# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:11:00 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: (4-{6-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-4-yl}phenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#C[C@@H](C)c2cc3OCOc3c(c2)c4ccc(CC(O)=O)cc4
#
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
 O71  O71  '(4-{6-[(2S)-4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl]-2H-1,3-benzodioxol-4-yl}phenyl)acetic acid'  ligand  56  33  .  2021-08-17  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_O71
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
 O71  C4   C  CR6    0   0.264  -6.0423   0.9790   0.4970
 O71  C5   C  CR6    0  -0.340  -4.9348   0.2747   0.0293
 O71  C6   C  CR6    0   0.452  -5.0649  -0.3118  -1.2571
 O71  N1   N  N      0  -0.502  -6.1852  -0.1990  -1.9589
 O71  N3   N  N      0  -0.498  -7.1611   1.0887  -0.2081
 O71  C2   C  CR6    0   0.536  -7.1825   0.4879  -1.4032
 O71  CAI  C  CH2    0  -0.523  -5.9970   1.6967   1.8115
 O71  CAJ  C  CH3    0  -0.665  -5.4029   3.0969   1.6517
 O71  CAK  C  CSP    0   0.093  -3.7332   0.1289   0.7651
 O71  CAL  C  CSP    0   0.145  -2.6865  -0.0315   1.3458
 O71  CAM  C  CH1    0  -0.512  -1.4303  -0.2523   2.0586
 O71  CAN  C  CR6    0   0.160  -0.3562  -0.7749   1.1245
 O71  CAO  C  CR16   0  -0.415   0.9190  -0.2418   1.1852
 O71  CAP  C  CR6    0   0.016   1.9873  -0.7169   0.3986
 O71  CAQ  C  CR6    0   0.226   1.6723  -1.7537  -0.4537
 O71  CAR  C  CR6    0   0.332   0.3958  -2.2914  -0.5242
 O71  CAS  C  CR16   0  -0.404  -0.6401  -1.8341   0.2482
 O71  CAT  C  C      0   0.080   3.3337  -0.1269   0.4977
 O71  CAU  C  C1     0  -0.295   4.4834  -0.9177   0.4794
 O71  CAV  C  C1     0  -0.298   5.7388  -0.3460   0.6165
 O71  CAW  C  C      0   0.175   5.9000   1.0283   0.7725
 O71  CAX  C  C1     0  -0.297   4.7501   1.8140   0.7855
 O71  CAY  C  C1     0  -0.297   3.4909   1.2514   0.6527
 O71  CAZ  C  CH2    0  -0.700   7.2572   1.6379   0.9080
 O71  CBA  C  C      0   0.423   7.8999   2.0757  -0.4338
 O71  CBE  C  CH2    0   0.068   1.6292  -3.2321  -2.1110
 O71  CBG  C  CH3    0  -0.638  -1.6286  -1.1989   3.2515
 O71  NAG  N  NH2    0  -0.825  -4.0604  -1.0219  -1.7925
 O71  NAH  N  NH2    0  -0.819  -8.3305   0.5659  -2.1009
 O71  OBB  O  OC    -1  -0.623   9.0438   2.5619  -0.3384
 O71  OBC  O  O      0  -0.597   7.2378   1.9124  -1.4728
 O71  OBD  O  O2     0  -0.482   2.4792  -2.4069  -1.3278
 O71  OBF  O  O2     0  -0.487   0.3798  -3.2917  -1.4375
 O71  H1   H  HCH2   0   0.249  -7.0119   1.7711   2.2042
 O71  H2   H  HCH2   0   0.244  -5.4039   1.1299   2.5308
 O71  H3   H  HCH3   0   0.231  -4.3739   3.0501   1.2952
 O71  H4   H  HCH3   0   0.229  -5.9813   3.6885   0.9415
 O71  H5   H  HCH3   0   0.238  -5.4024   3.6234   2.6059
