# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 13:23:34 2020
#   Inital geometry file: a 136 line input string
#   Ligand name: 4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-5-methoxy-phenyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cc(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
 U75  U75  '4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-5-methoxy-phenyl]benzoic acid'  ligand  52  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U75
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
 U75  C4   C  CR6   0   0.267  -4.8944  -0.2059  -0.0091
 U75  C5   C  CR6   0  -0.321  -4.2222  -1.0338   0.8886
 U75  C6   C  CR6   0   0.468  -4.7944  -2.3151   1.1070
 U75  N1   N  N     0  -0.505  -5.9036  -2.6922   0.4819
 U75  N3   N  N     0  -0.500  -6.0030  -0.5869  -0.6308
 U75  CAI  C  CH3   0  -0.673  -3.2414   1.0808  -1.3822
 U75  CAH  C  CH2   0  -0.527  -4.3629   1.1553  -0.3459
 U75  C2   C  CR6   0   0.540  -6.4538  -1.8174  -0.3581
 U75  NAJ  N  NH2   0  -0.820  -7.5583  -2.2149  -1.0134
 U75  NAG  N  NH2   0  -0.825  -4.2400  -3.1790   1.9656
 U75  CAK  C  CSP   0   0.154  -3.0292  -0.6425   1.5434
 U75  CAL  C  CSP   0   0.022  -2.0032  -0.3176   2.0904
 U75  CAM  C  CH2   0  -0.673  -0.7460   0.1199   2.6849
 U75  CAN  C  CR6   0   0.153   0.0996   0.8804   1.6872
 U75  CAO  C  CR16  0  -0.407   1.3303   0.3895   1.2913
 U75  CAS  C  CR16  0  -0.421  -0.3752   2.0838   1.1683
 U75  CAR  C  CR6   0   0.424   0.3944   2.7934   0.2547
 U75  OBB  O  O2    0  -0.471   0.0231   3.9600  -0.3039
 U75  CBC  C  CH3   0  -0.442  -1.2278   4.5133   0.0514
 U75  CAQ  C  CR16  0  -0.425   1.6374   2.2959  -0.1417
 U75  CAP  C  CR6   0   0.131   2.1104   1.0961   0.3696
 U75  CAT  C  CR6   0   0.092   3.4215   0.5672  -0.0551
 U75  CAU  C  CR16  0  -0.297   4.4955   1.4227  -0.3096
 U75  CAV  C  CR16  0  -0.240   5.7233   0.9218  -0.7012
 U75  CAW  C  CR6   0  -0.096   5.9120  -0.4504  -0.8512
 U75  CAZ  C  C     0   0.532   7.2469  -0.9406  -1.2695
 U75  OBD  O  OH1   0  -0.594   7.3020  -2.2603  -1.3831
 U75  OBA  O  O     0  -0.439   8.1911  -0.2185  -1.4860
 U75  CAX  C  CR16  0  -0.243   4.8446  -1.3117  -0.6027
 U75  CAY  C  CR16  0  -0.296   3.6179  -0.8060  -0.2100
 U75  H1   H  HCH3  0   0.237  -2.3719   0.5540  -0.9887
 U75  H2   H  HCH3  0   0.233  -3.5738   0.5702  -2.2864
 U75  H3   H  HCH3  0   0.235  -2.9184   2.0825  -1.6668
 U75  H4   H  HCH2  0   0.249  -5.1842   1.7581  -0.7352
 U75  H5   H  HCH2  0   0.244  -3.9933   1.6478   0.5564
 U75  H6   H  HNH2  0   0.395  -8.0183  -3.0663  -0.7438
 U75  H7   H  HNH2  0   0.395  -8.0794  -1.5476  -1.5537
