# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 16:47:07 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-ethyl-5-[(3~{S})-3-(6-pyridin-4-yl-1,3-benzodioxol-4-yl)but-1-ynyl]pyrimidine-2,4-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#C[C@H](C)c2cc(cc3OCOc23)c4ccncc4
#
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
 5N1  5N1  6-ethyl-5-[(3~{S})-3-(6-pyridin-4-yl-1,3-benzodioxol-4-yl)but-1-ynyl]pyrimidine-2,4-diamine  ligand  50  29  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_5N1
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
 5N1  C4   C  CR6   0   0.259  -3.1515  -0.8495   0.8864
 5N1  C5   C  CR6   0  -0.352  -3.1558   0.2218  -0.0058
 5N1  C6   C  CR6   0   0.465  -4.3957   0.5027  -0.6398
 5N1  N1   N  N     0  -0.504  -5.4807  -0.2196  -0.3865
 5N1  N3   N  N     0  -0.498  -4.2393  -1.5670   1.1367
 5N1  CBC  C  CH3   0  -0.671  -1.0909  -2.2531   0.7164
 5N1  CBB  C  CH2   0  -0.521  -1.8893  -1.2728   1.5754
 5N1  C2   C  CR6   0   0.536  -5.3557  -1.2160   0.4880
 5N1  NBA  N  NH2   0  -0.820  -6.4661  -1.9232   0.7684
 5N1  NAZ  N  NH2   0  -0.825  -4.5104   1.5148  -1.5067
 5N1  CAG  C  CSP   0   0.108  -2.0027   0.9918  -0.2960
 5N1  CAH  C  CSP   0   0.142  -1.0311   1.6594  -0.5578
 5N1  CAI  C  CH1   0  -0.497   0.1585   2.4409  -0.8857
 5N1  CAJ  C  CH3   0  -0.640   0.2134   2.7536  -2.3887
 5N1  CAK  C  CR6   0   0.064   1.4190   1.7305  -0.4423
 5N1  CAL  C  CR16  0  -0.378   1.5566   0.3381  -0.4786
 5N1  CAP  C  CR56  0   0.252   2.5237   2.4279  -0.0135
 5N1  OAW  O  O     0  -0.481   2.6684   3.7664   0.1194
 5N1  CAX  C  CH2   0   0.070   4.0341   3.9914   0.4501
 5N1  OAY  O  O     0  -0.486   4.5954   2.7251   0.7698
 5N1  CAO  C  CR56  0   0.333   3.6928   1.7950   0.3792
 5N1  CAN  C  CR16  0  -0.416   3.8285   0.4325   0.3614
 5N1  CAM  C  CR6   0   0.100   2.7221  -0.3119  -0.0879
 5N1  CAQ  C  CR6   0   0.175   2.7911  -1.7837  -0.1246
 5N1  CAR  C  CR16  0  -0.381   3.5019  -2.5055   0.8335
 5N1  CAS  C  CR16  0  -0.061   3.5196  -3.8891   0.7667
 5N1  NAT  N  N     0  -0.410   2.8908  -4.5914  -0.1691
 5N1  CAU  C  CR16  0  -0.061   2.2159  -3.9057  -1.0853
 5N1  CAV  C  CR16  0  -0.380   2.1386  -2.5233  -1.1100
 5N1  H1   H  HCH3  0   0.234  -1.6603  -3.1617   0.5205
 5N1  H2   H  HCH3  0   0.232  -0.8244  -1.8117  -0.2439
 5N1  H3   H  HCH3  0   0.238  -0.1648  -2.5364   1.2161
 5N1  H4   H  HCH2  0   0.244  -1.2728  -0.4010   1.8006
 5N1  H5   H  HCH2  0   0.250  -2.1512  -1.7453   2.5229
 5N1  H6   H  HNH2  0   0.394  -7.2807  -1.8067   0.1918
