# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:34:07 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 5-chloro-N~4~-cyclopropyl-N~2~-[4-(2-methoxyethoxy)phenyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1ccc(Nc2ncc(Cl)c(NC3CC3)n2)cc1
#
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
 E9Z  E9Z  5-chloro-N~4~-cyclopropyl-N~2~-[4-(2-methoxyethoxy)phenyl]pyrimidine-2,4-diamine  ligand  42  23  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E9Z
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
 E9Z  N1    N   N     0  -0.498  -1.4997  -1.5005  -0.1013
 E9Z  C2    C   CR6   0   0.600  -1.6834  -0.2012   0.0993
 E9Z  N3    N   N     0  -0.512  -2.8592   0.4247   0.1956
 E9Z  C4    C   CR6   0   0.624  -3.9654  -0.2919   0.0719
 E9Z  C5    C   CR6   0  -0.245  -3.8663  -1.6904  -0.1397
 E9Z  C6    C   CR16  0   0.030  -2.6105  -2.2273  -0.2149
 E9Z  CAA   C   CH3   0  -0.396   8.8238  -0.4680  -0.9850
 E9Z  CAC   C   CR16  0  -0.295   1.3551  -0.8568  -0.0736
 E9Z  CAD   C   CR16  0  -0.343   1.5983   1.4564   0.4842
 E9Z  CAE   C   CR16  0  -0.339   2.7337  -0.9840  -0.0739
 E9Z  CAF   C   CR16  0  -0.370   2.9791   1.3299   0.4820
 E9Z  CAH   C   CH2   0  -0.159   7.1880   0.4336   0.4117
 E9Z  CAI   C   CH2   0  -0.219   5.7719   0.9431   0.4531
 E9Z  CAJ   C   CH2   0  -0.515  -6.4254   2.4341  -0.2396
 E9Z  CAK   C   CH2   0  -0.476  -5.0221   2.6969  -0.6934
 E9Z  NAN   N   NH1   0  -0.767  -0.6121   0.6247   0.2316
 E9Z  NAO   N   NH1   0  -0.667  -5.1516   0.3275   0.1483
 E9Z  OAP   O   O2    0  -0.483   7.5105   0.0217  -0.8899
 E9Z  OAQ   O   O2    0  -0.475   4.8957  -0.1341   0.1840
 E9Z  CAS   C   CR6   0   0.341   0.7599   0.3761   0.2101
 E9Z  CAT   C   CR6   0   0.370   3.5650   0.0983   0.2040
 E9Z  CAW   C   CH1   0  -0.082  -5.2835   1.7219   0.4088
 E9Z  CL5   CL  CL    0  -0.124  -5.2785  -2.6737  -0.3018
 E9Z  H6    H   HCR6  0   0.283  -2.4839  -3.2924  -0.3755
 E9Z  HAA   H   HCH3  0   0.205   9.5669   0.2927  -0.7165
 E9Z  HAAA  H   HCH3  0   0.205   8.9870  -1.3373  -0.3364
 E9Z  HAAB  H   HCH3  0   0.235   8.9971  -0.7707  -2.0170
 E9Z  HAC   H   HCR6  0   0.285   0.7452  -1.7182  -0.2914
 E9Z  HAD   H   HCR6  0   0.269   1.1686   2.4258   0.7095
 E9Z  HAE   H   HCR6  0   0.260   3.1743  -1.9479  -0.2977
 E9Z  HAF   H   HCR6  0   0.280   3.5720   2.2070   0.7025
 E9Z  HAH   H   HCH2  0   0.212   7.8462   1.2476   0.7477
 E9Z  HAHA  H   HCH2  0   0.210   7.3108  -0.3892   1.1306
 E9Z  HAI   H   HCH2  0   0.231   5.5862   1.3625   1.4483
 E9Z  HAIA  H   HCH2  0   0.229   5.6349   1.7489  -0.2776
 E9Z  HAJ   H   HCH2  0   0.260  -6.9368   3.1906   0.3402
 E9Z  HAJA  H   HCH2  0   0.259  -7.0679   1.8600  -0.8957
