# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 04:59:24 2021
#   Inital geometry file: a 89 line input string
#   Ligand name: ~{N}4-methyl-6-[4-(oxetan-3-yl)piperazin-1-yl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(nc(N)n1)N2CCN(CC2)C3COC3
#
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
 CJR  CJR  ~{N}4-methyl-6-[4-(oxetan-3-yl)piperazin-1-yl]pyrimidine-2,4-diamine  ligand  39  19  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CJR
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
 CJR  C01  C  CH3   0  -0.528  26.3763   6.9926  -18.6717
 CJR  N02  N  NH1   0  -0.648  26.0025   7.8126  -17.5514
 CJR  C03  C  CR6   0   0.523  26.8756   8.3989  -16.7107
 CJR  N04  N  N     0  -0.535  26.3359   9.0556  -15.6746
 CJR  C05  C  CR6   0   0.519  27.1965   9.6313  -14.8438
 CJR  N06  N  NH2   0  -0.824  26.6655  10.3375  -13.8115
 CJR  N07  N  N     0  -0.548  28.5233   9.6237  -14.9304
 CJR  C08  C  CR6   0   0.581  29.0624   8.9785  -15.9711
 CJR  C09  C  CR16  0  -0.570  28.2575   8.3230  -16.9109
 CJR  N10  N  NT    0  -0.509  30.4221   9.0128  -16.0664
 CJR  C11  C  CH2   0  -0.293  31.1386   8.2464  -17.0642
 CJR  C12  C  CH2   0  -0.299  32.4370   8.9388  -17.4442
 CJR  N13  N  NT    0  -0.428  33.2538   9.1741  -16.2703
 CJR  C14  C  CH2   0  -0.299  32.5282  10.0260  -15.3473
 CJR  C15  C  CH2   0  -0.298  31.2345   9.3637  -14.9152
 CJR  C16  C  C     0  -0.192  34.5918   9.6390  -16.5172
 CJR  C17  C  C     0  -0.149  35.4988   8.7763  -17.4030
 CJR  O18  O  O     0  -0.514  35.7134   9.8555  -18.3205
 CJR  C19  C  C     0  -0.155  34.8844  10.7435  -17.5593
 CJR  H1   H  HCH3  0   0.262  25.4730   6.6873  -19.1927
 CJR  H2   H  HCH3  0   0.234  27.0021   7.5382  -19.3810
 CJR  H3   H  HCH3  0   0.230  26.9154   6.0899  -18.3708
 CJR  H4   H  HNH1  0   0.385  25.0336   7.8510  -17.2852
 CJR  H5   H  HNH2  0   0.383  25.7056  10.1579  -13.5723
 CJR  H6   H  HNH2  0   0.383  27.2738  10.5584  -13.0423
 CJR  H7   H  HCR6  0   0.264  28.6624   7.7702  -17.7418
 CJR  H8   H  HCH2  0   0.258  30.5447   8.1535  -17.9700
 CJR  H9   H  HCH2  0   0.227  31.3517   7.2338  -16.6986
 CJR  H10  H  HCH2  0   0.254  32.9624   8.2970  -18.1530
 CJR  H11  H  HCH2  0   0.206  32.1872   9.8737  -17.9706
 CJR  H13  H  HCH2  0   0.245  33.1389  10.2008  -14.4589
 CJR  H14  H  HCH2  0   0.205  32.3026  11.0112  -15.7890
 CJR  H15  H  HCH2  0   0.267  30.6763  10.0350  -14.2699
 CJR  H16  H  HCH2  0   0.220  31.4711   8.4622  -14.3345
 CJR  H17  H  H     0   0.267  35.0417   9.8586  -15.5474
 CJR  H18  H  H     0   0.217  35.0226   7.9100  -17.8717
 CJR  H19  H  H     0   0.226  36.4236   8.4409  -16.9257
 CJR  H20  H  H     0   0.221  35.4371  11.6074  -17.1792
 CJR  H21  H  H     0   0.214  34.0233  11.1062  -18.1287

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
 CJR  C01  N02  single    1.438  0.020  1.438
 CJR  C17  O18  single    1.433  0.020  1.433
 CJR  C17  C16  single    1.533  0.020  1.533
 CJR  O18  C19  single    1.434  0.020  1.434
 CJR  N02  C03  single    1.346  0.020  1.346
 CJR  C12  C11  single    1.520  0.020  1.520