 5N1  H7   H  HNH2  0   0.395  -6.3781  -2.7839   1.2792
 5N1  H8   H  HNH2  0   0.404  -3.7090   2.0502  -1.7910
 5N1  H9   H  HNH2  0   0.399  -5.3731   1.6517  -2.0040
 5N1  H10  H  HCH1  0   0.287   0.0930   3.3925  -0.3487
 5N1  H11  H  HCH3  0   0.235   0.2771   1.8357  -2.9723
 5N1  H12  H  HCH3  0   0.244  -0.6773   3.2991  -2.6992
 5N1  H13  H  HCH3  0   0.245   1.0842   3.3685  -2.6143
 5N1  H14  H  HCR6  0   0.254   0.7045  -0.2467  -0.8008
 5N1  H15  H  HCH2  0   0.238   4.5560   4.4249  -0.4088
 5N1  H16  H  HCH2  0   0.249   4.1005   4.6537   1.3130
 5N1  H17  H  HCR6  0   0.275   4.7515  -0.0446   0.6621
 5N1  H18  H  HCR6  0   0.267   4.0193  -2.0065   1.6423
 5N1  H19  H  HCR6  0   0.264   4.0647  -4.4546   1.5144
 5N1  H20  H  HCR6  0   0.264   1.7101  -4.4843  -1.8503
 5N1  H21  H  HCR6  0   0.268   1.5876  -2.0361  -1.9036

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
 5N1  CAU  NAT  aromatic  1.329  0.020  1.329
 5N1  CAU  CAV  aromatic  1.385  0.020  1.385
 5N1  NAT  CAS  aromatic  1.328  0.020  1.328
 5N1  CAV  CAQ  aromatic  1.394  0.020  1.394
 5N1  CAS  CAR  aromatic  1.385  0.020  1.385
 5N1  CAQ  CAR  aromatic  1.394  0.020  1.394
 5N1  CAQ  CAM  single    1.474  0.020  1.474
 5N1  CAJ  CAI  single    1.536  0.020  1.536
 5N1  CAM  CAN  aromatic  1.407  0.020  1.407
 5N1  CAM  CAL  aromatic  1.391  0.020  1.391
 5N1  CAN  CAO  aromatic  1.369  0.020  1.369
 5N1  CAL  CAK  aromatic  1.400  0.020  1.400
 5N1  CAO  CAP  aromatic  1.386  0.020  1.386
 5N1  CAO  OAY  single    1.354  0.020  1.354
 5N1  CAK  CAP  aromatic  1.375  0.020  1.375
 5N1  CAK  CAI  single    1.513  0.020  1.513
 5N1  CAP  OAW  single    1.353  0.020  1.353
 5N1  CAI  CAH  single    1.461  0.020  1.461
 5N1  OAY  CAX  single    1.421  0.020  1.421
 5N1  OAW  CAX  single    1.423  0.020  1.423
 5N1  CAH  CAG  triple    1.208  0.020  1.208
 5N1  CAG  C5   single    1.417  0.020  1.417
 5N1  NAZ  C6   single    1.338  0.020  1.338
 5N1  C5   C6   aromatic  1.421  0.020  1.421
 5N1  C5   C4   aromatic  1.394  0.020  1.394
 5N1  CBC  CBB  single    1.528  0.020  1.528
 5N1  C6   N1   aromatic  1.328  0.020  1.328
 5N1  CBB  C4   single    1.499  0.020  1.499
 5N1  C4   N3   aromatic  1.327  0.020  1.327
 5N1  N1   C2   aromatic  1.332  0.020  1.332
 5N1  N3   C2   aromatic  1.338  0.020  1.338
 5N1  C2   NBA  single    1.346  0.020  1.346
 5N1  CBC  H1   single    0.970  0.020  1.090
 5N1  CBC  H2   single    0.970  0.020  1.090
 5N1  CBC  H3   single    0.970  0.020  1.090
