# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 15:31:37 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-5'-methoxy[1,1'-biphenyl]-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#C[C@H](C)c2cc(OC)cc(c2)c3ccc(cc3)C(O)=O
#
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
 G6Y  G6Y  '3'-[(2R)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-5'-methoxy[1,1'-biphenyl]-4-carboxylic acid'  ligand  54  31  .  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_G6Y
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
 G6Y  C4   C  C      0   0.266  -5.5966  -0.9606   0.3664
 G6Y  C5   C  C      0  -0.338  -4.4176  -0.2940   0.0400
 G6Y  C6   C  C      0   0.450  -4.4681   0.5418  -1.1072
 G6Y  N1   N  N      0  -0.502  -5.5818   0.6766  -1.8162
 G6Y  N3   N  N      0  -0.498  -6.7087  -0.8201  -0.3442
 G6Y  CBE  C  CH3    0  -0.667  -5.1637  -3.3073   1.0995
 G6Y  CBD  C  CH2    0  -0.523  -5.6450  -1.9178   1.5182
 G6Y  C2   C  C      0   0.537  -6.6499  -0.0029  -1.4017
 G6Y  NAG  N  NH2    0  -0.820  -7.7879   0.1668  -2.0998
 G6Y  NAH  N  NH2    0  -0.826  -3.3915   1.2407  -1.4961
 G6Y  CAI  C  CSP    0   0.093  -3.2152  -0.4109   0.7792
 G6Y  CAJ  C  CSP    0   0.141  -2.1518  -0.4560   1.3499
 G6Y  CAK  C  CH1    0  -0.508  -0.8636  -0.4630   2.0390
 G6Y  CBC  C  CH3    0  -0.640  -1.0013   0.0541   3.4779
 G6Y  CAL  C  C      0   0.194   0.1572   0.3470   1.2617
 G6Y  CAM  C  C1     0  -0.428   1.4387  -0.1558   1.0669
 G6Y  CAQ  C  C1     0  -0.413  -0.1691   1.6045   0.7792
 G6Y  CAP  C  C      0   0.429   0.7774   2.3595   0.0876
 G6Y  OAX  O  O2     0  -0.472   0.3654   3.5616  -0.3553
 G6Y  CAY  C  CH3    0  -0.439   1.2644   4.3536  -1.1055
 G6Y  CAO  C  C1     0  -0.477   2.0556   1.8494  -0.1158
 G6Y  CAN  C  C      0   0.146   2.3948   0.5885   0.3799
 G6Y  CAR  C  C      0   0.076   3.7564   0.0558   0.1691
 G6Y  CAS  C  C1     0  -0.302   3.9719  -1.3060  -0.0509
 G6Y  CAT  C  C1     0  -0.275   5.2513  -1.8024  -0.2443
 G6Y  CAU  C  C      0  -0.110   6.3607  -0.9608  -0.2266
 G6Y  CAZ  C  C      0   0.395   7.7666  -1.5072  -0.4387
 G6Y  OBB  O  O      0  -0.593   7.8661  -2.7362  -0.6174
 G6Y  OBA  O  OC    -1  -0.593   8.6959  -0.6775  -0.4154
 G6Y  CAV  C  C1     0  -0.275   6.1460   0.3975  -0.0083
 G6Y  CAW  C  C1     0  -0.301   4.8691   0.8990   0.1866
 G6Y  H1   H  HCH3   0   0.230  -5.7682  -3.6997   0.2815
 G6Y  H2   H  HCH3   0   0.231  -4.1248  -3.2832   0.7707
 G6Y  H3   H  HCH3   0   0.239  -5.2350  -4.0042   1.9341
 G6Y  H4   H  HCH2   0   0.244  -5.0297  -1.5493   2.3409
 G6Y  H5   H  HCH2   0   0.249  -6.6730  -1.9777   1.8779
 G6Y  H6   H  HNH2   0   0.394  -7.7531   0.6300  -2.9907
 G6Y  H7   H  HNH2   0   0.395  -8.5636  -0.4475  -1.9247