 U75  H8   H  HNH2  0   0.405  -3.3506  -2.9888   2.3932
 U75  H9   H  HNH2  0   0.398  -4.6093  -4.1107   2.0417
 U75  H10  H  HCH2  0   0.289  -0.9475   0.7486   3.5577
 U75  H11  H  HCH2  0   0.287  -0.1953  -0.7480   3.0536
 U75  H12  H  HCR6  0   0.254   1.6962  -0.5372   1.7159
 U75  H13  H  HCR6  0   0.275  -1.3467   2.4423   1.4848
 U75  H14  H  HCH3  0   0.232  -1.2932   4.7236   1.1219
 U75  H15  H  HCH3  0   0.264  -1.3208   5.4475  -0.4969
 U75  H16  H  HCH3  0   0.224  -2.0584   3.8599  -0.2304
 U75  H17  H  HCR6  0   0.263   2.2141   2.8508  -0.8718
 U75  H18  H  HCR6  0   0.263   4.3806   2.4910  -0.1799
 U75  H19  H  HCR6  0   0.267   6.5417   1.6050  -0.8836
 U75  H20  H  HOH1  0   0.488   8.1895  -2.5329  -1.6593
 U75  H21  H  HCR6  0   0.270   4.9551  -2.3809  -0.7179
 U75  H22  H  HCR6  0   0.265   2.7980  -1.4922  -0.0415

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
 U75  NAG  C6   single    1.338  0.020  1.338
 U75  N1   C6   aromatic  1.328  0.020  1.328
 U75  N1   C2   aromatic  1.332  0.020  1.332
 U75  NAJ  C2   single    1.344  0.020  1.344
 U75  C6   C5   aromatic  1.420  0.020  1.420
 U75  C2   N3   aromatic  1.339  0.020  1.339
 U75  OBA  CAZ  double    1.208  0.020  1.208
 U75  C5   CAK  single    1.416  0.020  1.416
 U75  C5   C4   aromatic  1.394  0.020  1.394
 U75  N3   C4   aromatic  1.327  0.020  1.327
 U75  CAX  CAY  aromatic  1.384  0.020  1.384
 U75  CAX  CAW  aromatic  1.394  0.020  1.394
 U75  CAK  CAL  triple    1.207  0.020  1.207
 U75  C4   CAH  single    1.500  0.020  1.500
 U75  CAY  CAT  aromatic  1.396  0.020  1.396
 U75  CAL  CAM  single    1.458  0.020  1.458
 U75  CAZ  CAW  single    1.482  0.020  1.482
 U75  CAZ  OBD  single    1.326  0.020  1.326
 U75  CAI  CAH  single    1.529  0.020  1.529
 U75  CAW  CAV  aromatic  1.393  0.020  1.393
 U75  CAM  CAN  single    1.513  0.020  1.513
 U75  CAO  CAN  aromatic  1.383  0.020  1.383
 U75  CAO  CAP  aromatic  1.399  0.020  1.399
 U75  CAN  CAS  aromatic  1.394  0.020  1.394
 U75  CAT  CAP  single    1.476  0.020  1.476
 U75  CAT  CAU  aromatic  1.396  0.020  1.396
 U75  CAP  CAQ  aromatic  1.387  0.020  1.387
 U75  CAV  CAU  aromatic  1.383  0.020  1.383
 U75  CAS  CAR  aromatic  1.389  0.020  1.389
 U75  CAQ  CAR  aromatic  1.396  0.020  1.396
 U75  CAR  OBB  single    1.346  0.020  1.346
 U75  OBB  CBC  single    1.413  0.020  1.413
 U75  CAI  H1   single    0.970  0.020  1.090
 U75  CAI  H2   single    0.970  0.020  1.090
 U75  CAI  H3   single    0.970  0.020  1.090
 U75  CAH  H4   single    0.970  0.020  1.090
 U75  CAH  H5   single    0.970  0.020  1.090
 U75  NAJ  H6   single    0.860  0.020  1.020
 U75  NAJ  H7   single    0.860  0.020  1.020
