# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 19:42:12 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-ethyl-5-{(3S)-3-[2-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}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(ccc2OC)c3ccncc3
#
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
 G8J  G8J  6-ethyl-5-{(3S)-3-[2-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine  ligand  51  28  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G8J
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
 G8J  C4   C  CR6   0   0.263  -4.0803   0.0685   0.5443
 G8J  C5   C  CR6   0  -0.344  -2.8427   0.1203  -0.0942
 G8J  C6   C  CR6   0   0.453  -2.6237   1.2365  -0.9428
 G8J  N1   N  N     0  -0.501  -3.5473   2.1728  -1.1074
 G8J  N3   N  N     0  -0.496  -5.0043   1.0050   0.3730
 G8J  CAJ  C  CH3   0  -0.665  -3.9588  -0.6744   2.9224
 G8J  CAI  C  CH2   0  -0.521  -4.4040  -1.0348   1.5051
 G8J  C2   C  CR6   0   0.539  -4.6936   2.0175  -0.4443
 G8J  NAG  N  NH2   0  -0.820  -5.6380   2.9542  -0.6367
 G8J  NAH  N  NH2   0  -0.828  -1.4508   1.3943  -1.5838
 G8J  CAK  C  CSP   0   0.097  -1.8256  -0.8482   0.0872
 G8J  CAL  C  CSP   0   0.157  -0.9141  -1.6304   0.2088
 G8J  CAM  C  CH1   0  -0.487   0.2063  -2.5554   0.3534
 G8J  CAZ  C  CH3   0  -0.642   0.2812  -3.0954   1.7904
 G8J  CAN  C  CR6   0   0.050   1.5145  -1.8974  -0.0471
 G8J  CAO  C  CR16  0  -0.358   1.7114  -0.5367   0.1048
 G8J  CAS  C  CR6   0   0.352   2.5741  -2.6785  -0.5359
 G8J  OBA  O  O2    0  -0.465   2.3420  -3.9962  -0.6482
 G8J  CBB  C  CH3   0  -0.438   3.3693  -4.8370  -1.1375
 G8J  CAR  C  CR16  0  -0.368   3.7822  -2.0727  -0.8736
 G8J  CAQ  C  CR16  0  -0.307   3.9463  -0.7055  -0.7151
 G8J  CAP  C  CR6   0   0.098   2.9168   0.0879  -0.2210
 G8J  CAT  C  CR6   0   0.184   3.0818   1.5410  -0.0534
 G8J  CAU  C  CR16  0  -0.386   2.0128   2.4243  -0.2081
 G8J  CAV  C  CR16  0  -0.062   2.2223   3.7827  -0.0385
 G8J  NAW  N  N     0  -0.411   3.3999   4.3165   0.2667
 G8J  CAX  C  CR16  0  -0.061   4.4202   3.4784   0.4134
 G8J  CAY  C  CR16  0  -0.386   4.3163   2.1051   0.2684
 G8J  H1   H  HCH3  0   0.238  -4.2164  -1.4727   3.6182
 G8J  H2   H  HCH3  0   0.231  -2.8801  -0.5228   2.9713
 G8J  H3   H  HCH3  0   0.230  -4.4462   0.2387   3.2648
 G8J  H4   H  HCH2  0   0.250  -5.4812  -1.2061   1.4904
 G8J  H5   H  HCH2  0   0.245  -3.9183  -1.9606   1.1936
 G8J  H6   H  HNH2  0   0.396  -5.4067   3.8005  -1.1262
 G8J  H7   H  HNH2  0   0.396  -6.4586   2.9542  -0.0575