 G6Y  H8   H  HNH2   0   0.398  -3.4130   1.7190  -2.3806
 G6Y  H9   H  HNH2   0   0.402  -2.4881   1.0419  -1.1012
 G6Y  H10  H  HCH1   0   0.284  -0.5071  -1.4967   2.0873
 G6Y  H11  H  HCH3   0   0.233  -1.3472   1.0874   3.4887
 G6Y  H12  H  HCH3   0   0.242  -1.7133  -0.5527   4.0368
 G6Y  H13  H  HCH3   0   0.242  -0.0390   0.0076   3.9875
 G6Y  H14  H  H      0   0.250   1.6941  -1.1272   1.4726
 G6Y  H15  H  H      0   0.258  -1.1622   2.0117   0.9327
 G6Y  H16  H  HCH3   0   0.228   2.1524   4.6255  -0.5292
 G6Y  H17  H  HCH3   0   0.230   1.5803   3.8520  -2.0238
 G6Y  H18  H  HCH3   0   0.261   0.7289   5.2623  -1.3688
 G6Y  H19  H  H      0   0.277   2.7905   2.4070  -0.6807
 G6Y  H20  H  H      0   0.248   3.1299  -1.9859  -0.0930
 G6Y  H21  H  H      0   0.244   5.3895  -2.8615  -0.4176
 G6Y  H23  H  H      0   0.244   6.9909   1.0725   0.0165
 G6Y  H24  H  H      0   0.246   4.7413   1.9579   0.3755

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
 G6Y  NAH  C6   single    1.341  0.020  1.341
 G6Y  CBC  CAK  single    1.535  0.020  1.535
 G6Y  C6   N1   aromatic  1.327  0.020  1.327
 G6Y  C6   C5   aromatic  1.420  0.020  1.420
 G6Y  N1   C2   aromatic  1.332  0.020  1.332
 G6Y  CAJ  CAK  single    1.461  0.020  1.461
 G6Y  CAJ  CAI  triple    1.208  0.020  1.208
 G6Y  CAK  CAL  single    1.517  0.020  1.517
 G6Y  CAI  C5   single    1.416  0.020  1.416
 G6Y  C5   C4   aromatic  1.393  0.020  1.393
 G6Y  C2   NAG  single    1.346  0.020  1.346
 G6Y  C2   N3   aromatic  1.338  0.020  1.338
 G6Y  CAL  CAM  aromatic  1.390  0.020  1.390
 G6Y  CAL  CAQ  aromatic  1.386  0.020  1.386
 G6Y  CAM  CAN  aromatic  1.393  0.020  1.393
 G6Y  C4   N3   aromatic  1.327  0.020  1.327
 G6Y  C4   CBD  single    1.499  0.020  1.499
 G6Y  CAQ  CAP  aromatic  1.394  0.020  1.394
 G6Y  CAS  CAT  aromatic  1.386  0.020  1.386
 G6Y  CAS  CAR  aromatic  1.396  0.020  1.396
 G6Y  CAT  CAU  aromatic  1.393  0.020  1.393
 G6Y  CAN  CAR  single    1.477  0.020  1.477
 G6Y  CAN  CAO  aromatic  1.397  0.020  1.397
 G6Y  CBD  CBE  single    1.529  0.020  1.529
 G6Y  OBB  CAZ  deloc     1.246  0.020  1.246
 G6Y  CAR  CAW  aromatic  1.396  0.020  1.396
 G6Y  CAP  CAO  aromatic  1.391  0.020  1.391
 G6Y  CAP  OAX  single    1.346  0.020  1.346
 G6Y  CAU  CAZ  single    1.523  0.020  1.523
 G6Y  CAU  CAV  aromatic  1.392  0.020  1.392
 G6Y  CAZ  OBA  deloc     1.246  0.020  1.246
 G6Y  CAW  CAV  aromatic  1.386  0.020  1.386
 G6Y  OAX  CAY  single    1.414  0.020  1.414
 G6Y  CBE  H1   single    0.970  0.020  1.090
 G6Y  CBE  H2   single    0.970  0.020  1.090
 G6Y  CBE  H3   single    0.970  0.020  1.090
 G6Y  CBD  H4   single    0.970  0.020  1.090
