# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 11:17:05 2021
#   Inital geometry file: a 83 line input string
#   Ligand name: ~{N}4-cyclopropyl-6-piperidin-1-yl-pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(NC2CC2)cc(n1)N3CCCCC3
#
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
 CJ9  CJ9  ~{N}4-cyclopropyl-6-piperidin-1-yl-pyrimidine-2,4-diamine  ligand  36  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_CJ9
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
 CJ9  N01  N  NH2   0  -0.824  27.0629  10.5172  -13.6465
 CJ9  C02  C  CR6   0   0.508  27.6883   9.5896  -14.4414
 CJ9  N03  N  N     0  -0.538  28.9627   9.3528  -14.1733
 CJ9  C04  C  CR6   0   0.566  29.5932   8.4738  -14.9615
 CJ9  C05  C  CR16  0  -0.542  28.9298   7.8678  -16.0370
 CJ9  C06  C  CR6   0   0.515  27.5911   8.2095  -16.2147
 CJ9  N07  N  NH1   0  -0.660  26.8433   7.7102  -17.2298
 CJ9  C08  C  CH1   0  -0.097  27.2683   6.6841  -18.1100
 CJ9  C09  C  CH2   0  -0.484  28.2633   7.0182  -19.1823
 CJ9  C10  C  CH2   0  -0.509  26.8324   6.7756  -19.5370
 CJ9  N11  N  N     0  -0.532  26.9528   9.0620  -15.4066
 CJ9  N12  N  NT    0  -0.480  30.8853   8.1912  -14.6414
 CJ9  C13  C  CH2   0  -0.335  31.7289   7.3746  -15.4889
 CJ9  C14  C  CH2   0  -0.431  32.5547   8.2431  -16.4325
 CJ9  C15  C  CH2   0  -0.442  33.3796   9.2431  -15.6259
 CJ9  C16  C  CH2   0  -0.437  32.5018  10.0286  -14.6545
 CJ9  C17  C  CH2   0  -0.325  31.6551   9.0896  -13.7978
 CJ9  H1   H  HNH2  0   0.377  26.0586  10.4548  -13.6359
 CJ9  H2   H  HNH2  0   0.378  27.4688  10.6456  -12.7346
 CJ9  H3   H  HCR6  0   0.265  29.4123   7.1851  -16.7152
 CJ9  H4   H  HNH1  0   0.380  25.8623   7.9297  -17.1830
 CJ9  H5   H  HCH1  0   0.260  27.3339   5.6836  -17.6858
 CJ9  H6   H  HCH2  0   0.255  28.9968   6.2672  -19.4448
 CJ9  H7   H  HCH2  0   0.257  28.6281   8.0361  -19.2173
 CJ9  H8   H  HCH2  0   0.257  26.2341   7.6309  -19.8238
 CJ9  H9   H  HCH2  0   0.258  26.5707   5.8575  -20.0453
 CJ9  H10  H  HCH2  0   0.259  31.1390   6.6344  -16.0245
 CJ9  H11  H  HCH2  0   0.244  32.4005   6.8057  -14.8374
 CJ9  H12  H  HCH2  0   0.235  33.2044   7.6146  -17.0458
 CJ9  H13  H  HCH2  0   0.222  31.8816   8.7709  -17.1156
 CJ9  H14  H  HCH2  0   0.215  34.1450   8.7001  -15.0600
 CJ9  H15  H  HCH2  0   0.236  33.9148   9.9227  -16.2919
 CJ9  H16  H  HCH2  0   0.234  33.1167  10.6594  -14.0085
 CJ9  H17  H  HCH2  0   0.220  31.8348  10.6974  -15.2074
 CJ9  H18  H  HCH2  0   0.265  30.9788   9.6412  -13.1524
 CJ9  H19  H  HCH2  0   0.230  32.3037   8.4815  -13.1583

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
 CJ9  C10  C09  single    1.494  0.020  1.494
 CJ9  C10  C08  single    1.495  0.020  1.495
 CJ9  C09  C08  single    1.500  0.020  1.500
 CJ9  C08  N07  single    1.417  0.020  1.417
 CJ9  N07  C06  single    1.356  0.020  1.356
 CJ9  C14  C13  single    1.525  0.020  1.525
 CJ9  C14  C15  single    1.527  0.020  1.527