 5N1  CBB  H4   single    0.970  0.020  1.090
 5N1  CBB  H5   single    0.970  0.020  1.090
 5N1  NBA  H6   single    0.890  0.020  1.040
 5N1  NBA  H7   single    0.890  0.020  1.040
 5N1  NAZ  H8   single    0.860  0.020  1.020
 5N1  NAZ  H9   single    0.860  0.020  1.020
 5N1  CAI  H10  single    0.970  0.020  1.090
 5N1  CAJ  H11  single    0.970  0.020  1.090
 5N1  CAJ  H12  single    0.970  0.020  1.090
 5N1  CAJ  H13  single    0.970  0.020  1.090
 5N1  CAL  H14  single    0.930  0.020  1.080
 5N1  CAX  H15  single    0.970  0.020  1.090
 5N1  CAX  H16  single    0.970  0.020  1.090
 5N1  CAN  H17  single    0.930  0.020  1.080
 5N1  CAR  H18  single    0.930  0.020  1.080
 5N1  CAS  H19  single    0.930  0.020  1.080
 5N1  CAU  H20  single    0.930  0.020  1.080
 5N1  CAV  H21  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
 5N1  CBB  C4   N3   116.81  3.000
 5N1  N3   C4   C5   122.25  3.000
 5N1  CBB  C4   C5   120.91  3.000
 5N1  CAG  C5   C6   120.76  3.000
 5N1  C6   C5   C4   116.12  3.000
 5N1  CAG  C5   C4   123.11  3.000
 5N1  NAZ  C6   N1   117.72  3.000
 5N1  N1   C6   C5   121.36  3.000
 5N1  NAZ  C6   C5   120.91  3.000
 5N1  C2   N1   C6   117.10  3.000
 5N1  C2   N3   C4   116.79  3.000
 5N1  H3   CBC  H2   107.55  3.000
 5N1  H3   CBC  H1   108.04  3.000
 5N1  H2   CBC  H1   107.88  3.000
 5N1  H3   CBC  CBB  110.66  3.000
 5N1  H2   CBC  CBB  111.29  3.000
 5N1  H1   CBC  CBB  111.27  3.000
 5N1  H5   CBB  H4   107.60  3.000
 5N1  H5   CBB  CBC  109.62  3.000
 5N1  H4   CBB  CBC  109.47  3.000
 5N1  H5   CBB  C4   108.63  3.000
 5N1  H4   CBB  C4   110.18  3.000
 5N1  CBC  CBB  C4   111.26  3.000
 5N1  NBA  C2   N3   116.71  3.000
 5N1  NBA  C2   N1   116.91  3.000
 5N1  N3   C2   N1   126.37  3.000
 5N1  H7   NBA  H6   117.52  3.000
 5N1  H7   NBA  C2   118.93  3.000
 5N1  H6   NBA  C2   119.23  3.000
 5N1  H9   NAZ  H8   118.16  3.000
 5N1  H9   NAZ  C6   119.82  3.000
 5N1  H8   NAZ  C6   121.21  3.000
 5N1  CAH  CAG  C5   180.00  3.000
 5N1  CAI  CAH  CAG  180.00  3.000
 5N1  H10  CAI  CAK  108.31  3.000
 5N1  H10  CAI  CAJ  107.77  3.000
 5N1  CAK  CAI  CAJ  110.64  3.000
 5N1  H10  CAI  CAH  107.83  3.000
 5N1  CAK  CAI  CAH  111.19  3.000
 5N1  CAJ  CAI  CAH  110.96  3.000
 5N1  H13  CAJ  H12  108.16  3.000
 5N1  H13  CAJ  H11  108.52  3.000
 5N1  H12  CAJ  H11  108.48  3.000
 5N1  H13  CAJ  CAI  110.24  3.000
 5N1  H12  CAJ  CAI  110.59  3.000
 5N1  H11  CAJ  CAI  110.77  3.000
 5N1  CAP  CAK  CAL  115.70  3.000
 5N1  CAP  CAK  CAI  121.50  3.000
 5N1  CAL  CAK  CAI  122.77  3.000