 G6Y  CBD  H5   single    0.970  0.020  1.090
 G6Y  NAG  H6   single    0.890  0.020  1.040
 G6Y  NAG  H7   single    0.890  0.020  1.040
 G6Y  NAH  H8   single    0.890  0.020  1.040
 G6Y  NAH  H9   single    0.890  0.020  1.040
 G6Y  CAK  H10  single    0.970  0.020  1.090
 G6Y  CBC  H11  single    0.970  0.020  1.090
 G6Y  CBC  H12  single    0.970  0.020  1.090
 G6Y  CBC  H13  single    0.970  0.020  1.090
 G6Y  CAM  H14  single    0.930  0.020  1.080
 G6Y  CAQ  H15  single    0.930  0.020  1.080
 G6Y  CAY  H16  single    0.970  0.020  1.090
 G6Y  CAY  H17  single    0.970  0.020  1.090
 G6Y  CAY  H18  single    0.970  0.020  1.090
 G6Y  CAO  H19  single    0.930  0.020  1.080
 G6Y  CAS  H20  single    0.930  0.020  1.080
 G6Y  CAT  H21  single    0.930  0.020  1.080
 G6Y  CAV  H23  single    0.930  0.020  1.080
 G6Y  CAW  H24  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
 G6Y  CBD  C4   N3   116.88  3.000
 G6Y  CBD  C4   C5   120.87  3.000
 G6Y  N3   C4   C5   122.21  3.000
 G6Y  CAI  C5   C6   120.03  3.000
 G6Y  CAI  C5   C4   123.83  3.000
 G6Y  C6   C5   C4   116.15  3.000
 G6Y  NAH  C6   N1   117.76  3.000
 G6Y  N1   C6   C5   121.41  3.000
 G6Y  NAH  C6   C5   120.82  3.000
 G6Y  C2   N1   C6   117.05  3.000
 G6Y  C2   N3   C4   116.81  3.000
 G6Y  H3   CBE  H2   107.91  3.000
 G6Y  H3   CBE  H1   107.95  3.000
 G6Y  H2   CBE  H1   108.06  3.000
 G6Y  H3   CBE  CBD  110.54  3.000
 G6Y  H2   CBE  CBD  111.26  3.000
 G6Y  H1   CBE  CBD  110.98  3.000
 G6Y  H5   CBD  H4   107.54  3.000
 G6Y  H5   CBD  CBE  109.70  3.000
 G6Y  H4   CBD  CBE  109.62  3.000
 G6Y  H5   CBD  C4   108.60  3.000
 G6Y  H4   CBD  C4   110.21  3.000
 G6Y  CBE  CBD  C4   111.09  3.000
 G6Y  NAG  C2   N3   116.74  3.000
 G6Y  N3   C2   N1   126.36  3.000
 G6Y  NAG  C2   N1   116.89  3.000
 G6Y  H7   NAG  H6   117.58  3.000
 G6Y  H7   NAG  C2   119.03  3.000
 G6Y  H6   NAG  C2   119.26  3.000
 G6Y  H9   NAH  H8   117.29  3.000
 G6Y  H9   NAH  C6   120.28  3.000
 G6Y  H8   NAH  C6   119.05  3.000
 G6Y  CAJ  CAI  C5   180.00  3.000
 G6Y  CAK  CAJ  CAI  180.00  3.000
 G6Y  H10  CAK  CAL  107.91  3.000
 G6Y  H10  CAK  CBC  107.81  3.000
 G6Y  CAL  CAK  CBC  111.15  3.000
 G6Y  H10  CAK  CAJ  108.21  3.000
 G6Y  CAL  CAK  CAJ  110.43  3.000
 G6Y  CBC  CAK  CAJ  111.19  3.000
 G6Y  H13  CBC  H12  108.26  3.000
 G6Y  H13  CBC  H11  108.43  3.000
 G6Y  H12  CBC  H11  108.39  3.000
 G6Y  H13  CBC  CAK  110.16  3.000
 G6Y  H12  CBC  CAK  110.60  3.000
 G6Y  H11  CBC  CAK  110.92  3.000
 G6Y  CAQ  CAL  CAM  119.77  3.000
 G6Y  CAQ  CAL  CAK  120.28  3.000
 G6Y  CAM  CAL  CAK  119.92  3.000
 G6Y  H14  CAM  CAN  120.14  3.000
 G6Y  H14  CAM  CAL  119.29  3.000
 G6Y  CAN  CAM  CAL  120.56  3.000
 G6Y  H15  CAQ  CAP  119.25  3.000