 G8J  H8   H  HNH2  0   0.400  -0.8320   0.6065  -1.6806
 G8J  H9   H  HNH2  0   0.396  -1.3951   2.0951  -2.3039
 G8J  H10  H  HCH1  0   0.282   0.0232  -3.4023  -0.3141
 G8J  H11  H  HCH3  0   0.232   0.4566  -2.2843   2.4969
 G8J  H12  H  HCH3  0   0.241  -0.6491  -3.5934   2.0628
 G8J  H13  H  HCH3  0   0.244   1.0921  -3.8169   1.8853
 G8J  H14  H  HCR6  0   0.254   0.9005   0.0549   0.5133
 G8J  H15  H  HCH3  0   0.263   2.9646  -5.8457  -1.1401
 G8J  H16  H  HCH3  0   0.232   3.6621  -4.5713  -2.1560
 G8J  H17  H  HCH3  0   0.232   4.2540  -4.8129  -0.4964
 G8J  H18  H  HCR6  0   0.284   4.6061  -2.6494  -1.2707
 G8J  H19  H  HCR6  0   0.261   4.8891  -0.2612  -1.0079
 G8J  H20  H  HCR6  0   0.253   1.0254   2.0734  -0.4798
 G8J  H21  H  HCR6  0   0.264   1.3950   4.4726  -0.1633
 G8J  H22  H  HCR6  0   0.264   5.3774   3.9196   0.6686
 G8J  H23  H  HCR6  0   0.267   5.1899   1.4866   0.4266

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
 G8J  NAH  C6   single    1.346  0.020  1.346
 G8J  N1   C6   aromatic  1.325  0.020  1.325
 G8J  N1   C2   aromatic  1.333  0.020  1.333
 G8J  C6   C5   aromatic  1.419  0.020  1.419
 G8J  CAZ  CAM  single    1.537  0.020  1.537
 G8J  NAG  C2   single    1.344  0.020  1.344
 G8J  C2   N3   aromatic  1.338  0.020  1.338
 G8J  C5   CAK  single    1.416  0.020  1.416
 G8J  C5   C4   aromatic  1.394  0.020  1.394
 G8J  CAK  CAL  triple    1.207  0.020  1.207
 G8J  CAL  CAM  single    1.460  0.020  1.460
 G8J  CAM  CAN  single    1.518  0.020  1.518
 G8J  N3   C4   aromatic  1.327  0.020  1.327
 G8J  C4   CAI  single    1.498  0.020  1.498
 G8J  OBA  CAS  single    1.343  0.020  1.343
 G8J  OBA  CBB  single    1.415  0.020  1.415
 G8J  CAN  CAS  aromatic  1.404  0.020  1.404
 G8J  CAN  CAO  aromatic  1.383  0.020  1.383
 G8J  CAS  CAR  aromatic  1.393  0.020  1.393
 G8J  CAO  CAP  aromatic  1.396  0.020  1.396
 G8J  CAI  CAJ  single    1.529  0.020  1.529
 G8J  CAU  CAV  aromatic  1.385  0.020  1.385
 G8J  CAU  CAT  aromatic  1.395  0.020  1.395
 G8J  CAR  CAQ  aromatic  1.386  0.020  1.386
 G8J  CAP  CAQ  aromatic  1.390  0.020  1.390
 G8J  CAP  CAT  single    1.472  0.020  1.472
 G8J  CAV  NAW  aromatic  1.328  0.020  1.328
 G8J  CAT  CAY  aromatic  1.395  0.020  1.395
 G8J  NAW  CAX  aromatic  1.329  0.020  1.329
 G8J  CAY  CAX  aromatic  1.385  0.020  1.385
 G8J  CAJ  H1   single    0.970  0.020  1.090
 G8J  CAJ  H2   single    0.970  0.020  1.090
 G8J  CAJ  H3   single    0.970  0.020  1.090
 G8J  CAI  H4   single    0.970  0.020  1.090
 G8J  CAI  H5   single    0.970  0.020  1.090
