# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 23:27:12 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: ~{N}-[3-[(5-chloranyl-2-phenylazanyl-pyrimidin-4-yl)amino]phenyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cnc(Nc2ccccc2)nc1Nc3cccc(NC(=O)C=C)c3
#
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
 E3Z  E3Z  ~{N}-[3-[(5-chloranyl-2-phenylazanyl-pyrimidin-4-yl)amino]phenyl]prop-2-enamide  ligand  42  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E3Z
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
 E3Z  C4   C   CR6   0   0.668   0.6150   2.0688  -0.0907
 E3Z  C5   C   CR6   0  -0.250   1.7350   2.9367  -0.0737
 E3Z  C6   C   CR16  0   0.062   2.9746   2.3584  -0.0068
 E3Z  N1   N   N     0  -0.483   3.1619   1.0415   0.0371
 E3Z  N3   N   N     0  -0.546   0.8092   0.7646  -0.0494
 E3Z  CAA  C   CR16  0  -0.300   4.5636  -1.5233   0.2500
 E3Z  CAB  C   CR16  0  -0.225   5.5641  -2.4858   0.3076
 E3Z  CAC  C   CR16  0  -0.256   5.2727  -3.8386   0.2212
 E3Z  CAD  C   CR16  0  -0.222   3.9473  -4.2297   0.0735
 E3Z  CAE  C   CR16  0  -0.321   2.9395  -3.2844   0.0125
 E3Z  CAF  C   CR6   0   0.381   3.2318  -1.9173   0.1003
 E3Z  C2   C   CR6   0   0.652   2.0621   0.3036   0.0107
 E3Z  CL5  CL  CL    0  -0.098   1.5533   4.6527  -0.1285
 E3Z  NAO  N   NH1   0  -0.783  -0.6332   2.5825  -0.1491
 E3Z  CAP  C   CR6   0   0.433  -1.8849   1.9671  -0.1515
 E3Z  CAU  C   CR16  0  -0.420  -2.0980   0.5969  -0.0586
 E3Z  CAQ  C   CR16  0  -0.357  -2.9879   2.8230  -0.2485
 E3Z  CAR  C   CR16  0  -0.228  -4.2634   2.2970  -0.2512
 E3Z  CAS  C   CR16  0  -0.362  -4.4948   0.9304  -0.1581
 E3Z  CAT  C   CR6   0   0.409  -3.3973   0.0781  -0.0601
 E3Z  NAV  N   NH1   0  -0.758  -3.4879  -1.3117   0.0451
 E3Z  CAW  C   C     0   0.521  -4.5854  -2.1130   0.0443
 E3Z  OAX  O   O     0  -0.435  -5.7313  -1.7088  -0.0565
 E3Z  CAY  C   C1    0  -0.314  -4.2474  -3.5536   0.1788
 E3Z  CAZ  C   C2    0  -0.432  -5.1899  -4.4889   0.1907
 E3Z  H1   H   HCR6  0   0.272   3.8625   2.9803   0.0130
 E3Z  H3   H   HCR6  0   0.238   6.5902  -2.1611   0.4255
 E3Z  H4   H   HCR6  0   0.235   6.0617  -4.5769   0.2692
 E3Z  H5   H   HCR6  0   0.236   3.6929  -5.2794   0.0035
 E3Z  H6   H   HCR6  0   0.220   1.9107  -3.6051  -0.1061
 E3Z  H8   H   HNH1  0   0.397  -0.6770   3.5901  -0.1875
 E3Z  H9   H   HCR6  0   0.280  -1.2573  -0.0746   0.0143
 E3Z  H10  H   HCR6  0   0.248  -2.8423   3.8941  -0.3200
 E3Z  H11  H   HCR6  0   0.247  -5.1087   2.9682  -0.3274
 E3Z  H12  H   HCR6  0   0.283  -5.5037   0.5549  -0.1613
 E3Z  H13  H   HNH1  0   0.384  -2.6016  -1.7841   0.1379
 E3Z  H14  H   H     0   0.232  -3.2024  -3.8296   0.2690
 E3Z  H16  H   H     0   0.261  -6.2403  -4.2433   0.1042
 E3Z  H17  H   H     0   0.248  -4.9361  -5.5351   0.2870
 E3Z  NAG  N   NH1   0  -0.766   2.1426  -1.0530   0.0424