 G6Y  H15  CAQ  CAL  120.48  3.000
 G6Y  CAP  CAQ  CAL  120.28  3.000
 G6Y  CAO  CAP  OAX  124.10  3.000
 G6Y  OAX  CAP  CAQ  116.05  3.000
 G6Y  CAO  CAP  CAQ  119.85  3.000
 G6Y  CAY  OAX  CAP  118.72  3.000
 G6Y  H18  CAY  H17  108.81  3.000
 G6Y  H18  CAY  H16  108.66  3.000
 G6Y  H17  CAY  H16  108.81  3.000
 G6Y  H18  CAY  OAX  106.48  3.000
 G6Y  H17  CAY  OAX  111.87  3.000
 G6Y  H16  CAY  OAX  112.10  3.000
 G6Y  H19  CAO  CAN  119.06  3.000
 G6Y  H19  CAO  CAP  120.77  3.000
 G6Y  CAN  CAO  CAP  120.15  3.000
 G6Y  CAR  CAN  CAO  119.92  3.000
 G6Y  CAO  CAN  CAM  119.39  3.000
 G6Y  CAR  CAN  CAM  120.69  3.000
 G6Y  CAW  CAR  CAS  117.91  3.000
 G6Y  CAW  CAR  CAN  121.00  3.000
 G6Y  CAS  CAR  CAN  121.09  3.000
 G6Y  H20  CAS  CAT  119.17  3.000
 G6Y  H20  CAS  CAR  119.90  3.000
 G6Y  CAT  CAS  CAR  120.92  3.000
 G6Y  H21  CAT  CAU  119.46  3.000
 G6Y  H21  CAT  CAS  119.40  3.000
 G6Y  CAU  CAT  CAS  121.14  3.000
 G6Y  CAV  CAU  CAZ  120.94  3.000
 G6Y  CAV  CAU  CAT  117.95  3.000
 G6Y  CAZ  CAU  CAT  121.11  3.000
 G6Y  OBA  CAZ  OBB  126.87  3.000
 G6Y  OBA  CAZ  CAU  116.54  3.000
 G6Y  OBB  CAZ  CAU  116.59  3.000
 G6Y  H23  CAV  CAW  119.38  3.000
 G6Y  H23  CAV  CAU  119.47  3.000
 G6Y  CAW  CAV  CAU  121.15  3.000
 G6Y  H24  CAW  CAV  119.15  3.000
 G6Y  H24  CAW  CAR  119.90  3.000
 G6Y  CAV  CAW  CAR  120.94  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
 G6Y  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 G6Y  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 G6Y  CONST_03  C2   N1   C6   C5     0.00   0.0  0
 G6Y  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 G6Y  CONST_05  N3   C2   N1   C6     0.00   0.0  0
 G6Y  CONST_06  N3   C4   C5   C6     0.00   0.0  0
 G6Y  CONST_07  CAR  CAN  CAM  CAL  180.00   0.0  0
 G6Y  CONST_08  CAO  CAN  CAM  CAL    0.00   0.0  0
 G6Y  CONST_09  CAO  CAP  CAQ  CAL    0.00   0.0  0
 G6Y  CONST_10  CAP  CAQ  CAL  CAM    0.00   0.0  0
 G6Y  CONST_13  CAP  CAO  CAN  CAM    0.00   0.0  0
 G6Y  CONST_14  CAN  CAM  CAL  CAQ    0.00   0.0  0
 G6Y  CONST_15  CAN  CAO  CAP  CAQ    0.00   0.0  0
 G6Y  CONST_16  CAR  CAN  CAO  CAP  180.00   0.0  0
 G6Y  CONST_19  CAT  CAS  CAR  CAN  180.00   0.0  0
 G6Y  CONST_20  CAV  CAW  CAR  CAN  180.00   0.0  0
 G6Y  CONST_21  CAU  CAT  CAS  CAR    0.00   0.0  0
 G6Y  CONST_22  CAU  CAV  CAW  CAR    0.00   0.0  0
 G6Y  CONST_23  CAV  CAU  CAT  CAS    0.00   0.0  0
 G6Y  CONST_24  CAV  CAW  CAR  CAS    0.00   0.0  0
 G6Y  CONST_25  CAW  CAR  CAS  CAT    0.00   0.0  0
 G6Y  CONST_26  CAW  CAV  CAU  CAT    0.00   0.0  0
 G6Y  CONST_27  NAH  C6   C5   C4   180.00   0.0  0
 G6Y  CONST_28  NAG  C2   N3   C4   180.00   0.0  0
 G6Y  CONST_29  NAG  C2   N1   C6   180.00   0.0  0