 CJR  C12  N13  single    1.449  0.020  1.449
 CJR  C11  N10  single    1.448  0.020  1.448
 CJR  C19  C16  single    1.546  0.020  1.546
 CJR  C09  C03  aromatic  1.398  0.020  1.398
 CJR  C09  C08  aromatic  1.400  0.020  1.400
 CJR  C16  N13  single    1.438  0.020  1.438
 CJR  C03  N04  aromatic  1.340  0.020  1.340
 CJR  N13  C14  single    1.451  0.020  1.451
 CJR  N04  C05  aromatic  1.328  0.020  1.328
 CJR  C08  N10  single    1.363  0.020  1.363
 CJR  C08  N07  aromatic  1.338  0.020  1.338
 CJR  N10  C15  single    1.452  0.020  1.452
 CJR  C14  C15  single    1.516  0.020  1.516
 CJR  C05  N07  aromatic  1.330  0.020  1.330
 CJR  C05  N06  single    1.359  0.020  1.359
 CJR  C01  H1   single    0.970  0.020  1.090
 CJR  C01  H2   single    0.970  0.020  1.090
 CJR  C01  H3   single    0.970  0.020  1.090
 CJR  N02  H4   single    0.860  0.020  1.020
 CJR  N06  H5   single    0.890  0.020  1.040
 CJR  N06  H6   single    0.890  0.020  1.040
 CJR  C09  H7   single    0.930  0.020  1.080
 CJR  C11  H8   single    0.970  0.020  1.090
 CJR  C11  H9   single    0.970  0.020  1.090
 CJR  C12  H10  single    0.970  0.020  1.090
 CJR  C12  H11  single    0.970  0.020  1.090
 CJR  C14  H13  single    0.970  0.020  1.090
 CJR  C14  H14  single    0.970  0.020  1.090
 CJR  C15  H15  single    0.970  0.020  1.090
 CJR  C15  H16  single    0.970  0.020  1.090
 CJR  C16  H17  single    0.970  0.020  1.090
 CJR  C17  H18  single    0.970  0.020  1.090
 CJR  C17  H19  single    0.970  0.020  1.090
 CJR  C19  H20  single    0.970  0.020  1.090
 CJR  C19  H21  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
 CJR  H3   C01  H2   107.97  3.000
 CJR  H3   C01  H1   108.05  3.000
 CJR  H2   C01  H1   107.79  3.000
 CJR  H3   C01  N02  112.61  3.000
 CJR  H2   C01  N02  111.72  3.000
 CJR  H1   C01  N02  108.53  3.000
 CJR  H4   N02  C03  116.29  3.000
 CJR  H4   N02  C01  118.59  3.000
 CJR  C03  N02  C01  124.49  3.000
 CJR  C09  C03  N04  122.36  3.000
 CJR  N04  C03  N02  115.78  3.000
 CJR  C09  C03  N02  121.86  3.000
 CJR  C05  N04  C03  115.80  3.000
 CJR  N07  C05  N06  116.26  3.000
 CJR  N06  C05  N04  116.58  3.000
 CJR  N07  C05  N04  127.13  3.000
 CJR  H6   N06  H5   115.78  3.000
 CJR  H6   N06  C05  117.32  3.000
 CJR  H5   N06  C05  117.45  3.000
 CJR  C08  N07  C05  117.10  3.000
 CJR  N10  C08  C09  122.56  3.000
 CJR  N10  C08  N07  116.36  3.000
 CJR  C09  C08  N07  121.08  3.000
 CJR  H7   C09  C08  122.81  3.000
 CJR  H7   C09  C03  120.65  3.000
 CJR  C08  C09  C03  116.53  3.000
 CJR  C15  N10  C11  113.41  3.000
 CJR  C15  N10  C08  120.57  3.000
 CJR  C11  N10  C08  121.90  3.000
 CJR  H9   C11  H8   107.74  3.000
 CJR  H9   C11  C12  109.75  3.000
 CJR  H8   C11  C12  107.30  3.000
 CJR  H9   C11  N10  110.78  3.000
 CJR  H8   C11  N10  110.43  3.000
 CJR  C12  C11  N10  110.73  3.000
 CJR  H11  C12  H10  107.33  3.000
 CJR  H11  C12  N13  112.16  3.000
 CJR  H10  C12  N13  110.51  3.000
 CJR  H11  C12  C11  108.20  3.000
 CJR  H10  C12  C11  107.81  3.000
 CJR  N13  C12  C11  110.67  3.000
 CJR  C16  N13  C14  112.63  3.000
 CJR  C14  N13  C12  109.20  3.000