 G8J  NAG  H6   single    0.860  0.020  1.020
 G8J  NAG  H7   single    0.860  0.020  1.020
 G8J  NAH  H8   single    0.890  0.020  1.040
 G8J  NAH  H9   single    0.890  0.020  1.040
 G8J  CAM  H10  single    0.970  0.020  1.090
 G8J  CAZ  H11  single    0.970  0.020  1.090
 G8J  CAZ  H12  single    0.970  0.020  1.090
 G8J  CAZ  H13  single    0.970  0.020  1.090
 G8J  CAO  H14  single    0.930  0.020  1.080
 G8J  CBB  H15  single    0.970  0.020  1.090
 G8J  CBB  H16  single    0.970  0.020  1.090
 G8J  CBB  H17  single    0.970  0.020  1.090
 G8J  CAR  H18  single    0.930  0.020  1.080
 G8J  CAQ  H19  single    0.930  0.020  1.080
 G8J  CAU  H20  single    0.930  0.020  1.080
 G8J  CAV  H21  single    0.930  0.020  1.080
 G8J  CAX  H22  single    0.930  0.020  1.080
 G8J  CAY  H23  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
 G8J  CAI  C4   N3   116.88  3.000
 G8J  CAI  C4   C5   120.87  3.000
 G8J  N3   C4   C5   122.22  3.000
 G8J  CAK  C5   C6   120.25  3.000
 G8J  CAK  C5   C4   123.62  3.000
 G8J  C6   C5   C4   116.12  3.000
 G8J  NAH  C6   N1   117.73  3.000
 G8J  N1   C6   C5   121.49  3.000
 G8J  NAH  C6   C5   120.76  3.000
 G8J  C2   N1   C6   117.06  3.000
 G8J  C2   N3   C4   116.83  3.000
 G8J  H3   CAJ  H2   108.17  3.000
 G8J  H3   CAJ  H1   107.90  3.000
 G8J  H2   CAJ  H1   107.88  3.000
 G8J  H3   CAJ  CAI  111.00  3.000
 G8J  H2   CAJ  CAI  111.25  3.000
 G8J  H1   CAJ  CAI  110.51  3.000
 G8J  H5   CAI  H4   107.61  3.000
 G8J  H5   CAI  CAJ  109.58  3.000
 G8J  H4   CAI  CAJ  109.71  3.000
 G8J  H5   CAI  C4   110.21  3.000
 G8J  H4   CAI  C4   108.68  3.000
 G8J  CAJ  CAI  C4   110.98  3.000
 G8J  NAG  C2   N3   116.85  3.000
 G8J  N3   C2   N1   126.28  3.000
 G8J  NAG  C2   N1   116.85  3.000
 G8J  H7   NAG  H6   117.97  3.000
 G8J  H7   NAG  C2   119.44  3.000
 G8J  H6   NAG  C2   119.68  3.000
 G8J  H9   NAH  H8   116.25  3.000
 G8J  H9   NAH  C6   118.08  3.000
 G8J  H8   NAH  C6   119.33  3.000
 G8J  CAL  CAK  C5   180.00  3.000
 G8J  CAM  CAL  CAK  180.00  3.000
 G8J  H10  CAM  CAN  108.59  3.000
 G8J  H10  CAM  CAZ  107.86  3.000
 G8J  CAN  CAM  CAZ  110.91  3.000
 G8J  H10  CAM  CAL  107.56  3.000
 G8J  CAN  CAM  CAL  111.13  3.000
 G8J  CAZ  CAM  CAL  110.65  3.000
 G8J  H13  CAZ  H12  108.12  3.000
 G8J  H13  CAZ  H11  108.46  3.000
 G8J  H12  CAZ  H11  108.39  3.000
 G8J  H13  CAZ  CAM  110.51  3.000
 G8J  H12  CAZ  CAM  110.64  3.000
 G8J  H11  CAZ  CAM  110.63  3.000
 G8J  CAS  CAN  CAO  118.55  3.000
 G8J  CAO  CAN  CAM  121.34  3.000