 E3Z  H2   H   HCR6  0   0.281   4.8174  -0.4786   0.3218
 E3Z  H7   H   HNH1  0   0.372   1.2418  -1.5035  -0.0136

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
 E3Z  OAX  CAW  double    1.219  0.020  1.219
 E3Z  NAG  CAF  single    1.392  0.020  1.392
 E3Z  NAG  C2   single    1.359  0.020  1.359
 E3Z  CAA  CAF  aromatic  1.397  0.020  1.397
 E3Z  CAA  CAB  aromatic  1.389  0.020  1.389
 E3Z  N1   C2   aromatic  1.325  0.020  1.325
 E3Z  N1   C6   aromatic  1.331  0.020  1.331
 E3Z  CAF  CAE  aromatic  1.401  0.020  1.401
 E3Z  NAV  CAW  single    1.359  0.020  1.359
 E3Z  NAV  CAT  single    1.397  0.020  1.397
 E3Z  C2   N3   aromatic  1.336  0.020  1.336
 E3Z  CAB  CAC  aromatic  1.386  0.020  1.386
 E3Z  CAE  CAD  aromatic  1.383  0.020  1.383
 E3Z  C6   C5   aromatic  1.369  0.020  1.369
 E3Z  CAW  CAY  single    1.486  0.020  1.486
 E3Z  CAC  CAD  aromatic  1.390  0.020  1.390
 E3Z  N3   C4   aromatic  1.319  0.020  1.319
 E3Z  C5   C4   aromatic  1.417  0.020  1.417
 E3Z  C5   CL5  single    1.727  0.020  1.727
 E3Z  CAU  CAT  aromatic  1.399  0.020  1.399
 E3Z  CAU  CAP  aromatic  1.390  0.020  1.390
 E3Z  CAT  CAS  aromatic  1.393  0.020  1.393
 E3Z  C4   NAO  single    1.351  0.020  1.351
 E3Z  NAO  CAP  single    1.395  0.020  1.395
 E3Z  CAP  CAQ  aromatic  1.400  0.020  1.400
 E3Z  CAS  CAR  aromatic  1.389  0.020  1.389
 E3Z  CAY  CAZ  double    1.328  0.020  1.328
 E3Z  CAQ  CAR  aromatic  1.380  0.020  1.380
 E3Z  C6   H1   single    0.930  0.020  1.080
 E3Z  CAA  H2   single    0.930  0.020  1.080
 E3Z  CAB  H3   single    0.930  0.020  1.080
 E3Z  CAC  H4   single    0.930  0.020  1.080
 E3Z  CAD  H5   single    0.930  0.020  1.080
 E3Z  CAE  H6   single    0.930  0.020  1.080
 E3Z  NAG  H7   single    0.860  0.020  1.020
 E3Z  NAO  H8   single    0.860  0.020  1.020
 E3Z  CAU  H9   single    0.930  0.020  1.080
 E3Z  CAQ  H10  single    0.930  0.020  1.080
 E3Z  CAR  H11  single    0.930  0.020  1.080
 E3Z  CAS  H12  single    0.930  0.020  1.080
 E3Z  NAV  H13  single    0.860  0.020  1.020
 E3Z  CAY  H14  single    0.930  0.020  1.080
 E3Z  CAZ  H16  single    0.930  0.020  1.080
 E3Z  CAZ  H17  single    0.930  0.020  1.080

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
 E3Z  NAO  C4   N3   120.88  3.000
 E3Z  NAO  C4   C5   119.86  3.000
 E3Z  N3   C4   C5   119.26  3.000
 E3Z  CL5  C5   C6   121.10  3.000
 E3Z  CL5  C5   C4   121.68  3.000
 E3Z  C6   C5   C4   117.22  3.000
 E3Z  H1   C6   N1   116.85  3.000
 E3Z  H1   C6   C5   119.99  3.000
 E3Z  N1   C6   C5   123.15  3.000
 E3Z  C2   N1   C6   115.70  3.000
 E3Z  C2   N3   C4   118.71  3.000
 E3Z  H2   CAA  CAF  120.35  3.000
 E3Z  H2   CAA  CAB  119.95  3.000
 E3Z  CAF  CAA  CAB  119.70  3.000
 E3Z  H3   CAB  CAC  119.90  3.000
 E3Z  H3   CAB  CAA  118.63  3.000
 E3Z  CAC  CAB  CAA  121.47  3.000
 E3Z  H4   CAC  CAD  120.55  3.000