 O71  H6   H  HCH1   0   0.285  -1.0916   0.7127   2.4491
 O71  H7   H  HCR6   0   0.253   1.1116   0.5660   1.8815
 O71  H8   H  HCR6   0   0.265  -1.6283  -2.2744   0.1881
 O71  H9   H  H      0   0.246   4.4034  -1.9930   0.3870
 O71  H10  H  H      0   0.244   6.6114  -0.9888   0.6138
 O71  H11  H  H      0   0.243   4.8383   2.8878   0.9026
 O71  H12  H  H      0   0.249   2.6199   1.8953   0.6597
 O71  H13  H  HCH2   0   0.246   7.2139   2.5133   1.5631
 O71  H14  H  HCH2   0   0.245   7.9377   0.9347   1.3974
 O71  H15  H  HCH2   0   0.233   1.4950  -2.7911  -3.1049
 O71  H16  H  HCH2   0   0.247   2.0551  -4.2318  -2.1904
 O71  H17  H  HCH3   0   0.242  -0.6901  -1.3128   3.7939
 O71  H18  H  HCH3   0   0.241  -2.3756  -0.8027   3.9390
 O71  H19  H  HCH3   0   0.232  -1.9556  -2.1836   2.9179
 O71  H20  H  HNH2   0   0.400  -3.1393  -0.9731  -1.3917
 O71  H21  H  HNH2   0   0.397  -4.1276  -1.3112  -2.7536
 O71  H22  H  HNH2   0   0.394  -8.3390   0.2815  -3.0646
 O71  H23  H  HNH2   0   0.395  -9.0410   1.2102  -1.8012

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
 O71  OBC  CBA  deloc     1.243  0.020  1.243
 O71  OBB  CBA  deloc     1.247  0.020  1.247
 O71  CBA  CAZ  single    1.551  0.020  1.551
 O71  CAZ  CAW  single    1.494  0.020  1.494
 O71  NAG  C6   single    1.342  0.020  1.342
 O71  CAV  CAW  aromatic  1.392  0.020  1.392
 O71  CAV  CAU  aromatic  1.386  0.020  1.386
 O71  CAW  CAX  aromatic  1.393  0.020  1.393
 O71  N1   C6   aromatic  1.327  0.020  1.327
 O71  N1   C2   aromatic  1.332  0.020  1.332
 O71  NAH  C2   single    1.346  0.020  1.346
 O71  C6   C5   aromatic  1.420  0.020  1.420
 O71  C2   N3   aromatic  1.338  0.020  1.338
 O71  CAU  CAT  aromatic  1.396  0.020  1.396
 O71  CAX  CAY  aromatic  1.386  0.020  1.386
 O71  C5   CAK  single    1.417  0.020  1.417
 O71  C5   C4   aromatic  1.393  0.020  1.393
 O71  N3   C4   aromatic  1.327  0.020  1.327
 O71  CAT  CAY  aromatic  1.396  0.020  1.396
 O71  CAT  CAP  single    1.473  0.020  1.473
 O71  CAK  CAL  triple    1.208  0.020  1.208
 O71  C4   CAI  single    1.498  0.020  1.498
 O71  CAL  CAM  single    1.461  0.020  1.461
 O71  CAO  CAP  aromatic  1.409  0.020  1.409
 O71  CAO  CAN  aromatic  1.383  0.020  1.383
 O71  CAJ  CAI  single    1.529  0.020  1.529
 O71  CAP  CAQ  aromatic  1.379  0.020  1.379
 O71  CAM  CAN  single    1.516  0.020  1.516
 O71  CAM  CBG  single    1.536  0.020  1.536
 O71  CAN  CAS  aromatic  1.404  0.020  1.404
 O71  CAQ  OBD  single    1.357  0.020  1.357
 O71  CAQ  CAR  aromatic  1.387  0.020  1.387
 O71  CAS  CAR  aromatic  1.371  0.020  1.371
 O71  OBD  CBE  single    1.420  0.020  1.420
 O71  CAR  OBF  single    1.355  0.020  1.355
 O71  CBE  OBF  single    1.421  0.020  1.421
 O71  CAI  H1   single    0.970  0.020  1.090
 O71  CAI  H2   single    0.970  0.020  1.090