 U75  NAG  H8   single    0.860  0.020  1.020
 U75  NAG  H9   single    0.860  0.020  1.020
 U75  CAM  H10  single    0.970  0.020  1.090
 U75  CAM  H11  single    0.970  0.020  1.090
 U75  CAO  H12  single    0.930  0.020  1.080
 U75  CAS  H13  single    0.930  0.020  1.080
 U75  CBC  H14  single    0.970  0.020  1.090
 U75  CBC  H15  single    0.970  0.020  1.090
 U75  CBC  H16  single    0.970  0.020  1.090
 U75  CAQ  H17  single    0.930  0.020  1.080
 U75  CAU  H18  single    0.930  0.020  1.080
 U75  CAV  H19  single    0.930  0.020  1.080
 U75  OBD  H20  single    0.850  0.020  0.980
 U75  CAX  H21  single    0.930  0.020  1.080
 U75  CAY  H22  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
 U75  CAH  C4   N3   116.84  3.000
 U75  CAH  C4   C5   120.86  3.000
 U75  N3   C4   C5   122.28  3.000
 U75  CAK  C5   C6   121.18  3.000
 U75  CAK  C5   C4   122.67  3.000
 U75  C6   C5   C4   116.15  3.000
 U75  NAG  C6   N1   117.69  3.000
 U75  N1   C6   C5   121.36  3.000
 U75  NAG  C6   C5   120.95  3.000
 U75  C2   N1   C6   117.09  3.000
 U75  C2   N3   C4   116.74  3.000
 U75  H3   CAI  H2   107.70  3.000
 U75  H3   CAI  H1   107.57  3.000
 U75  H2   CAI  H1   108.44  3.000
 U75  H3   CAI  CAH  110.45  3.000
 U75  H2   CAI  CAH  111.18  3.000
 U75  H1   CAI  CAH  111.35  3.000
 U75  H5   CAH  H4   107.48  3.000
 U75  H5   CAH  CAI  109.50  3.000
 U75  H4   CAH  CAI  109.73  3.000
 U75  H5   CAH  C4   110.09  3.000
 U75  H4   CAH  C4   108.36  3.000
 U75  CAI  CAH  C4   111.59  3.000
 U75  NAJ  C2   N3   116.69  3.000
 U75  N3   C2   N1   126.39  3.000
 U75  NAJ  C2   N1   116.91  3.000
 U75  H7   NAJ  H6   118.02  3.000
 U75  H7   NAJ  C2   119.48  3.000
 U75  H6   NAJ  C2   119.74  3.000
 U75  H9   NAG  H8   117.93  3.000
 U75  H9   NAG  C6   119.66  3.000
 U75  H8   NAG  C6   121.16  3.000
 U75  CAL  CAK  C5   180.00  3.000
 U75  CAM  CAL  CAK  180.00  3.000
 U75  H11  CAM  H10  106.27  3.000
 U75  H11  CAM  CAN  109.89  3.000
 U75  H10  CAM  CAN  109.89  3.000
 U75  H11  CAM  CAL  109.52  3.000
 U75  H10  CAM  CAL  109.81  3.000
 U75  CAN  CAM  CAL  111.34  3.000
 U75  CAS  CAN  CAO  120.20  3.000
 U75  CAS  CAN  CAM  119.28  3.000
 U75  CAO  CAN  CAM  120.52  3.000
 U75  H12  CAO  CAP  120.14  3.000
 U75  H12  CAO  CAN  119.48  3.000
 U75  CAP  CAO  CAN  120.37  3.000
 U75  H13  CAS  CAR  121.34  3.000
 U75  H13  CAS  CAN  118.86  3.000
 U75  CAR  CAS  CAN  119.81  3.000
 U75  CAQ  CAR  OBB  115.89  3.000
 U75  OBB  CAR  CAS  124.26  3.000
 U75  CAQ  CAR  CAS  119.85  3.000
 U75  CBC  OBB  CAR  118.64  3.000
 U75  H16  CBC  H15  108.57  3.000
 U75  H16  CBC  H14  108.78  3.000
 U75  H15  CBC  H14  108.88  3.000