 CJ9  C06  C05  aromatic  1.393  0.020  1.393
 CJ9  C06  N11  aromatic  1.337  0.020  1.337
 CJ9  C05  C04  aromatic  1.402  0.020  1.402
 CJ9  C13  N12  single    1.448  0.020  1.448
 CJ9  N11  C02  aromatic  1.323  0.020  1.323
 CJ9  C15  C16  single    1.527  0.020  1.527
 CJ9  C04  N12  single    1.361  0.020  1.361
 CJ9  C04  N03  aromatic  1.338  0.020  1.338
 CJ9  N12  C17  single    1.453  0.020  1.453
 CJ9  C02  N03  aromatic  1.324  0.020  1.324
 CJ9  C02  N01  single    1.372  0.020  1.372
 CJ9  C16  C17  single    1.527  0.020  1.527
 CJ9  N01  H1   single    0.890  0.020  1.040
 CJ9  N01  H2   single    0.890  0.020  1.040
 CJ9  C05  H3   single    0.930  0.020  1.080
 CJ9  N07  H4   single    0.860  0.020  1.020
 CJ9  C08  H5   single    0.970  0.020  1.090
 CJ9  C09  H6   single    0.970  0.020  1.090
 CJ9  C09  H7   single    0.970  0.020  1.090
 CJ9  C10  H8   single    0.970  0.020  1.090
 CJ9  C10  H9   single    0.970  0.020  1.090
 CJ9  C13  H10  single    0.970  0.020  1.090
 CJ9  C13  H11  single    0.970  0.020  1.090
 CJ9  C14  H12  single    0.970  0.020  1.090
 CJ9  C14  H13  single    0.970  0.020  1.090
 CJ9  C15  H14  single    0.970  0.020  1.090
 CJ9  C15  H15  single    0.970  0.020  1.090
 CJ9  C16  H16  single    0.970  0.020  1.090
 CJ9  C16  H17  single    0.970  0.020  1.090
 CJ9  C17  H18  single    0.970  0.020  1.090
 CJ9  C17  H19  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
 CJ9  H2   N01  H1   113.64  3.000
 CJ9  H2   N01  C02  115.29  3.000
 CJ9  H1   N01  C02  114.77  3.000
 CJ9  N11  C02  N03  127.70  3.000
 CJ9  N03  C02  N01  116.26  3.000
 CJ9  N11  C02  N01  116.02  3.000
 CJ9  C04  N03  C02  116.86  3.000
 CJ9  N12  C04  C05  122.70  3.000
 CJ9  N12  C04  N03  116.43  3.000
 CJ9  C05  C04  N03  120.86  3.000
 CJ9  H3   C05  C06  120.39  3.000
 CJ9  H3   C05  C04  123.06  3.000
 CJ9  C06  C05  C04  116.53  3.000
 CJ9  N11  C06  N07  115.08  3.000
 CJ9  N11  C06  C05  122.56  3.000
 CJ9  N07  C06  C05  122.35  3.000
 CJ9  H4   N07  C08  118.63  3.000
 CJ9  H4   N07  C06  114.99  3.000
 CJ9  C08  N07  C06  124.48  3.000
 CJ9  H5   C08  C10  116.48  3.000
 CJ9  H5   C08  C09  116.30  3.000
 CJ9  C10  C08  C09   59.84  3.000
 CJ9  H5   C08  N07  116.19  3.000
 CJ9  C09  C08  N07  118.78  3.000
 CJ9  C10  C08  N07  117.46  3.000
 CJ9  H7   C09  H6   114.62  3.000
 CJ9  H7   C09  C10  117.90  3.000
 CJ9  H6   C09  C10  118.62  3.000
 CJ9  H7   C09  C08  117.14  3.000
 CJ9  H6   C09  C08  117.93  3.000
 CJ9  C10  C09  C08   59.89  3.000
 CJ9  H9   C10  H8   114.36  3.000
 CJ9  H9   C10  C09  118.76  3.000
 CJ9  H8   C10  C09  117.65  3.000
 CJ9  H9   C10  C08  117.85  3.000
 CJ9  H8   C10  C08  117.55  3.000
 CJ9  C09  C10  C08   60.27  3.000
 CJ9  C06  N11  C02  115.46  3.000
 CJ9  C17  N12  C13  112.32  3.000
 CJ9  C17  N12  C04  120.74  3.000
 CJ9  C13  N12  C04  122.18  3.000
 CJ9  H11  C13  H10  105.79  3.000
 CJ9  H11  C13  C14  109.38  3.000