 O71  CAJ  H3   single    0.970  0.020  1.090
 O71  CAJ  H4   single    0.970  0.020  1.090
 O71  CAJ  H5   single    0.970  0.020  1.090
 O71  CAM  H6   single    0.970  0.020  1.090
 O71  CAO  H7   single    0.930  0.020  1.080
 O71  CAS  H8   single    0.930  0.020  1.080
 O71  CAU  H9   single    0.930  0.020  1.080
 O71  CAV  H10  single    0.930  0.020  1.080
 O71  CAX  H11  single    0.930  0.020  1.080
 O71  CAY  H12  single    0.930  0.020  1.080
 O71  CAZ  H13  single    0.970  0.020  1.090
 O71  CAZ  H14  single    0.970  0.020  1.090
 O71  CBE  H15  single    0.970  0.020  1.090
 O71  CBE  H16  single    0.970  0.020  1.090
 O71  CBG  H17  single    0.970  0.020  1.090
 O71  CBG  H18  single    0.970  0.020  1.090
 O71  CBG  H19  single    0.970  0.020  1.090
 O71  NAG  H20  single    0.890  0.020  1.040
 O71  NAG  H21  single    0.890  0.020  1.040
 O71  NAH  H22  single    0.890  0.020  1.040
 O71  NAH  H23  single    0.890  0.020  1.040

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
 O71  CAI  C4   N3   116.87  3.000
 O71  CAI  C4   C5   120.84  3.000
 O71  N3   C4   C5   122.25  3.000
 O71  CAK  C5   C6   120.39  3.000
 O71  CAK  C5   C4   123.50  3.000
 O71  C6   C5   C4   116.11  3.000
 O71  NAG  C6   N1   117.78  3.000
 O71  N1   C6   C5   121.44  3.000
 O71  NAG  C6   C5   120.77  3.000
 O71  C2   N1   C6   117.08  3.000
 O71  C2   N3   C4   116.81  3.000
 O71  NAH  C2   N3   116.80  3.000
 O71  N3   C2   N1   126.31  3.000
 O71  NAH  C2   N1   116.88  3.000
 O71  H2   CAI  H1   107.69  3.000
 O71  H2   CAI  CAJ  109.47  3.000
 O71  H1   CAI  CAJ  109.67  3.000
 O71  H2   CAI  C4   110.24  3.000
 O71  H1   CAI  C4   108.69  3.000
 O71  CAJ  CAI  C4   111.02  3.000
 O71  H5   CAJ  H4   107.97  3.000
 O71  H5   CAJ  H3   107.86  3.000
 O71  H4   CAJ  H3   108.12  3.000
 O71  H5   CAJ  CAI  110.55  3.000
 O71  H4   CAJ  CAI  111.02  3.000
 O71  H3   CAJ  CAI  111.20  3.000
 O71  CAL  CAK  C5   180.00  3.000
 O71  CAM  CAL  CAK  180.00  3.000
 O71  H6   CAM  CBG  107.83  3.000
 O71  H6   CAM  CAN  107.73  3.000
 O71  CBG  CAM  CAN  110.95  3.000
 O71  H6   CAM  CAL  107.86  3.000
 O71  CBG  CAM  CAL  111.16  3.000
 O71  CAN  CAM  CAL  111.14  3.000
 O71  CAS  CAN  CAO  120.30  3.000
 O71  CAS  CAN  CAM  120.09  3.000
 O71  CAO  CAN  CAM  119.54  3.000
 O71  H7   CAO  CAP  118.37  3.000
 O71  H7   CAO  CAN  118.64  3.000
 O71  CAP  CAO  CAN  122.98  3.000
 O71  CAT  CAP  CAQ  123.47  3.000
 O71  CAQ  CAP  CAO  115.18  3.000
 O71  CAT  CAP  CAO  121.35  3.000
 O71  OBD  CAQ  CAR  109.14  3.000
 O71  CAR  CAQ  CAP  122.23  3.000
 O71  OBD  CAQ  CAP  128.63  3.000
 O71  OBF  CAR  CAS  128.12  3.000
 O71  OBF  CAR  CAQ  109.35  3.000
 O71  CAS  CAR  CAQ  122.52  3.000
 O71  H8   CAS  CAR  121.50  3.000
 O71  H8   CAS  CAN  121.72  3.000
 O71  CAR  CAS  CAN  116.79  3.000
