# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 00:27:47 2021
#   Inital geometry file: a 95 line input string
#   Ligand name: ~{N}4-cyclopropyl-5-ethyl-6-piperidin-1-yl-pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1c(NC2CC2)nc(N)nc1N3CCCCC3
#
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
 CGX  CGX  ~{N}4-cyclopropyl-5-ethyl-6-piperidin-1-yl-pyrimidine-2,4-diamine  ligand  42  19  .  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_CGX
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
 CGX  C5   C  CR6   0  -0.088  28.4496   7.8015  -16.9352
 CGX  C4   C  CR6   0   0.503  27.0554   7.9680  -17.0819
 CGX  C2   C  CR6   0   0.510  27.0802   9.7985  -15.7570
 CGX  C6   C  CR6   0   0.458  29.0704   8.7675  -16.1355
 CGX  CAA  C  CH2   0  -0.437  32.2464   8.8462  -14.2425
 CGX  CAB  C  CH2   0  -0.442  33.2735   8.8866  -15.3665
 CGX  CAC  C  CH2   0  -0.433  32.7121   8.2176  -16.6145
 CGX  CAD  C  CH2   0  -0.284  30.9103   9.4254  -14.6884
 CGX  CAF  C  CH2   0  -0.324  31.3636   8.8164  -16.9794
 CGX  CAJ  C  CH2   0  -0.575  29.1404   6.5897  -17.5000
 CGX  CAK  C  CH3   0  -0.656  29.3415   6.5966  -19.0183
 CGX  CAQ  C  CH1   0  -0.075  24.9009   7.1082  -17.8367
 CGX  CAR  C  CH2   0  -0.518  24.2383   6.5373  -19.0481
 CGX  CAS  C  CH2   0  -0.478  24.2093   8.0156  -18.8024
 CGX  N1   N  N     0  -0.522  28.3885   9.7513  -15.5417
 CGX  N3   N  N     0  -0.514  26.3773   8.9630  -16.5117
 CGX  NAE  N  NT    0  -0.497  30.4304   8.7141  -15.8632
 CGX  NAO  N  NH2   0  -0.826  26.3996  10.8277  -15.1848
 CGX  NAP  N  NH1   0  -0.681  26.3241   7.0855  -17.8082
 CGX  H1   H  HCH2  0   0.216  32.0960   7.8127  -13.9159
 CGX  H2   H  HCH2  0   0.231  32.6020   9.4058  -13.3743
 CGX  H3   H  HCH2  0   0.233  34.2051   8.4086  -15.0569
 CGX  H4   H  HCH2  0   0.212  33.5170   9.9293  -15.5969
 CGX  H5   H  HCH2  0   0.219  32.5919   7.1436  -16.4408
 CGX  H6   H  HCH2  0   0.233  33.3960   8.3320  -17.4584
 CGX  H7   H  HCH2  0   0.199  31.0258  10.5008  -14.8890
 CGX  H8   H  HCH2  0   0.243  30.1785   9.3304  -13.8884
 CGX  H9   H  HCH2  0   0.221  31.4991   9.8742  -17.2550
 CGX  H10  H  HCH2  0   0.260  30.9562   8.3229  -17.8564
 CGX  H11  H  HCH2  0   0.243  28.5701   5.6929  -17.2295
 CGX  H12  H  HCH2  0   0.260  30.1047   6.4580  -17.0063
 CGX  H13  H  HCH3  0   0.232  29.8091   5.6680  -19.3477
 CGX  H14  H  HCH3  0   0.220  28.3990   6.6982  -19.5569
 CGX  H15  H  HCH3  0   0.230  29.9803   7.4199  -19.3390
 CGX  H16  H  HCH1  0   0.254  24.4066   6.9450  -16.8827