 CJ9  H10  C13  C14  112.12  3.000
 CJ9  H11  C13  N12  107.59  3.000
 CJ9  H10  C13  N12  110.86  3.000
 CJ9  C14  C13  N12  110.88  3.000
 CJ9  H13  C14  H12  107.02  3.000
 CJ9  H13  C14  C15  110.25  3.000
 CJ9  H12  C14  C15  110.62  3.000
 CJ9  H13  C14  C13  109.13  3.000
 CJ9  H12  C14  C13  109.98  3.000
 CJ9  C15  C14  C13  109.79  3.000
 CJ9  H15  C15  H14  106.32  3.000
 CJ9  H15  C15  C16  110.47  3.000
 CJ9  H14  C15  C16  109.15  3.000
 CJ9  H15  C15  C14  110.51  3.000
 CJ9  H14  C15  C14  109.00  3.000
 CJ9  C16  C15  C14  111.25  3.000
 CJ9  H17  C16  H16  106.79  3.000
 CJ9  H17  C16  C17  108.73  3.000
 CJ9  H16  C16  C17  109.59  3.000
 CJ9  H17  C16  C15  110.09  3.000
 CJ9  H16  C16  C15  110.47  3.000
 CJ9  C17  C16  C15  111.06  3.000
 CJ9  H19  C17  H18  107.69  3.000
 CJ9  H19  C17  C16  109.92  3.000
 CJ9  H18  C17  C16  111.50  3.000
 CJ9  H19  C17  N12  108.03  3.000
 CJ9  H18  C17  N12  109.23  3.000
 CJ9  C16  C17  N12  110.38  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
 CJ9  CONST_01  C05  C06  N11  C02     0.00   0.0  0
 CJ9  CONST_02  C05  C04  N03  C02     0.00   0.0  0
 CJ9  CONST_03  C06  C05  C04  N03     0.00   0.0  0
 CJ9  CONST_04  C06  N11  C02  N03     0.00   0.0  0
 CJ9  CONST_05  N11  C06  C05  C04     0.00   0.0  0
 CJ9  CONST_06  N11  C02  N03  C04     0.00   0.0  0
 CJ9  CONST_07  N12  C04  N03  C02   180.00   0.0  0
 CJ9  CONST_08  N12  C04  C05  C06   180.00   0.0  0
 CJ9  CONST_09  C06  N11  C02  N01   180.00   0.0  0
 CJ9  CONST_10  C04  N03  C02  N01   180.00   0.0  0
 CJ9  CONST_11  N07  C06  N11  C02   180.00   0.0  0
 CJ9  CONST_12  N07  C06  C05  C04   180.00   0.0  0
 CJ9  CONST_13  C08  N07  C06  C05     0.00   0.0  0
 CJ9  CONST_14  N11  C06  N07  C08   180.00   0.0  0
 CJ9  CONST_15  H3   C05  C04  N03   180.00   0.0  0
 CJ9  CONST_18  H4   N07  C06  C05   180.00   0.0  0
 CJ9  Var_01    C13  N12  C04  N03  -173.10  30.0  2
 CJ9  Var_02    C14  C13  N12  C04    94.39  30.0  1
 CJ9  Var_03    C16  C17  N12  C04   -96.33  30.0  1
 CJ9  Var_04    C15  C14  C13  N12    56.56  30.0  1
 CJ9  Var_05    C15  C16  C17  N12   -54.51  30.0  1
 CJ9  Var_06    C16  C15  C14  C13   -52.44  30.0  1
 CJ9  Var_07    C17  C16  C15  C14    51.95  30.0  1
 CJ9  Var_08    C10  C08  N07  C06  -144.00  30.0  2
 CJ9  Var_09    C09  C10  C08  N07   109.00  30.0  1
 CJ9  Var_10    H6   C09  C10  C08   107.48  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
 CJ9  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
 CJ9  plan-1  N01  0.020
 CJ9  plan-1  C02  0.020
 CJ9  plan-1  N03  0.020
 CJ9  plan-1  C04  0.020
 CJ9  plan-1  C05  0.020
 CJ9  plan-1  C06  0.020
 CJ9  plan-1  N07  0.020
 CJ9  plan-1  N11  0.020
 CJ9  plan-1  N12  0.020
 CJ9  plan-1  H3   0.020
 CJ9  plan-2  N01  0.020
 CJ9  plan-2  C02  0.020
 CJ9  plan-2  H1   0.020
 CJ9  plan-2  H2   0.020
 CJ9  plan-3  C06  0.020
 CJ9  plan-3  N07  0.020
 CJ9  plan-3  C08  0.020
 CJ9  plan-3  H4   0.020