 CJR  C16  N13  C12  115.97  3.000
 CJR  H14  C14  H13  107.28  3.000
 CJR  H14  C14  C15  109.25  3.000
 CJR  H13  C14  C15  108.37  3.000
 CJR  H14  C14  N13  111.84  3.000
 CJR  H13  C14  N13  109.39  3.000
 CJR  C15  C14  N13  110.59  3.000
 CJR  H16  C15  H15  107.71  3.000
 CJR  H16  C15  C14  108.99  3.000
 CJR  H15  C15  C14  109.75  3.000
 CJR  H16  C15  N10  109.97  3.000
 CJR  H15  C15  N10  109.45  3.000
 CJR  C14  C15  N10  110.91  3.000
 CJR  H17  C16  C19  112.15  3.000
 CJR  H17  C16  C17  112.50  3.000
 CJR  C19  C16  C17   84.30  3.000
 CJR  H17  C16  N13  107.22  3.000
 CJR  C19  C16  N13  121.52  3.000
 CJR  C17  C16  N13  117.88  3.000
 CJR  H19  C17  H18  108.20  3.000
 CJR  H19  C17  O18  112.58  3.000
 CJR  H18  C17  O18  112.79  3.000
 CJR  H19  C17  C16  114.87  3.000
 CJR  H18  C17  C16  115.82  3.000
 CJR  O18  C17  C16   91.99  3.000
 CJR  C19  O18  C17   92.28  3.000
 CJR  H21  C19  H20  108.46  3.000
 CJR  H21  C19  O18  112.59  3.000
 CJR  H20  C19  O18  112.43  3.000
 CJR  H21  C19  C16  116.01  3.000
 CJR  H20  C19  C16  115.19  3.000
 CJR  O18  C19  C16   91.43  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
 CJR  CONST_01  N07  C08  C09  C03     0.00   0.0  0
 CJR  CONST_02  N07  C05  N04  C03     0.00   0.0  0
 CJR  CONST_03  C08  C09  C03  N04     0.00   0.0  0
 CJR  CONST_04  C08  N07  C05  N04     0.00   0.0  0
 CJR  CONST_05  C09  C03  N04  C05     0.00   0.0  0
 CJR  CONST_06  C09  C08  N07  C05     0.00   0.0  0
 CJR  CONST_07  N10  C08  C09  C03   180.00   0.0  0
 CJR  CONST_08  N10  C08  N07  C05   180.00   0.0  0
 CJR  CONST_09  C08  C09  C03  N02   180.00   0.0  0
 CJR  CONST_10  C05  N04  C03  N02   180.00   0.0  0
 CJR  CONST_11  N06  C05  N04  C03   180.00   0.0  0
 CJR  CONST_12  C08  N07  C05  N06   180.00   0.0  0
 CJR  CONST_13  H7   C09  C03  N04   180.00   0.0  0
 CJR  CONST_14  C09  C03  N02  C01     0.00   0.0  0
 CJR  CONST_15  N04  C03  N02  C01   180.00   0.0  0
 CJR  CONST_16  H4   N02  C03  N04     0.00   0.0  0
 CJR  Var_01    C11  N10  C08  N07   173.69  30.0  2
 CJR  Var_02    C12  C11  N10  C08   150.92  30.0  1
 CJR  Var_03    C14  C15  N10  C08  -150.53  30.0  1
 CJR  Var_04    N13  C12  C11  N10    55.94  30.0  1
 CJR  Var_05    N13  C14  C15  N10   -55.76  30.0  1
 CJR  Var_06    C16  N13  C12  C11   170.96  30.0  1
 CJR  Var_07    C15  C14  N13  C12    60.41  30.0  1
 CJR  Var_08    H20  C19  O18  C17   117.96  30.0  1
 CJR  Var_09    H18  C17  O18  C19   119.30  30.0  1
 CJR  Var_10    H1   C01  N02  C03  -177.80  30.0  3

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
 CJR  chir_01  C16  C17  C19  N13  negativ

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
 CJR  plan-1  N02  0.020
 CJR  plan-1  C03  0.020
 CJR  plan-1  N04  0.020
 CJR  plan-1  C05  0.020
 CJR  plan-1  N06  0.020
 CJR  plan-1  N07  0.020
 CJR  plan-1  C08  0.020
 CJR  plan-1  C09  0.020
 CJR  plan-1  N10  0.020
 CJR  plan-1  H7   0.020
 CJR  plan-2  C01  0.020
 CJR  plan-2  N02  0.020
 CJR  plan-2  C03  0.020
 CJR  plan-2  H4   0.020
 CJR  plan-3  C05  0.020
 CJR  plan-3  N06  0.020
 CJR  plan-3  H5   0.020
 CJR  plan-3  H6   0.020