 CGX  H17  H  HCH2  0   0.256  23.3291   5.9694  -18.9013
 CGX  H18  H  HCH2  0   0.253  24.8715   6.1668  -19.8452
 CGX  H19  H  HCH2  0   0.249  24.8358   8.6410  -19.4247
 CGX  H20  H  HCH2  0   0.249  23.2786   8.4719  -18.4912
 CGX  H21  H  HNH2  0   0.383  25.4006  10.7336  -15.1149
 CGX  H22  H  HNH2  0   0.383  26.8444  11.2993  -14.4158
 CGX  H23  H  HNH1  0   0.399  26.7652   6.2250  -18.0846

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
 CGX  CAS  CAR  single    1.499  0.020  1.499
 CGX  CAS  CAQ  single    1.495  0.020  1.495
 CGX  CAR  CAQ  single    1.494  0.020  1.494
 CGX  CAK  CAJ  single    1.532  0.020  1.532
 CGX  CAQ  NAP  single    1.424  0.020  1.424
 CGX  CAJ  C5   single    1.505  0.020  1.505
 CGX  NAP  C4   single    1.357  0.020  1.357
 CGX  CAF  CAC  single    1.520  0.020  1.520
 CGX  CAF  NAE  single    1.459  0.020  1.459
 CGX  CAC  CAB  single    1.523  0.020  1.523
 CGX  C5   C4   aromatic  1.412  0.020  1.412
 CGX  C5   C6   aromatic  1.399  0.020  1.399
 CGX  C4   N3   aromatic  1.332  0.020  1.332
 CGX  C6   NAE  single    1.388  0.020  1.388
 CGX  C6   N1   aromatic  1.336  0.020  1.336
 CGX  NAE  CAD  single    1.455  0.020  1.455
 CGX  N3   C2   aromatic  1.327  0.020  1.327
 CGX  CAB  CAA  single    1.523  0.020  1.523
 CGX  N1   C2   aromatic  1.327  0.020  1.327
 CGX  C2   NAO  single    1.360  0.020  1.360
 CGX  CAD  CAA  single    1.523  0.020  1.523
 CGX  CAA  H1   single    0.970  0.020  1.090
 CGX  CAA  H2   single    0.970  0.020  1.090
 CGX  CAB  H3   single    0.970  0.020  1.090
 CGX  CAB  H4   single    0.970  0.020  1.090
 CGX  CAC  H5   single    0.970  0.020  1.090
 CGX  CAC  H6   single    0.970  0.020  1.090
 CGX  CAD  H7   single    0.970  0.020  1.090
 CGX  CAD  H8   single    0.970  0.020  1.090
 CGX  CAF  H9   single    0.970  0.020  1.090
 CGX  CAF  H10  single    0.970  0.020  1.090
 CGX  CAJ  H11  single    0.970  0.020  1.090
 CGX  CAJ  H12  single    0.970  0.020  1.090
 CGX  CAK  H13  single    0.970  0.020  1.090
 CGX  CAK  H14  single    0.970  0.020  1.090
 CGX  CAK  H15  single    0.970  0.020  1.090
 CGX  CAQ  H16  single    0.970  0.020  1.090
 CGX  CAR  H17  single    0.970  0.020  1.090
 CGX  CAR  H18  single    0.970  0.020  1.090
 CGX  CAS  H19  single    0.970  0.020  1.090
 CGX  CAS  H20  single    0.970  0.020  1.090
 CGX  NAO  H21  single    0.890  0.020  1.040
 CGX  NAO  H22  single    0.890  0.020  1.040
 CGX  NAP  H23  single    0.890  0.020  1.040

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
 CGX  CAJ  C5   C6   124.52  3.000