 E3Z  H4   CAC  CAB  120.66  3.000
 E3Z  CAD  CAC  CAB  118.79  3.000
 E3Z  H5   CAD  CAE  119.26  3.000
 E3Z  H5   CAD  CAC  120.26  3.000
 E3Z  CAE  CAD  CAC  120.48  3.000
 E3Z  H6   CAE  CAF  119.57  3.000
 E3Z  H6   CAE  CAD  119.61  3.000
 E3Z  CAF  CAE  CAD  120.82  3.000
 E3Z  NAG  CAF  CAE  116.12  3.000
 E3Z  CAE  CAF  CAA  118.75  3.000
 E3Z  NAG  CAF  CAA  125.13  3.000
 E3Z  NAG  C2   N3   113.63  3.000
 E3Z  N3   C2   N1   125.95  3.000
 E3Z  NAG  C2   N1   120.42  3.000
 E3Z  H8   NAO  CAP  113.67  3.000
 E3Z  H8   NAO  C4   114.92  3.000
 E3Z  CAP  NAO  C4   131.41  3.000
 E3Z  CAQ  CAP  CAU  119.13  3.000
 E3Z  CAQ  CAP  NAO  115.95  3.000
 E3Z  CAU  CAP  NAO  124.92  3.000
 E3Z  H9   CAU  CAT  119.55  3.000
 E3Z  H9   CAU  CAP  119.92  3.000
 E3Z  CAT  CAU  CAP  120.53  3.000
 E3Z  H10  CAQ  CAR  120.07  3.000
 E3Z  H10  CAQ  CAP  120.22  3.000
 E3Z  CAR  CAQ  CAP  119.71  3.000
 E3Z  H11  CAR  CAS  119.00  3.000
 E3Z  H11  CAR  CAQ  119.07  3.000
 E3Z  CAS  CAR  CAQ  121.93  3.000
 E3Z  H12  CAS  CAT  121.68  3.000
 E3Z  H12  CAS  CAR  119.93  3.000
 E3Z  CAT  CAS  CAR  118.39  3.000
 E3Z  NAV  CAT  CAS  124.26  3.000
 E3Z  CAS  CAT  CAU  120.32  3.000
 E3Z  NAV  CAT  CAU  115.42  3.000
 E3Z  H13  NAV  CAW  115.69  3.000
 E3Z  H13  NAV  CAT  114.58  3.000
 E3Z  CAW  NAV  CAT  129.73  3.000
 E3Z  CAY  CAW  OAX  122.86  3.000
 E3Z  CAY  CAW  NAV  112.83  3.000
 E3Z  OAX  CAW  NAV  124.31  3.000
 E3Z  H14  CAY  CAZ  120.26  3.000
 E3Z  H14  CAY  CAW  118.25  3.000
 E3Z  CAZ  CAY  CAW  121.49  3.000
 E3Z  H17  CAZ  H16  117.05  3.000
 E3Z  H17  CAZ  CAY  121.06  3.000
 E3Z  H16  CAZ  CAY  121.89  3.000
 E3Z  H7   NAG  C2   113.05  3.000
 E3Z  H7   NAG  CAF  115.08  3.000
 E3Z  C2   NAG  CAF  131.85  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
 E3Z  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 E3Z  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 E3Z  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 E3Z  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 E3Z  CONST_05  N3   C2   N1   C6      0.00   0.0  0
 E3Z  CONST_06  N3   C4   C5   C6      0.00   0.0  0
 E3Z  CONST_07  CAD  CAE  CAF  CAA     0.00   0.0  0
 E3Z  CONST_08  CAD  CAC  CAB  CAA     0.00   0.0  0
 E3Z  CONST_09  CAE  CAF  CAA  CAB     0.00   0.0  0
 E3Z  CONST_10  CAE  CAD  CAC  CAB     0.00   0.0  0
 E3Z  CONST_11  CAF  CAA  CAB  CAC     0.00   0.0  0
 E3Z  CONST_12  CAF  CAE  CAD  CAC     0.00   0.0  0
 E3Z  CONST_13  CAS  CAT  CAU  CAP     0.00   0.0  0
 E3Z  CONST_14  CAS  CAR  CAQ  CAP     0.00   0.0  0
 E3Z  CONST_15  CAR  CAS  CAT  CAU     0.00   0.0  0
 E3Z  CONST_16  CAR  CAQ  CAP  CAU     0.00   0.0  0
 E3Z  CONST_17  CAT  CAU  CAP  CAQ     0.00   0.0  0
 E3Z  CONST_18  CAT  CAS  CAR  CAQ     0.00   0.0  0
 E3Z  CONST_19  NAG  C2   N3   C4    180.00   0.0  0
 E3Z  CONST_20  NAG  C2   N1   C6    180.00   0.0  0