 E9Z  HAK   H   HCH2  0   0.255  -4.7173   2.2979  -1.6519
 E9Z  HAKA  H   HCH2  0   0.254  -4.5583   3.6377  -0.4275
 E9Z  HNAN  H   HNH1  0   0.405  -0.8720   1.5841   0.4030
 E9Z  HNAO  H   HNH1  0   0.399  -5.9844  -0.2387   0.1613
 E9Z  HAW   H   HCH1  0   0.267  -5.0098   2.0335   1.4123

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
 E9Z  C6   N1    aromatic  1.332  0.020  1.332
 E9Z  N1   C2    aromatic  1.327  0.020  1.327
 E9Z  C2   NAN   single    1.359  0.020  1.359
 E9Z  C2   N3    aromatic  1.335  0.020  1.335
 E9Z  C4   N3    aromatic  1.324  0.020  1.324
 E9Z  C5   C4    aromatic  1.418  0.020  1.418
 E9Z  C4   NAO   single    1.340  0.020  1.340
 E9Z  CL5  C5    single    1.728  0.020  1.728
 E9Z  C6   C5    aromatic  1.368  0.020  1.368
 E9Z  C6   H6    single    0.930  0.020  1.080
 E9Z  OAP  CAA   single    1.405  0.020  1.405
 E9Z  CAA  HAA   single    0.970  0.020  1.090
 E9Z  CAA  HAAA  single    0.970  0.020  1.090
 E9Z  CAA  HAAB  single    0.970  0.020  1.090
 E9Z  CAS  CAC   aromatic  1.398  0.020  1.398
 E9Z  CAC  CAE   aromatic  1.384  0.020  1.384
 E9Z  CAC  HAC   single    0.930  0.020  1.080
 E9Z  CAS  CAD   aromatic  1.395  0.020  1.395
 E9Z  CAD  CAF   aromatic  1.387  0.020  1.387
 E9Z  CAD  HAD   single    0.930  0.020  1.080
 E9Z  CAE  CAT   aromatic  1.393  0.020  1.393
 E9Z  CAE  HAE   single    0.930  0.020  1.080
 E9Z  CAF  CAT   aromatic  1.392  0.020  1.392
 E9Z  CAF  HAF   single    0.930  0.020  1.080
 E9Z  CAI  CAH   single    1.506  0.020  1.506
 E9Z  CAH  OAP   single    1.403  0.020  1.403
 E9Z  CAH  HAH   single    0.970  0.020  1.090
 E9Z  CAH  HAHA  single    0.970  0.020  1.090
 E9Z  OAQ  CAI   single    1.414  0.020  1.414
 E9Z  CAI  HAI   single    0.970  0.020  1.090
 E9Z  CAI  HAIA  single    0.970  0.020  1.090
 E9Z  CAW  CAJ   single    1.494  0.020  1.494
 E9Z  CAK  CAJ   single    1.498  0.020  1.498
 E9Z  CAJ  HAJ   single    0.970  0.020  1.090
 E9Z  CAJ  HAJA  single    0.970  0.020  1.090
 E9Z  CAW  CAK   single    1.495  0.020  1.495
 E9Z  CAK  HAK   single    0.970  0.020  1.090
 E9Z  CAK  HAKA  single    0.970  0.020  1.090
 E9Z  NAN  CAS   single    1.395  0.020  1.395
 E9Z  NAN  HNAN  single    0.860  0.020  1.020
 E9Z  NAO  CAW   single    1.425  0.020  1.425
 E9Z  NAO  HNAO  single    0.860  0.020  1.020
 E9Z  CAT  OAQ   single    1.351  0.020  1.351
 E9Z  CAW  HAW   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
 E9Z  C6    N1   C2    115.56  3.000
 E9Z  NAN   C2   N3    113.71  3.000
 E9Z  N3    C2   N1    126.26  3.000
 E9Z  NAN   C2   N1    120.02  3.000
 E9Z  C4    N3   C2    118.37  3.000
 E9Z  NAO   C4   C5    121.74  3.000
 E9Z  NAO   C4   N3    118.95  3.000
 E9Z  C5    C4   N3    119.31  3.000