 O71  CAY  CAT  CAU  117.92  3.000
 O71  CAY  CAT  CAP  120.39  3.000
 O71  CAU  CAT  CAP  121.67  3.000
 O71  H9   CAU  CAV  119.02  3.000
 O71  H9   CAU  CAT  120.22  3.000
 O71  CAV  CAU  CAT  120.73  3.000
 O71  H10  CAV  CAW  119.50  3.000
 O71  H10  CAV  CAU  118.96  3.000
 O71  CAW  CAV  CAU  121.53  3.000
 O71  CAZ  CAW  CAX  121.27  3.000
 O71  CAX  CAW  CAV  117.53  3.000
 O71  CAZ  CAW  CAV  121.20  3.000
 O71  H11  CAX  CAY  119.12  3.000
 O71  H11  CAX  CAW  119.52  3.000
 O71  CAY  CAX  CAW  121.36  3.000
 O71  H12  CAY  CAX  119.26  3.000
 O71  H12  CAY  CAT  119.81  3.000
 O71  CAX  CAY  CAT  120.93  3.000
 O71  H14  CAZ  H13  105.73  3.000
 O71  H14  CAZ  CBA  108.10  3.000
 O71  H13  CAZ  CBA  107.97  3.000
 O71  H14  CAZ  CAW  110.08  3.000
 O71  H13  CAZ  CAW  110.17  3.000
 O71  CBA  CAZ  CAW  114.41  3.000
 O71  OBC  CBA  OBB  127.16  3.000
 O71  OBB  CBA  CAZ  115.10  3.000
 O71  OBC  CBA  CAZ  117.74  3.000
 O71  H16  CBE  H15  110.56  3.000
 O71  H16  CBE  OBF  109.86  3.000
 O71  H15  CBE  OBF  109.84  3.000
 O71  H16  CBE  OBD  109.83  3.000
 O71  H15  CBE  OBD  109.86  3.000
 O71  OBF  CBE  OBD  106.82  3.000
 O71  H19  CBG  H18  108.41  3.000
 O71  H19  CBG  H17  108.44  3.000
 O71  H18  CBG  H17  108.32  3.000
 O71  H19  CBG  CAM  110.97  3.000
 O71  H18  CBG  CAM  110.76  3.000
 O71  H17  CBG  CAM  109.86  3.000
 O71  H21  NAG  H20  117.12  3.000
 O71  H21  NAG  C6   118.92  3.000
 O71  H20  NAG  C6   120.07  3.000
 O71  H23  NAH  H22  117.49  3.000
 O71  H23  NAH  C2   119.06  3.000
 O71  H22  NAH  C2   119.22  3.000
 O71  CBE  OBD  CAQ  106.20  3.000
 O71  CBE  OBF  CAR  106.16  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
 O71  CONST_01  N1   C6   C5   C4     0.00   0.0  0
 O71  CONST_02  N1   C2   N3   C4     0.00   0.0  0
 O71  CONST_03  C2   N1   C6   C5     0.00   0.0  0
 O71  CONST_04  C2   N3   C4   C5     0.00   0.0  0
 O71  CONST_05  N3   C2   N1   C6     0.00   0.0  0
 O71  CONST_06  N3   C4   C5   C6     0.00   0.0  0
 O71  CONST_07  CAT  CAP  CAO  CAN  180.00   0.0  0
 O71  CONST_08  CAQ  CAP  CAO  CAN    0.00   0.0  0
 O71  CONST_09  CAQ  CAR  CAS  CAN    0.00   0.0  0
 O71  CONST_12  CAR  CAQ  CAP  CAO    0.00   0.0  0
 O71  CONST_13  CAR  CAS  CAN  CAO    0.00   0.0  0
 O71  CONST_14  CAV  CAU  CAT  CAP  180.00   0.0  0
 O71  CONST_15  CAX  CAY  CAT  CAP  180.00   0.0  0
 O71  CONST_16  CAS  CAN  CAO  CAP    0.00   0.0  0
 O71  CONST_17  CAS  CAR  CAQ  CAP    0.00   0.0  0
 O71  CONST_20  CAT  CAP  CAQ  CAR  180.00   0.0  0
 O71  CONST_21  CAW  CAV  CAU  CAT    0.00   0.0  0
 O71  CONST_22  CAW  CAX  CAY  CAT    0.00   0.0  0
 O71  CONST_23  CAX  CAW  CAV  CAU    0.00   0.0  0
 O71  CONST_24  CAX  CAY  CAT  CAU    0.00   0.0  0
 O71  CONST_25  CAY  CAX  CAW  CAV    0.00   0.0  0
 O71  CONST_26  CAY  CAT  CAU  CAV    0.00   0.0  0