 E3Z  CONST_21  NAO  C4   C5   C6    180.00   0.0  0
 E3Z  CONST_22  CL5  C5   C6   N1    180.00   0.0  0
 E3Z  CONST_23  CL5  C5   C4   N3    180.00   0.0  0
 E3Z  CONST_24  NAG  CAF  CAA  CAB   180.00   0.0  0
 E3Z  CONST_25  NAG  CAF  CAE  CAD   180.00   0.0  0
 E3Z  CONST_26  NAO  C4   N3   C2    180.00   0.0  0
 E3Z  CONST_27  CAT  CAU  CAP  NAO   180.00   0.0  0
 E3Z  CONST_28  CAR  CAQ  CAP  NAO   180.00   0.0  0
 E3Z  CONST_29  NAV  CAT  CAU  CAP   180.00   0.0  0
 E3Z  CONST_30  NAV  CAT  CAS  CAR   180.00   0.0  0
 E3Z  CONST_31  H1   C6   C5   C4    180.00   0.0  0
 E3Z  CONST_32  H6   CAE  CAF  CAA   180.00   0.0  0
 E3Z  CONST_33  H4   CAC  CAB  CAA   180.00   0.0  0
 E3Z  CONST_34  H5   CAD  CAC  CAB   180.00   0.0  0
 E3Z  CONST_35  H2   CAA  CAB  CAC   180.00   0.0  0
 E3Z  CONST_36  H3   CAB  CAC  CAD   180.00   0.0  0
 E3Z  CONST_37  H11  CAR  CAQ  CAP   180.00   0.0  0
 E3Z  CONST_38  H12  CAS  CAT  CAU   180.00   0.0  0
 E3Z  CONST_39  H10  CAQ  CAP  CAU   180.00   0.0  0
 E3Z  CONST_40  H9   CAU  CAP  CAQ   180.00   0.0  0
 E3Z  CONST_41  CAW  NAV  CAT  CAU   180.00   0.0  0
 E3Z  CONST_42  CAW  NAV  CAT  CAS     0.00   0.0  0
 E3Z  CONST_43  H13  NAV  CAT  CAU     0.00   0.0  0
 E3Z  CONST_44  OAX  CAW  NAV  CAT     0.00   0.0  0
 E3Z  CONST_45  CAY  CAW  NAV  CAT   180.00   0.0  0
 E3Z  Var_01    CAU  CAP  NAO  C4      1.52  30.0  2
 E3Z  Var_02    CAP  NAO  C4   C5   -178.57  30.0  2
 E3Z  Var_03    CAF  NAG  C2   N1     -0.11  30.0  1
 E3Z  Var_04    C2   NAG  CAF  CAA     5.50  30.0  3
 E3Z  Var_05    CAZ  CAY  CAW  NAV  -179.64  30.0  2
 E3Z  Var_06    H16  CAZ  CAY  CAW    -0.06   0.0  2

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
 E3Z  plan-1  C4   0.020
 E3Z  plan-1  C5   0.020
 E3Z  plan-1  C6   0.020
 E3Z  plan-1  N1   0.020
 E3Z  plan-1  N3   0.020
 E3Z  plan-1  C2   0.020
 E3Z  plan-1  CL5  0.020
 E3Z  plan-1  NAO  0.020
 E3Z  plan-1  H1   0.020
 E3Z  plan-1  NAG  0.020
 E3Z  plan-2  CAA  0.020
 E3Z  plan-2  CAB  0.020
 E3Z  plan-2  CAC  0.020
 E3Z  plan-2  CAD  0.020
 E3Z  plan-2  CAE  0.020
 E3Z  plan-2  CAF  0.020
 E3Z  plan-2  H3   0.020
 E3Z  plan-2  H4   0.020
 E3Z  plan-2  H5   0.020
 E3Z  plan-2  H6   0.020
 E3Z  plan-2  NAG  0.020
 E3Z  plan-2  H2   0.020
 E3Z  plan-3  NAO  0.020
 E3Z  plan-3  CAP  0.020
 E3Z  plan-3  CAU  0.020
 E3Z  plan-3  CAQ  0.020
 E3Z  plan-3  CAR  0.020
 E3Z  plan-3  CAS  0.020
 E3Z  plan-3  CAT  0.020
 E3Z  plan-3  NAV  0.020
 E3Z  plan-3  H9   0.020
 E3Z  plan-3  H10  0.020
 E3Z  plan-3  H11  0.020
 E3Z  plan-3  H12  0.020
 E3Z  plan-4  CAT  0.020
 E3Z  plan-4  NAV  0.020
 E3Z  plan-4  CAW  0.020
 E3Z  plan-4  OAX  0.020
 E3Z  plan-4  CAY  0.020
 E3Z  plan-4  H13  0.020
 E3Z  plan-5  CAW  0.020
 E3Z  plan-5  CAY  0.020
 E3Z  plan-5  CAZ  0.020
 E3Z  plan-5  H14  0.020
 E3Z  plan-5  H16  0.020
 E3Z  plan-5  H17  0.020

