02  aromatic  1.328  0.020  1.328
 CJL  C16  C17  single    1.520  0.020  1.520
 CJL  C04  N12  single    1.360  0.020  1.360
 CJL  C04  N03  aromatic  1.338  0.020  1.338
 CJL  N12  C17  single    1.450  0.020  1.450
 CJL  C02  N03  aromatic  1.329  0.020  1.329
 CJL  C02  N01  single    1.359  0.020  1.359
 CJL  C10  H1   single    0.970  0.020  1.090
 CJL  C10  H2   single    0.970  0.020  1.090
 CJL  C13  H3   single    0.970  0.020  1.090
 CJL  C13  H4   single    0.970  0.020  1.090
 CJL  C18  H5   single    0.970  0.020  1.090
 CJL  C17  H6   single    0.970  0.020  1.090
 CJL  C17  H7   single    0.970  0.020  1.090
 CJL  C16  H8   single    0.970  0.020  1.090
 CJL  C16  H9   single    0.970  0.020  1.090
 CJL  C14  H10  single    0.970  0.020  1.090
 CJL  C14  H11  single    0.970  0.020  1.090
 CJL  C19  H12  single    0.970  0.020  1.090
 CJL  C19  H13  single    0.970  0.020  1.090
 CJL  C21  H14  single    0.970  0.020  1.090
 CJL  C21  H15  single    0.970  0.020  1.090
 CJL  C05  H16  single    0.930  0.020  1.080
 CJL  C08  H17  single    0.970  0.020  1.090
 CJL  C09  H18  single    0.970  0.020  1.090
 CJL  C09  H19  single    0.970  0.020  1.090
 CJL  N01  H20  single    0.890  0.020  1.040
 CJL  N01  H21  single    0.890  0.020  1.040
 CJL  N07  H22  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
 CJL  H2   C10  H1   114.77  3.000
 CJL  H2   C10  C09  117.78  3.000
 CJL  H1   C10  C09  118.70  3.000
 CJL  H2   C10  C08  117.18  3.000
 CJL  H1   C10  C08  117.75  3.000
 CJL  C09  C10  C08   59.80  3.000
 CJL  H4   C13  H3   106.91  3.000
 CJL  H4   C13  N12  108.74  3.000
 CJL  H3   C13  N12  111.61  3.000
 CJL  H4   C13  C14  109.44  3.000
 CJL  H3   C13  C14  109.71  3.000
 CJL  N12  C13  C14  110.34  3.000
 CJL  H5   C18  N15  112.16  3.000
 CJL  H5   C18  C21  112.86  3.000
 CJL  N15  C18  C21  116.03  3.000
 CJL  H5   C18  C19  112.88  3.000
 CJL  N15  C18  C19  116.01  3.000
 CJL  C21  C18  C19   84.22  3.000
 CJL  H7   C17  H6   108.22  3.000
 CJL  H7   C17  N12  109.72  3.000
 CJL  H6   C17  N12  108.60  3.000
 CJL  H7   C17  C16  110.39  3.000
 CJL  H6   C17  C16  109.46  3.000
 CJL  N12  C17  C16  110.40  3.000
 CJL  H9   C16  H8   107.21  3.000
 CJL  H9   C16  N15  111.80  3.000
 CJL  H8   C16  N15  109.22  3.000
 CJL  H9   C16  C17  109.14  3.000
 CJL  H8   C16  C17  108.95  3.000
 CJL  N15  C16  C17  110.43  3.000
 CJL  H11  C14  H10  107.23  3.000
 CJL  H11  C14  N15  109.34  3.000
 CJL  H10  C14  N15  111.92  3.000
 CJL  H11  C14  C13  108.81  3.000
 CJL  H10  C14  C13  109.10  3.000
 CJL  N15  C14  C13  110.35  3.000
 CJL  H13  C19  H12  109.06  3.000
 CJL  H13  C19  O20  112.51  3.000
 CJL  H12  C19  O20  112.32  3.000
 CJL  H13  C19  C18  116.28  3.000
 CJL  H12  C19  C18  114.01  3.000
 CJL  O20  C19  C18   91.85  3.000
 CJL  H15  C21  H14  109.03  3.000
 CJL  H15  C21  O20  112.33  3.000
 CJL  H14  C21  O20  112.54  3.000
 CJL  H15  C21  C18  114.02  3.000
 CJL  H14  C21  C18  116.26  3.000
 CJL  O20  C21  C18   91.85  3.000
 CJL  C04  N12  C17  121.92  3.000
 CJL  C17  N12  C13  111.63  3.000
 CJL  C04  N12  C13  123.78  3.000
 CJL  N11  C02  N03  127.10  3.000
 CJL  N03  C02  N01  116.30  3.000
 CJL  N11  C02  N01  116.58  3.000
 CJL  N03  C04  C05  120.92  3.000