 G8J  CAS  CAN  CAM  120.06  3.000
 G8J  H14  CAO  CAP  119.33  3.000
 G8J  H14  CAO  CAN  118.16  3.000
 G8J  CAP  CAO  CAN  122.50  3.000
 G8J  CAR  CAS  OBA  123.81  3.000
 G8J  CAR  CAS  CAN  119.80  3.000
 G8J  OBA  CAS  CAN  116.39  3.000
 G8J  CBB  OBA  CAS  119.12  3.000
 G8J  H17  CBB  H16  108.94  3.000
 G8J  H17  CBB  H15  108.86  3.000
 G8J  H16  CBB  H15  108.86  3.000
 G8J  H17  CBB  OBA  111.83  3.000
 G8J  H16  CBB  OBA  111.87  3.000
 G8J  H15  CBB  OBA  106.38  3.000
 G8J  H18  CAR  CAQ  118.55  3.000
 G8J  H18  CAR  CAS  121.19  3.000
 G8J  CAQ  CAR  CAS  120.26  3.000
 G8J  H19  CAQ  CAP  120.45  3.000
 G8J  H19  CAQ  CAR  118.49  3.000
 G8J  CAP  CAQ  CAR  121.05  3.000
 G8J  CAT  CAP  CAQ  121.38  3.000
 G8J  CAT  CAP  CAO  120.78  3.000
 G8J  CAQ  CAP  CAO  117.83  3.000
 G8J  CAY  CAT  CAU  116.59  3.000
 G8J  CAY  CAT  CAP  121.64  3.000
 G8J  CAU  CAT  CAP  121.77  3.000
 G8J  H20  CAU  CAV  119.12  3.000
 G8J  H20  CAU  CAT  121.43  3.000
 G8J  CAV  CAU  CAT  119.44  3.000
 G8J  H21  CAV  NAW  116.55  3.000
 G8J  H21  CAV  CAU  119.64  3.000
 G8J  NAW  CAV  CAU  123.81  3.000
 G8J  CAX  NAW  CAV  116.91  3.000
 G8J  H22  CAX  CAY  119.63  3.000
 G8J  H22  CAX  NAW  116.56  3.000
 G8J  CAY  CAX  NAW  123.81  3.000
 G8J  H23  CAY  CAX  119.40  3.000
 G8J  H23  CAY  CAT  121.14  3.000
 G8J  CAX  CAY  CAT  119.45  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
 G8J  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 G8J  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 G8J  CONST_03  C2   N1   C6   C5     0.00   0.0  0
 G8J  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 G8J  CONST_05  N3   C2   N1   C6     0.00   0.0  0
 G8J  CONST_06  N3   C4   C5   C6     0.00   0.0  0
 G8J  CONST_07  CAQ  CAR  CAS  CAN    0.00   0.0  0
 G8J  CONST_08  CAQ  CAP  CAO  CAN    0.00   0.0  0
 G8J  CONST_09  CAT  CAP  CAO  CAN  180.00   0.0  0
 G8J  CONST_10  CAR  CAS  CAN  CAO    0.00   0.0  0
 G8J  CONST_11  CAR  CAQ  CAP  CAO    0.00   0.0  0
 G8J  CONST_14  CAP  CAO  CAN  CAS    0.00   0.0  0
 G8J  CONST_15  CAP  CAQ  CAR  CAS    0.00   0.0  0
 G8J  CONST_16  CAT  CAP  CAQ  CAR  180.00   0.0  0
 G8J  CONST_19  CAV  CAU  CAT  CAP  180.00   0.0  0
 G8J  CONST_20  CAX  CAY  CAT  CAP  180.00   0.0  0
 G8J  CONST_21  NAW  CAV  CAU  CAT    0.00   0.0  0
 G8J  CONST_22  NAW  CAX  CAY  CAT    0.00   0.0  0
 G8J  CONST_23  CAX  NAW  CAV  CAU    0.00   0.0  0
 G8J  CONST_24  CAX  CAY  CAT  CAU    0.00   0.0  0
 G8J  CONST_25  CAY  CAT  CAU  CAV    0.00   0.0  0
 G8J  CONST_26  CAY  CAX  NAW  CAV    0.00   0.0  0