 CGX  C6   C5   C4   114.59  3.000
 CGX  CAJ  C5   C4   120.62  3.000
 CGX  NAP  C4   N3   116.13  3.000
 CGX  N3   C4   C5   123.11  3.000
 CGX  NAP  C4   C5   120.74  3.000
 CGX  NAO  C2   N3   116.77  3.000
 CGX  NAO  C2   N1   116.88  3.000
 CGX  N3   C2   N1   126.31  3.000
 CGX  NAE  C6   N1   116.18  3.000
 CGX  N1   C6   C5   122.40  3.000
 CGX  NAE  C6   C5   121.35  3.000
 CGX  H2   CAA  H1   106.93  3.000
 CGX  H2   CAA  CAD  108.88  3.000
 CGX  H1   CAA  CAD  109.03  3.000
 CGX  H2   CAA  CAB  110.69  3.000
 CGX  H1   CAA  CAB  109.76  3.000
 CGX  CAD  CAA  CAB  111.44  3.000
 CGX  H4   CAB  H3   106.66  3.000
 CGX  H4   CAB  CAC  109.13  3.000
 CGX  H3   CAB  CAC  110.76  3.000
 CGX  H4   CAB  CAA  109.29  3.000
 CGX  H3   CAB  CAA  110.76  3.000
 CGX  CAC  CAB  CAA  110.15  3.000
 CGX  H6   CAC  H5   107.11  3.000
 CGX  H6   CAC  CAF  109.20  3.000
 CGX  H5   CAC  CAF  109.10  3.000
 CGX  H6   CAC  CAB  110.87  3.000
 CGX  H5   CAC  CAB  109.96  3.000
 CGX  CAF  CAC  CAB  110.52  3.000
 CGX  H8   CAD  H7   106.85  3.000
 CGX  H8   CAD  NAE  109.22  3.000
 CGX  H7   CAD  NAE  111.43  3.000
 CGX  H8   CAD  CAA  109.97  3.000
 CGX  H7   CAD  CAA  109.45  3.000
 CGX  NAE  CAD  CAA  109.87  3.000
 CGX  H10  CAF  H9   106.29  3.000
 CGX  H10  CAF  NAE  110.26  3.000
 CGX  H9   CAF  NAE  109.73  3.000
 CGX  H10  CAF  CAC  110.35  3.000
 CGX  H9   CAF  CAC  109.22  3.000
 CGX  NAE  CAF  CAC  110.88  3.000
 CGX  H12  CAJ  H11  104.43  3.000
 CGX  H12  CAJ  CAK  109.45  3.000
 CGX  H11  CAJ  CAK  108.45  3.000
 CGX  H12  CAJ  C5   109.45  3.000
 CGX  H11  CAJ  C5   109.10  3.000
 CGX  CAK  CAJ  C5   115.39  3.000
 CGX  H15  CAK  H14  106.91  3.000
 CGX  H15  CAK  H13  107.63  3.000
 CGX  H14  CAK  H13  107.50  3.000
 CGX  H15  CAK  CAJ  111.84  3.000
 CGX  H14  CAK  CAJ  112.13  3.000
 CGX  H13  CAK  CAJ  110.60  3.000
 CGX  H16  CAQ  NAP  115.76  3.000
 CGX  H16  CAQ  CAS  116.61  3.000
 CGX  NAP  CAQ  CAS  119.02  3.000
 CGX  H16  CAQ  CAR  116.92  3.000
 CGX  NAP  CAQ  CAR  116.97  3.000
 CGX  CAS  CAQ  CAR   60.20  3.000
 CGX  H18  CAR  H17  114.30  3.000
 CGX  H18  CAR  CAS  117.99  3.000
 CGX  H17  CAR  CAS  118.62  3.000
 CGX  H18  CAR  CAQ  117.91  3.000
 CGX  H17  CAR  CAQ  117.59  3.000
 CGX  CAS  CAR  CAQ   59.92  3.000
 CGX  H20  CAS  H19  114.81  3.000
 CGX  H20  CAS  CAR  118.66  3.000
 CGX  H19  CAS  CAR  117.68  3.000
 CGX  H20  CAS  CAQ  117.91  3.000
 CGX  H19  CAS  CAQ  117.03  3.000
 CGX  CAR  CAS  CAQ   59.88  3.000
 CGX  C6   N1   C2   117.21  3.000
 CGX  C2   N3   C4   116.35  3.000