 5N1  H14  CAL  CAM  119.40  3.000
 5N1  H14  CAL  CAK  117.89  3.000
 5N1  CAM  CAL  CAK  122.69  3.000
 5N1  CAO  CAP  OAW  109.49  3.000
 5N1  OAW  CAP  CAK  128.20  3.000
 5N1  CAO  CAP  CAK  122.30  3.000
 5N1  CAX  OAW  CAP  106.38  3.000
 5N1  H16  CAX  H15  110.59  3.000
 5N1  H16  CAX  OAY  109.83  3.000
 5N1  H15  CAX  OAY  109.94  3.000
 5N1  H16  CAX  OAW  109.79  3.000
 5N1  H15  CAX  OAW  109.74  3.000
 5N1  OAY  CAX  OAW  106.88  3.000
 5N1  CAO  OAY  CAX  106.49  3.000
 5N1  CAN  CAO  OAY  128.42  3.000
 5N1  OAY  CAO  CAP  109.29  3.000
 5N1  CAN  CAO  CAP  122.29  3.000
 5N1  H17  CAN  CAM  121.76  3.000
 5N1  H17  CAN  CAO  121.32  3.000
 5N1  CAM  CAN  CAO  116.91  3.000
 5N1  CAQ  CAM  CAN  119.96  3.000
 5N1  CAN  CAM  CAL  120.10  3.000
 5N1  CAQ  CAM  CAL  119.94  3.000
 5N1  CAV  CAQ  CAR  116.72  3.000
 5N1  CAR  CAQ  CAM  121.58  3.000
 5N1  CAV  CAQ  CAM  121.70  3.000
 5N1  H18  CAR  CAS  119.38  3.000
 5N1  H18  CAR  CAQ  121.24  3.000
 5N1  CAS  CAR  CAQ  119.37  3.000
 5N1  H19  CAS  NAT  116.61  3.000
 5N1  H19  CAS  CAR  119.60  3.000
 5N1  NAT  CAS  CAR  123.78  3.000
 5N1  CAU  NAT  CAS  116.96  3.000
 5N1  H20  CAU  CAV  119.60  3.000
 5N1  H20  CAU  NAT  116.62  3.000
 5N1  CAV  CAU  NAT  123.78  3.000
 5N1  H21  CAV  CAU  119.41  3.000
 5N1  H21  CAV  CAQ  121.19  3.000
 5N1  CAU  CAV  CAQ  119.39  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
 5N1  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 5N1  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 5N1  CONST_03  C2   N1   C6   C5     0.00   0.0  0
 5N1  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 5N1  CONST_05  N3   C4   C5   C6     0.00   0.0  0
 5N1  CONST_06  N3   C2   N1   C6     0.00   0.0  0
 5N1  CONST_07  CAQ  CAM  CAL  CAK  180.00   0.0  0
 5N1  CONST_08  CAN  CAM  CAL  CAK    0.00   0.0  0
 5N1  CONST_09  CAN  CAO  CAP  CAK    0.00   0.0  0
 5N1  CONST_12  CAO  CAN  CAM  CAL    0.00   0.0  0
 5N1  CONST_13  CAO  CAP  CAK  CAL    0.00   0.0  0
 5N1  CONST_14  CAM  CAN  CAO  CAP    0.00   0.0  0
 5N1  CONST_15  CAM  CAL  CAK  CAP    0.00   0.0  0
 5N1  CONST_16  CAQ  CAM  CAN  CAO  180.00   0.0  0
 5N1  CONST_19  CAU  CAV  CAQ  CAM  180.00   0.0  0
 5N1  CONST_20  CAS  CAR  CAQ  CAM  180.00   0.0  0
 5N1  CONST_21  NAT  CAU  CAV  CAQ    0.00   0.0  0
 5N1  CONST_22  NAT  CAS  CAR  CAQ    0.00   0.0  0
 5N1  CONST_23  CAU  NAT  CAS  CAR    0.00   0.0  0
 5N1  CONST_24  CAU  CAV  CAQ  CAR    0.00   0.0  0
 5N1  CONST_25  CAV  CAU  NAT  CAS    0.00   0.0  0
 5N1  CONST_26  CAV  CAQ  CAR  CAS    0.00   0.0  0