 CJL  N03  C04  N12  116.53  3.000
 CJL  C05  C04  N12  122.53  3.000
 CJL  H16  C05  C06  120.31  3.000
 CJL  H16  C05  C04  123.16  3.000
 CJL  C06  C05  C04  116.52  3.000
 CJL  N11  C06  N07  115.37  3.000
 CJL  N11  C06  C05  122.60  3.000
 CJL  N07  C06  C05  122.03  3.000
 CJL  H17  C08  N07  115.98  3.000
 CJL  H17  C08  C09  116.74  3.000
 CJL  N07  C08  C09  117.44  3.000
 CJL  H17  C08  C10  116.37  3.000
 CJL  N07  C08  C10  118.75  3.000
 CJL  C09  C08  C10   59.99  3.000
 CJL  H19  C09  H18  114.55  3.000
 CJL  H19  C09  C08  117.67  3.000
 CJL  H18  C09  C08  117.42  3.000
 CJL  H19  C09  C10  118.71  3.000
 CJL  H18  C09  C10  117.72  3.000
 CJL  C08  C09  C10   60.22  3.000
 CJL  C04  N03  C02  117.18  3.000
 CJL  H22  N07  C08  118.06  3.000
 CJL  H22  N07  C06  115.59  3.000
 CJL  C08  N07  C06  123.70  3.000
 CJL  C06  N11  C02  115.69  3.000
 CJL  C14  N15  C16  110.93  3.000
 CJL  C16  N15  C18  111.29  3.000
 CJL  C14  N15  C18  111.20  3.000
 CJL  C21  O20  C19   91.63  3.000
 CJL  H21  N01  H20  115.66  3.000
 CJL  H21  N01  C02  117.23  3.000
 CJL  H20  N01  C02  117.24  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
 CJL  CONST_01  C05  C06  N11  C02     0.00   0.0  0
 CJL  CONST_02  C05  C04  N03  C02     0.00   0.0  0
 CJL  CONST_03  N11  C06  C05  C04     0.00   0.0  0
 CJL  CONST_04  N11  C02  N03  C04     0.00   0.0  0
 CJL  CONST_05  N03  C04  C05  C06     0.00   0.0  0
 CJL  CONST_06  N03  C02  N11  C06     0.00   0.0  0
 CJL  CONST_07  C06  C05  C04  N12   180.00   0.0  0
 CJL  CONST_08  C02  N03  C04  N12   180.00   0.0  0
 CJL  CONST_09  N07  C06  N11  C02   180.00   0.0  0
 CJL  CONST_10  N07  C06  C05  C04   180.00   0.0  0
 CJL  CONST_11  N01  C02  N03  C04   180.00   0.0  0
 CJL  CONST_12  N01  C02  N11  C06   180.00   0.0  0
 CJL  CONST_13  C08  N07  C06  C05     0.00   0.0  0
 CJL  CONST_14  N11  C06  N07  C08   180.00   0.0  0
 CJL  CONST_15  H16  C05  C04  N12     0.00   0.0  0
 CJL  CONST_16  H22  N07  C06  C05   180.00   0.0  0
 CJL  Var_01    C18  N15  C14  C13   178.09  30.0  1
 CJL  Var_02    C05  C04  N12  C13    13.72  30.0  3
 CJL  Var_03    C16  C17  N12  C13    56.67  30.0  1
 CJL  Var_04    C17  C16  N15  C18  -178.29  30.0  1
 CJL  Var_05    C14  C13  N12  C17   -56.83  30.0  1
 CJL  Var_06    N15  C14  C13  N12    56.75  30.0  1
 CJL  Var_07    N15  C16  C17  N12   -56.37  30.0  1
 CJL  Var_08    N07  C08  C09  C10   109.03  30.0  1
 CJL  Var_09    C06  N07  C08  C10   -78.06  30.0  3
 CJL  Var_10    H14  C21  O20  C19   124.76  30.0  1
 CJL  Var_11    H12  C19  O20  C21   111.71  30.0  1
 CJL  Var_12    H1   C10  C09  C08   107.19  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
 CJL  chir_01  C18  C21  C19  N15  positiv
 CJL  chir_02  C08  C09  C10  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
 CJL  plan-1  C06  0.020
 CJL  plan-1  C08  0.020
 CJL  plan-1  N07  0.020
 CJL  plan-1  H22  0.020
 CJL  plan-2  N12  0.020
 CJL  plan-2  C02  0.020
 CJL  plan-2  C04  0.020
 CJL  plan-2  C05  0.020
 CJL  plan-2  C06  0.020
 CJL  plan-2  N03  0.020
 CJL  plan-2  N07  0.020
 CJL  plan-2  N11  0.020
 CJL  plan-2  H16  0.020
 CJL  plan-2  N01  0.020
 CJL  plan-3  C02  0.020
 CJL  plan-3  H20  0.020
 CJL  plan-3  H21  0.020
 CJL  plan-3  N01  0.020