 E9Z  CL5   C5   C6    121.44  3.000
 E9Z  C6    C5   C4    117.35  3.000
 E9Z  CL5   C5   C4    121.20  3.000
 E9Z  H6    C6   C5    120.05  3.000
 E9Z  H6    C6   N1    116.81  3.000
 E9Z  C5    C6   N1    123.14  3.000
 E9Z  HAAB  CAA  HAAA  108.44  3.000
 E9Z  HAAB  CAA  HAA   108.47  3.000
 E9Z  HAAA  CAA  HAA   107.70  3.000
 E9Z  HAAB  CAA  OAP   108.05  3.000
 E9Z  HAAA  CAA  OAP   112.05  3.000
 E9Z  HAA   CAA  OAP   112.03  3.000
 E9Z  HAC   CAC  CAS   120.32  3.000
 E9Z  HAC   CAC  CAE   119.35  3.000
 E9Z  CAS   CAC  CAE   120.33  3.000
 E9Z  HAD   CAD  CAS   119.68  3.000
 E9Z  HAD   CAD  CAF   118.47  3.000
 E9Z  CAS   CAD  CAF   121.85  3.000
 E9Z  HAE   CAE  CAT   119.34  3.000
 E9Z  HAE   CAE  CAC   119.13  3.000
 E9Z  CAT   CAE  CAC   121.53  3.000
 E9Z  HAF   CAF  CAT   121.84  3.000
 E9Z  HAF   CAF  CAD   118.14  3.000
 E9Z  CAT   CAF  CAD   120.02  3.000
 E9Z  HAHA  CAH  HAH   106.70  3.000
 E9Z  HAHA  CAH  OAP   111.18  3.000
 E9Z  HAH   CAH  OAP   111.31  3.000
 E9Z  HAHA  CAH  CAI   109.90  3.000
 E9Z  HAH   CAH  CAI   107.70  3.000
 E9Z  OAP   CAH  CAI   109.94  3.000
 E9Z  HAIA  CAI  HAI   107.63  3.000
 E9Z  HAIA  CAI  OAQ   110.83  3.000
 E9Z  HAI   CAI  OAQ   111.06  3.000
 E9Z  HAIA  CAI  CAH   110.36  3.000
 E9Z  HAI   CAI  CAH   108.29  3.000
 E9Z  OAQ   CAI  CAH   108.64  3.000
 E9Z  HAJA  CAJ  HAJ   114.52  3.000
 E9Z  HAJA  CAJ  CAW   117.63  3.000
 E9Z  HAJ   CAJ  CAW   117.53  3.000
 E9Z  HAJA  CAJ  CAK   117.72  3.000
 E9Z  HAJ   CAJ  CAK   118.85  3.000
 E9Z  CAW   CAJ  CAK    59.94  3.000
 E9Z  HAKA  CAK  HAK   114.68  3.000
 E9Z  HAKA  CAK  CAW   117.44  3.000
 E9Z  HAK   CAK  CAW   117.51  3.000
 E9Z  HAKA  CAK  CAJ   118.66  3.000
 E9Z  HAK   CAK  CAJ   117.87  3.000
 E9Z  CAW   CAK  CAJ    59.89  3.000
 E9Z  HNAN  NAN  CAS   115.19  3.000
 E9Z  HNAN  NAN  C2    113.05  3.000
 E9Z  CAS   NAN  C2    131.73  3.000
 E9Z  HNAO  NAO  CAW   118.12  3.000
 E9Z  HNAO  NAO  C4    118.21  3.000
 E9Z  CAW   NAO  C4    123.00  3.000
 E9Z  CAH   OAP  CAA   112.34  3.000
 E9Z  CAT   OAQ  CAI   118.45  3.000
 E9Z  NAN   CAS  CAD   116.77  3.000
 E9Z  NAN   CAS  CAC   125.39  3.000
 E9Z  CAD   CAS  CAC   117.84  3.000
 E9Z  OAQ   CAT  CAF   124.74  3.000
 E9Z  OAQ   CAT  CAE   116.83  3.000
 E9Z  CAF   CAT  CAE   118.43  3.000
 E9Z  HAW   CAW  NAO   115.24  3.000
 E9Z  HAW   CAW  CAK   116.76  3.000
 E9Z  NAO   CAW  CAK   119.17  3.000
 E9Z  HAW   CAW  CAJ   117.20  3.000
 E9Z  NAO   CAW  CAJ   117.26  3.000
 E9Z  CAK   CAW  CAJ    60.17  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
 E9Z  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 E9Z  CONST_02  C4    N3   C2   N1      0.00   0.0  0