 5N1  CONST_27  NAZ  C6   C5   C4   180.00   0.0  0
 5N1  CONST_28  NBA  C2   N3   C4   180.00   0.0  0
 5N1  CONST_29  CBB  C4   C5   C6   180.00   0.0  0
 5N1  CONST_30  NBA  C2   N1   C6   180.00   0.0  0
 5N1  CONST_31  CAG  C5   C6   N1   180.00   0.0  0
 5N1  CONST_32  CAG  C5   C4   N3   180.00   0.0  0
 5N1  CONST_33  C2   N3   C4   CBB  180.00   0.0  0
 5N1  CONST_34  NAZ  C6   N1   C2   180.00   0.0  0
 5N1  CONST_35  CAM  CAL  CAK  CAI  180.00   0.0  0
 5N1  CONST_36  CAO  CAP  CAK  CAI  180.00   0.0  0
 5N1  CONST_37  OAW  CAP  CAK  CAI    0.00   0.0  0
 5N1  CONST_38  H17  CAN  CAM  CAL  180.00   0.0  0
 5N1  CONST_39  H14  CAL  CAK  CAP  180.00   0.0  0
 5N1  CONST_40  H21  CAV  CAQ  CAM    0.00   0.0  0
 5N1  CONST_41  H18  CAR  CAQ  CAM    0.00   0.0  0
 5N1  CONST_42  H20  CAU  CAV  CAQ  180.00   0.0  0
 5N1  CONST_43  H19  CAS  CAR  CAQ  180.00   0.0  0
 5N1  CONST_44  H8   NAZ  C6   C5     0.00   0.0  0
 5N1  CONST_45  H9   NAZ  C6   C5   180.00   0.0  0
 5N1  CONST_46  H6   NBA  C2   N1     0.00   0.0  0
 5N1  CONST_47  H7   NBA  C2   N1   180.00   0.0  0
 5N1  Var_01    OAY  CAX  OAW  CAP  -11.75  30.0  1
 5N1  Var_02    CAN  CAO  OAY  CAX  173.29  30.0  1
 5N1  Var_03    CAO  CAP  OAW  CAX    7.31  30.0  1
 5N1  Var_04    CBC  CBB  C4   C5   -86.31  30.0  1
 5N1  Var_05    H1   CBC  CBB  C4   -61.18  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
 5N1  chir_01  CAI  CAJ  CAK  CAH  positiv

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
 5N1  plan-1  C4   0.020
 5N1  plan-1  C5   0.020
 5N1  plan-1  C6   0.020
 5N1  plan-1  N1   0.020
 5N1  plan-1  N3   0.020
 5N1  plan-1  CBB  0.020
 5N1  plan-1  C2   0.020
 5N1  plan-1  NBA  0.020
 5N1  plan-1  NAZ  0.020
 5N1  plan-1  CAG  0.020
 5N1  plan-1  CAH  0.020
 5N1  plan-2  CAM  0.020
 5N1  plan-2  CAQ  0.020
 5N1  plan-2  CAR  0.020
 5N1  plan-2  CAS  0.020
 5N1  plan-2  NAT  0.020
 5N1  plan-2  CAU  0.020
 5N1  plan-2  CAV  0.020
 5N1  plan-2  H18  0.020
 5N1  plan-2  H19  0.020
 5N1  plan-2  H20  0.020
 5N1  plan-2  H21  0.020
 5N1  plan-3  CAI  0.020
 5N1  plan-3  CAK  0.020
 5N1  plan-3  CAL  0.020
 5N1  plan-3  CAP  0.020
 5N1  plan-3  OAW  0.020
 5N1  plan-3  OAY  0.020
 5N1  plan-3  CAO  0.020
 5N1  plan-3  CAN  0.020
 5N1  plan-3  CAM  0.020
 5N1  plan-3  CAQ  0.020
 5N1  plan-3  H14  0.020
 5N1  plan-3  H17  0.020
 5N1  plan-4  C2   0.020
 5N1  plan-4  NBA  0.020
 5N1  plan-4  H6   0.020
 5N1  plan-4  H7   0.020
 5N1  plan-5  C6   0.020
 5N1  plan-5  NAZ  0.020
 5N1  plan-5  H8   0.020
 5N1  plan-5  H9   0.020