 O71  CONST_27  OBD  CAQ  CAP  CAT    0.00   0.0  0
 O71  CONST_28  NAG  C6   C5   C4   180.00   0.0  0
 O71  CONST_29  NAH  C2   N3   C4   180.00   0.0  0
 O71  CONST_30  NAH  C2   N1   C6   180.00   0.0  0
 O71  CONST_31  CAI  C4   C5   C6   180.00   0.0  0
 O71  CONST_32  CAK  C5   C6   N1   180.00   0.0  0
 O71  CONST_33  CAK  C5   C4   N3   180.00   0.0  0
 O71  CONST_34  NAG  C6   N1   C2   180.00   0.0  0
 O71  CONST_35  CAI  C4   N3   C2   180.00   0.0  0
 O71  CONST_36  CAP  CAO  CAN  CAM  180.00   0.0  0
 O71  CONST_37  CAR  CAS  CAN  CAM  180.00   0.0  0
 O71  CONST_38  CAZ  CAW  CAV  CAU  180.00   0.0  0
 O71  CONST_39  CAZ  CAW  CAX  CAY  180.00   0.0  0
 O71  CONST_40  H8   CAS  CAN  CAO  180.00   0.0  0
 O71  CONST_41  H9   CAU  CAT  CAP    0.00   0.0  0
 O71  CONST_42  H12  CAY  CAT  CAP    0.00   0.0  0
 O71  CONST_43  H7   CAO  CAP  CAQ  180.00   0.0  0
 O71  CONST_44  H10  CAV  CAU  CAT  180.00   0.0  0
 O71  CONST_45  H11  CAX  CAY  CAT  180.00   0.0  0
 O71  CONST_46  H20  NAG  C6   C5     0.00   0.0  0
 O71  CONST_47  H21  NAG  C6   C5   180.00   0.0  0
 O71  CONST_48  H22  NAH  C2   N1     0.00   0.0  0
 O71  CONST_49  H23  NAH  C2   N1   180.00   0.0  0
 O71  Var_01    OBF  CBE  OBD  CAQ  -14.79  30.0  1
 O71  Var_02    OBD  CBE  OBF  CAR   14.92  30.0  1
 O71  Var_03    CAJ  CAI  C4   C5    85.36  30.0  2
 O71  Var_04    CBA  CAZ  CAW  CAV   91.15  30.0  2
 O71  Var_05    OBC  CBA  CAZ  CAW    1.45  30.0  1
 O71  Var_06    H3   CAJ  CAI  C4   -62.00  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
 O71  chir_01  CAM  CAL  CAN  CBG  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
 O71  plan-1  C4   0.020
 O71  plan-1  C5   0.020
 O71  plan-1  C6   0.020
 O71  plan-1  N1   0.020
 O71  plan-1  N3   0.020
 O71  plan-1  C2   0.020
 O71  plan-1  CAI  0.020
 O71  plan-1  CAK  0.020
 O71  plan-1  CAL  0.020
 O71  plan-1  NAG  0.020
 O71  plan-1  NAH  0.020
 O71  plan-2  CAP  0.020
 O71  plan-2  CAT  0.020
 O71  plan-2  CAU  0.020
 O71  plan-2  CAV  0.020
 O71  plan-2  CAW  0.020
 O71  plan-2  CAX  0.020
 O71  plan-2  CAY  0.020
 O71  plan-2  CAZ  0.020
 O71  plan-2  H9   0.020
 O71  plan-2  H10  0.020
 O71  plan-2  H11  0.020
 O71  plan-2  H12  0.020
 O71  plan-3  CAM  0.020
 O71  plan-3  CAN  0.020
 O71  plan-3  CAO  0.020
 O71  plan-3  CAP  0.020
 O71  plan-3  CAQ  0.020
 O71  plan-3  CAR  0.020
 O71  plan-3  CAS  0.020
 O71  plan-3  CAT  0.020
 O71  plan-3  OBD  0.020
 O71  plan-3  OBF  0.020
 O71  plan-3  H7   0.020
 O71  plan-3  H8   0.020
 O71  plan-4  C6   0.020
 O71  plan-4  NAG  0.020
 O71  plan-4  H20  0.020
 O71  plan-4  H21  0.020
 O71  plan-5  C2   0.020
 O71  plan-5  NAH  0.020
 O71  plan-5  H22  0.020
 O71  plan-5  H23  0.020
 O71  plan-6  CAZ  0.020
 O71  plan-6  CBA  0.020
 O71  plan-6  OBB  0.020
 O71  plan-6  OBC  0.020