 E9Z  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 E9Z  CONST_04  C5    C4   N3   C2      0.00   0.0  0
 E9Z  CONST_05  C6    N1   C2   N3      0.00   0.0  0
 E9Z  CONST_06  C6    C5   C4   N3      0.00   0.0  0
 E9Z  CONST_07  CAF   CAD  CAS  CAC     0.00   0.0  0
 E9Z  CONST_08  CAF   CAT  CAE  CAC     0.00   0.0  0
 E9Z  CONST_09  CAE   CAC  CAS  CAD     0.00   0.0  0
 E9Z  CONST_10  CAE   CAT  CAF  CAD     0.00   0.0  0
 E9Z  CONST_11  CAT   CAE  CAC  CAS     0.00   0.0  0
 E9Z  CONST_12  CAT   CAF  CAD  CAS     0.00   0.0  0
 E9Z  CONST_13  CL5   C5   C6   N1    180.00   0.0  0
 E9Z  CONST_14  NAO   C4   N3   C2    180.00   0.0  0
 E9Z  CONST_15  CL5   C5   C4   N3    180.00   0.0  0
 E9Z  CONST_16  NAN   C2   N3   C4    180.00   0.0  0
 E9Z  CONST_17  NAN   C2   N1   C6    180.00   0.0  0
 E9Z  CONST_18  NAO   C4   C5   C6    180.00   0.0  0
 E9Z  CONST_19  OAQ   CAT  CAE  CAC   180.00   0.0  0
 E9Z  CONST_20  OAQ   CAT  CAF  CAD   180.00   0.0  0
 E9Z  CONST_21  NAN   CAS  CAC  CAE   180.00   0.0  0
 E9Z  CONST_22  NAN   CAS  CAD  CAF   180.00   0.0  0
 E9Z  CONST_23  CAW   NAO  C4   N3      0.00   0.0  0
 E9Z  CONST_24  CAW   NAO  C4   C5    180.00   0.0  0
 E9Z  CONST_25  H6    C6   N1   C2    180.00   0.0  0
 E9Z  CONST_26  HAD   CAD  CAS  CAC   180.00   0.0  0
 E9Z  CONST_27  HAC   CAC  CAS  CAD   180.00   0.0  0
 E9Z  CONST_28  HAF   CAF  CAT  CAE   180.00   0.0  0
 E9Z  CONST_29  HAE   CAE  CAT  CAF   180.00   0.0  0
 E9Z  CONST_30  HNAO  NAO  C4   N3    180.00   0.0  0
 E9Z  Var_01    CAS   NAN  C2   N1     -0.62  30.0  2
 E9Z  Var_02    CAC   CAS  NAN  C2      5.47  30.0  2
 E9Z  Var_03    CAJ   CAW  NAO  C4    146.63  30.0  3
 E9Z  Var_04    NAO   CAW  CAK  CAJ   106.53  30.0  1
 E9Z  Var_05    HAI   CAI  OAQ  CAT    59.43  30.0  3
 E9Z  Var_06    CAI   CAH  OAP  CAA  -179.83  30.0  2
 E9Z  Var_07    OAQ   CAI  CAH  OAP    65.68  30.0  1
 E9Z  Var_08    HAA   CAA  OAP  CAH   -60.86  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
 E9Z  chir_01  CAW  CAJ  CAK  NAO  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
 E9Z  plan-1  N1    0.020
 E9Z  plan-1  C2    0.020
 E9Z  plan-1  N3    0.020
 E9Z  plan-1  C4    0.020
 E9Z  plan-1  C5    0.020
 E9Z  plan-1  C6    0.020
 E9Z  plan-1  NAN   0.020
 E9Z  plan-1  NAO   0.020
 E9Z  plan-1  CL5   0.020
 E9Z  plan-1  H6    0.020
 E9Z  plan-2  CAC   0.020
 E9Z  plan-2  CAD   0.020
 E9Z  plan-2  CAE   0.020
 E9Z  plan-2  CAF   0.020
 E9Z  plan-2  NAN   0.020
 E9Z  plan-2  OAQ   0.020
 E9Z  plan-2  CAS   0.020
 E9Z  plan-2  CAT   0.020
 E9Z  plan-2  HAC   0.020
 E9Z  plan-2  HAD   0.020
 E9Z  plan-2  HAE   0.020
 E9Z  plan-2  HAF   0.020
 E9Z  plan-3  C4    0.020
 E9Z  plan-3  NAO   0.020
 E9Z  plan-3  CAW   0.020
 E9Z  plan-3  HNAO  0.020