 U75  H16  CBC  OBB  111.94  3.000
 U75  H15  CBC  OBB  106.58  3.000
 U75  H14  CBC  OBB  112.00  3.000
 U75  H17  CAQ  CAP  120.66  3.000
 U75  H17  CAQ  CAR  118.86  3.000
 U75  CAP  CAQ  CAR  120.47  3.000
 U75  CAT  CAP  CAQ  120.44  3.000
 U75  CAQ  CAP  CAO  119.31  3.000
 U75  CAT  CAP  CAO  120.25  3.000
 U75  CAY  CAT  CAU  118.31  3.000
 U75  CAU  CAT  CAP  121.07  3.000
 U75  CAY  CAT  CAP  120.62  3.000
 U75  H18  CAU  CAV  119.07  3.000
 U75  H18  CAU  CAT  120.08  3.000
 U75  CAV  CAU  CAT  120.84  3.000
 U75  H19  CAV  CAW  120.10  3.000
 U75  H19  CAV  CAU  119.40  3.000
 U75  CAW  CAV  CAU  120.50  3.000
 U75  CAX  CAW  CAZ  122.39  3.000
 U75  CAZ  CAW  CAV  118.56  3.000
 U75  CAX  CAW  CAV  119.06  3.000
 U75  OBA  CAZ  OBD  123.17  3.000
 U75  OBD  CAZ  CAW  113.00  3.000
 U75  OBA  CAZ  CAW  123.83  3.000
 U75  H20  OBD  CAZ  110.04  3.000
 U75  H21  CAX  CAY  118.84  3.000
 U75  H21  CAX  CAW  120.92  3.000
 U75  CAY  CAX  CAW  120.24  3.000
 U75  H22  CAY  CAX  118.95  3.000
 U75  H22  CAY  CAT  119.99  3.000
 U75  CAX  CAY  CAT  121.05  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
 U75  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 U75  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 U75  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 U75  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 U75  CONST_05  N3   C2   N1   C6      0.00   0.0  0
 U75  CONST_06  N3   C4   C5   C6      0.00   0.0  0
 U75  CONST_07  CAT  CAP  CAO  CAN   180.00   0.0  0
 U75  CONST_08  CAQ  CAP  CAO  CAN     0.00   0.0  0
 U75  CONST_09  CAQ  CAR  CAS  CAN     0.00   0.0  0
 U75  CONST_10  CAR  CAS  CAN  CAO     0.00   0.0  0
 U75  CONST_13  CAR  CAQ  CAP  CAO     0.00   0.0  0
 U75  CONST_14  CAP  CAO  CAN  CAS     0.00   0.0  0
 U75  CONST_15  CAP  CAQ  CAR  CAS     0.00   0.0  0
 U75  CONST_16  CAT  CAP  CAQ  CAR   180.00   0.0  0
 U75  CONST_19  CAX  CAY  CAT  CAP   180.00   0.0  0
 U75  CONST_20  CAV  CAU  CAT  CAP   180.00   0.0  0
 U75  CONST_21  CAW  CAX  CAY  CAT     0.00   0.0  0
 U75  CONST_22  CAW  CAV  CAU  CAT     0.00   0.0  0
 U75  CONST_23  CAX  CAY  CAT  CAU     0.00   0.0  0
 U75  CONST_24  CAX  CAW  CAV  CAU     0.00   0.0  0
 U75  CONST_25  CAY  CAX  CAW  CAV     0.00   0.0  0
 U75  CONST_26  CAY  CAT  CAU  CAV     0.00   0.0  0
 U75  CONST_27  NAG  C6   C5   C4    180.00   0.0  0
 U75  CONST_28  NAJ  C2   N3   C4    180.00   0.0  0
 U75  CONST_29  NAJ  C2   N1   C6    180.00   0.0  0
 U75  CONST_30  CAH  C4   C5   C6    180.00   0.0  0
 U75  CONST_31  CAK  C5   C6   N1    180.00   0.0  0
 U75  CONST_32  CAK  C5   C4   N3    180.00   0.0  0