 G8J  CONST_27  NAH  C6   C5   C4   180.00   0.0  0
 G8J  CONST_28  NAG  C2   N3   C4   180.00   0.0  0
 G8J  CONST_29  NAG  C2   N1   C6   180.00   0.0  0
 G8J  CONST_30  CAI  C4   C5   C6   180.00   0.0  0
 G8J  CONST_31  CAK  C5   C6   N1   180.00   0.0  0
 G8J  CONST_32  CAK  C5   C4   N3   180.00   0.0  0
 G8J  CONST_33  C2   N3   C4   CAI  180.00   0.0  0
 G8J  CONST_34  NAH  C6   N1   C2   180.00   0.0  0
 G8J  CONST_35  CAR  CAS  CAN  CAM  180.00   0.0  0
 G8J  CONST_36  CAP  CAO  CAN  CAM  180.00   0.0  0
 G8J  CONST_37  OBA  CAS  CAN  CAO  180.00   0.0  0
 G8J  CONST_38  CAQ  CAR  CAS  OBA  180.00   0.0  0
 G8J  CONST_39  H18  CAR  CAS  CAN  180.00   0.0  0
 G8J  CONST_40  H19  CAQ  CAP  CAO  180.00   0.0  0
 G8J  CONST_41  H14  CAO  CAN  CAS  180.00   0.0  0
 G8J  CONST_42  H20  CAU  CAT  CAP    0.00   0.0  0
 G8J  CONST_43  H23  CAY  CAT  CAP    0.00   0.0  0
 G8J  CONST_44  H21  CAV  CAU  CAT  180.00   0.0  0
 G8J  CONST_45  H22  CAX  CAY  CAT  180.00   0.0  0
 G8J  CONST_47  H9   NAH  C6   C5   180.00   0.0  0
 G8J  CONST_48  H6   NAG  C2   N1     0.00   0.0  0
 G8J  CONST_49  H7   NAG  C2   N1   180.00   0.0  0
 G8J  Var_01    CAJ  CAI  C4   C5    88.12  30.0  2
 G8J  Var_02    CAR  CAS  OBA  CBB   -0.09  30.0  2
 G8J  Var_03    H1   CAJ  CAI  C4   178.83  30.0  3
 G8J  Var_04    H15  CBB  OBA  CAS  179.86  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
 G8J  chir_01  CAM  CAZ  CAL  CAN  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
 G8J  plan-1  C4   0.020
 G8J  plan-1  C5   0.020
 G8J  plan-1  C6   0.020
 G8J  plan-1  N1   0.020
 G8J  plan-1  N3   0.020
 G8J  plan-1  CAI  0.020
 G8J  plan-1  C2   0.020
 G8J  plan-1  NAG  0.020
 G8J  plan-1  NAH  0.020
 G8J  plan-1  CAK  0.020
 G8J  plan-1  CAL  0.020
 G8J  plan-2  CAM  0.020
 G8J  plan-2  CAN  0.020
 G8J  plan-2  CAO  0.020
 G8J  plan-2  CAS  0.020
 G8J  plan-2  OBA  0.020
 G8J  plan-2  CAR  0.020
 G8J  plan-2  CAQ  0.020
 G8J  plan-2  CAP  0.020
 G8J  plan-2  CAT  0.020
 G8J  plan-2  H14  0.020
 G8J  plan-2  H18  0.020
 G8J  plan-2  H19  0.020
 G8J  plan-3  CAP  0.020
 G8J  plan-3  CAT  0.020
 G8J  plan-3  CAU  0.020
 G8J  plan-3  CAV  0.020
 G8J  plan-3  NAW  0.020
 G8J  plan-3  CAX  0.020
 G8J  plan-3  CAY  0.020
 G8J  plan-3  H20  0.020
 G8J  plan-3  H21  0.020
 G8J  plan-3  H22  0.020
 G8J  plan-3  H23  0.020
 G8J  plan-4  C2   0.020
 G8J  plan-4  NAG  0.020
 G8J  plan-4  H6   0.020
 G8J  plan-4  H7   0.020
 G8J  plan-5  C6   0.020
 G8J  plan-5  NAH  0.020
 G8J  plan-5  H8   0.020
 G8J  plan-5  H9   0.020