 G6Y  CONST_30  CBD  C4   C5   C6   180.00   0.0  0
 G6Y  CONST_31  CAI  C5   C6   N1   180.00   0.0  0
 G6Y  CONST_32  CAI  C5   C4   N3   180.00   0.0  0
 G6Y  CONST_33  C2   N3   C4   CBD  180.00   0.0  0
 G6Y  CONST_34  NAH  C6   N1   C2   180.00   0.0  0
 G6Y  CONST_35  CAN  CAM  CAL  CAK  180.00   0.0  0
 G6Y  CONST_36  CAP  CAQ  CAL  CAK  180.00   0.0  0
 G6Y  CONST_37  OAX  CAP  CAQ  CAL  180.00   0.0  0
 G6Y  CONST_38  CAN  CAO  CAP  OAX  180.00   0.0  0
 G6Y  CONST_39  CAZ  CAU  CAT  CAS  180.00   0.0  0
 G6Y  CONST_40  CAW  CAV  CAU  CAZ  180.00   0.0  0
 G6Y  CONST_41  H15  CAQ  CAL  CAM  180.00   0.0  0
 G6Y  CONST_42  H19  CAO  CAN  CAM  180.00   0.0  0
 G6Y  CONST_43  H14  CAM  CAL  CAQ  180.00   0.0  0
 G6Y  CONST_44  H20  CAS  CAR  CAN    0.00   0.0  0
 G6Y  CONST_45  H24  CAW  CAR  CAN    0.00   0.0  0
 G6Y  CONST_46  H21  CAT  CAS  CAR  180.00   0.0  0
 G6Y  CONST_47  H23  CAV  CAW  CAR  180.00   0.0  0
 G6Y  CONST_48  H8   NAH  C6   C5   180.00   0.0  0
 G6Y  CONST_49  H9   NAH  C6   C5     0.00   0.0  0
 G6Y  CONST_50  H6   NAG  C2   N1     0.00   0.0  0
 G6Y  CONST_51  H7   NAG  C2   N1   180.00   0.0  0
 G6Y  Var_01    CBE  CBD  C4   C5   -84.24  30.0  2
 G6Y  Var_02    CAO  CAP  OAX  CAY    1.72  30.0  2
 G6Y  Var_03    OBB  CAZ  CAU  CAT   -0.47  30.0  2
 G6Y  Var_04    H1   CBE  CBD  C4   -58.30  30.0  3
 G6Y  Var_05    H16  CAY  OAX  CAP  -62.06  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
 G6Y  chir_01  CAK  CBC  CAJ  CAL  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
 G6Y  plan-1  C4   0.020
 G6Y  plan-1  C5   0.020
 G6Y  plan-1  C6   0.020
 G6Y  plan-1  N1   0.020
 G6Y  plan-1  N3   0.020
 G6Y  plan-1  CBD  0.020
 G6Y  plan-1  C2   0.020
 G6Y  plan-1  NAG  0.020
 G6Y  plan-1  NAH  0.020
 G6Y  plan-1  CAI  0.020
 G6Y  plan-1  CAJ  0.020
 G6Y  plan-2  CAK  0.020
 G6Y  plan-2  CAL  0.020
 G6Y  plan-2  CAM  0.020
 G6Y  plan-2  CAQ  0.020
 G6Y  plan-2  CAP  0.020
 G6Y  plan-2  OAX  0.020
 G6Y  plan-2  CAO  0.020
 G6Y  plan-2  CAN  0.020
 G6Y  plan-2  CAR  0.020
 G6Y  plan-2  H14  0.020
 G6Y  plan-2  H15  0.020
 G6Y  plan-2  H19  0.020
 G6Y  plan-3  CAN  0.020
 G6Y  plan-3  CAR  0.020
 G6Y  plan-3  CAS  0.020
 G6Y  plan-3  CAT  0.020
 G6Y  plan-3  CAU  0.020
 G6Y  plan-3  CAZ  0.020
 G6Y  plan-3  CAV  0.020
 G6Y  plan-3  CAW  0.020
 G6Y  plan-3  H20  0.020
 G6Y  plan-3  H21  0.020
 G6Y  plan-3  H23  0.020
 G6Y  plan-3  H24  0.020
 G6Y  plan-4  C2   0.020
 G6Y  plan-4  NAG  0.020
 G6Y  plan-4  H6   0.020
 G6Y  plan-4  H7   0.020
 G6Y  plan-5  C6   0.020
 G6Y  plan-5  NAH  0.020
 G6Y  plan-5  H8   0.020
 G6Y  plan-5  H9   0.020
 G6Y  plan-6  CAU  0.020
 G6Y  plan-6  CAZ  0.020
 G6Y  plan-6  OBB  0.020
 G6Y  plan-6  OBA  0.020