 U75  CONST_33  C2   N3   C4   CAH   180.00   0.0  0
 U75  CONST_34  NAG  C6   N1   C2    180.00   0.0  0
 U75  CONST_35  CAP  CAO  CAN  CAM   180.00   0.0  0
 U75  CONST_36  CAR  CAS  CAN  CAM   180.00   0.0  0
 U75  CONST_37  OBB  CAR  CAS  CAN   180.00   0.0  0
 U75  CONST_38  CAP  CAQ  CAR  OBB   180.00   0.0  0
 U75  CONST_39  CAZ  CAW  CAV  CAU   180.00   0.0  0
 U75  CONST_40  CAY  CAX  CAW  CAZ   180.00   0.0  0
 U75  CONST_41  H13  CAS  CAN  CAO   180.00   0.0  0
 U75  CONST_42  H17  CAQ  CAP  CAO   180.00   0.0  0
 U75  CONST_43  H12  CAO  CAN  CAS   180.00   0.0  0
 U75  CONST_44  H22  CAY  CAT  CAP     0.00   0.0  0
 U75  CONST_45  H18  CAU  CAT  CAP     0.00   0.0  0
 U75  CONST_46  H21  CAX  CAY  CAT   180.00   0.0  0
 U75  CONST_47  H19  CAV  CAU  CAT   180.00   0.0  0
 U75  CONST_48  H8   NAG  C6   C5      0.00   0.0  0
 U75  CONST_49  H9   NAG  C6   C5    180.00   0.0  0
 U75  CONST_50  H6   NAJ  C2   N1      0.00   0.0  0
 U75  CONST_51  H7   NAJ  C2   N1    180.00   0.0  0
 U75  CONST_52  H20  OBD  CAZ  CAW   180.00   0.0  0
 U75  Var_01    CAI  CAH  C4   C5     80.27  30.0  2
 U75  Var_02    CAO  CAN  CAM  CAL  -116.61  30.0  2
 U75  Var_03    CAQ  CAR  OBB  CBC   179.70  30.0  3
 U75  Var_04    OBA  CAZ  CAW  CAV     0.26  30.0  2
 U75  Var_05    CAN  CAM  CAL  CAK    -8.39  30.0  3
 U75  Var_06    H1   CAI  CAH  C4    -64.64  30.0  3
 U75  Var_07    H14  CBC  OBB  CAR    60.33  30.0  3

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
 U75  plan-1  C4   0.020
 U75  plan-1  C5   0.020
 U75  plan-1  C6   0.020
 U75  plan-1  N1   0.020
 U75  plan-1  N3   0.020
 U75  plan-1  CAH  0.020
 U75  plan-1  C2   0.020
 U75  plan-1  NAJ  0.020
 U75  plan-1  NAG  0.020
 U75  plan-1  CAK  0.020
 U75  plan-1  CAL  0.020
 U75  plan-2  CAM  0.020
 U75  plan-2  CAN  0.020
 U75  plan-2  CAO  0.020
 U75  plan-2  CAS  0.020
 U75  plan-2  CAR  0.020
 U75  plan-2  OBB  0.020
 U75  plan-2  CAQ  0.020
 U75  plan-2  CAP  0.020
 U75  plan-2  CAT  0.020
 U75  plan-2  H12  0.020
 U75  plan-2  H13  0.020
 U75  plan-2  H17  0.020
 U75  plan-3  CAP  0.020
 U75  plan-3  CAT  0.020
 U75  plan-3  CAU  0.020
 U75  plan-3  CAV  0.020
 U75  plan-3  CAW  0.020
 U75  plan-3  CAZ  0.020
 U75  plan-3  CAX  0.020
 U75  plan-3  CAY  0.020
 U75  plan-3  H18  0.020
 U75  plan-3  H19  0.020
 U75  plan-3  H21  0.020
 U75  plan-3  H22  0.020
 U75  plan-4  C2   0.020
 U75  plan-4  NAJ  0.020
 U75  plan-4  H6   0.020
 U75  plan-4  H7   0.020
 U75  plan-5  C6   0.020
 U75  plan-5  NAG  0.020
 U75  plan-5  H8   0.020
 U75  plan-5  H9   0.020
 U75  plan-6  CAW  0.020
 U75  plan-6  CAZ  0.020
 U75  plan-6  OBD  0.020
 U75  plan-6  OBA  0.020
 U75  plan-6  H20  0.020