 CGX  CAF  NAE  CAD  111.88  3.000
 CGX  CAD  NAE  C6   117.57  3.000
 CGX  CAF  NAE  C6   118.30  3.000
 CGX  H22  NAO  H21  115.46  3.000
 CGX  H22  NAO  C2   117.08  3.000
 CGX  H21  NAO  C2   117.10  3.000
 CGX  H23  NAP  CAQ  116.52  3.000
 CGX  H23  NAP  C4   117.86  3.000
 CGX  CAQ  NAP  C4   122.63  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
 CGX  CONST_01  C2   N3   C4   C5      0.00   0.0  0
 CGX  CONST_02  C2   N1   C6   C5      0.00   0.0  0
 CGX  CONST_03  N1   C6   C5   C4      0.00   0.0  0
 CGX  CONST_04  N1   C2   N3   C4      0.00   0.0  0
 CGX  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 CGX  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 CGX  CONST_07  NAE  C6   C5   C4    180.00   0.0  0
 CGX  CONST_08  NAE  C6   N1   C2    180.00   0.0  0
 CGX  CONST_09  NAO  C2   N3   C4    180.00   0.0  0
 CGX  CONST_10  NAP  C4   N3   C2    180.00   0.0  0
 CGX  CONST_11  NAP  C4   C5   C6    180.00   0.0  0
 CGX  CONST_12  NAO  C2   N1   C6    180.00   0.0  0
 CGX  CONST_13  N3   C4   C5   CAJ   180.00   0.0  0
 CGX  CONST_14  NAE  C6   C5   CAJ     0.00   0.0  0
 CGX  CONST_15  N1   C6   C5   CAJ   180.00   0.0  0
 CGX  CONST_16  CAQ  NAP  C4   C5    180.00   0.0  0
 CGX  CONST_17  N3   C4   NAP  CAQ     0.00   0.0  0
 CGX  CONST_18  H23  NAP  C4   C5      0.00   0.0  0
 CGX  Var_01    CAF  NAE  C6   C5     62.11  30.0  2
 CGX  Var_02    CAC  CAF  NAE  C6   -157.97  30.0  1
 CGX  Var_03    CAA  CAD  NAE  C6    158.26  30.0  1
 CGX  Var_04    CAF  CAC  CAB  CAA    52.81  30.0  1
 CGX  Var_05    NAE  CAF  CAC  CAB   -56.31  30.0  1
 CGX  Var_06    NAE  CAD  CAA  CAB    56.38  30.0  1
 CGX  Var_07    CAD  CAA  CAB  CAC   -53.32  30.0  1
 CGX  Var_08    CAS  CAQ  NAP  C4     85.23  30.0  2
 CGX  Var_09    NAP  CAQ  CAS  CAR   106.25  30.0  1
 CGX  Var_10    H17  CAR  CAS  CAQ   107.07  30.0  1
 CGX  Var_11    CAK  CAJ  C5   C4     75.69  30.0  2
 CGX  Var_12    H13  CAK  CAJ  C5   -177.62  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
 CGX  chir_01  CAQ  CAS  CAR  NAP  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
 CGX  plan-1  C5   0.020
 CGX  plan-1  C4   0.020
 CGX  plan-1  C2   0.020
 CGX  plan-1  C6   0.020
 CGX  plan-1  CAJ  0.020
 CGX  plan-1  N1   0.020
 CGX  plan-1  N3   0.020
 CGX  plan-1  NAE  0.020
 CGX  plan-1  NAO  0.020
 CGX  plan-1  NAP  0.020
 CGX  plan-2  C2   0.020
 CGX  plan-2  NAO  0.020
 CGX  plan-2  H21  0.020
 CGX  plan-2  H22  0.020
 CGX  plan-3  C4   0.020
 CGX  plan-3  CAQ  0.020
 CGX  plan-3  NAP  0.020
 CGX  plan-3  H23  0.020

