# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  2 18:56:44 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]-4-methoxy-phenyl]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1nc(N)nc(N)c1C#CCc2cc(ccc2OC)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
 U06  U06  '4-[3-[3-[2,4-bis(azanyl)-6-ethyl-pyrimidin-5-yl]prop-2-ynyl]-4-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_U06
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
 U06  C4   C  CR6   0   0.460   4.7622  -1.5238  -1.1407
 U06  C5   C  CR6   0  -0.203   4.0484  -0.5400  -0.4107
 U06  C6   C  CR6   0   0.268   4.4611  -0.3315   0.9037
 U06  N1   N  N     0  -0.590   5.4712  -1.0029   1.4435
 U06  N3   N  N     0  -0.530   5.7704  -2.1952  -0.5971
 U06  CAA  C  CH3   0  -0.645   2.4535   0.0432   2.3505
 U06  CAB  C  CH2   0  -0.594   3.7388   0.6442   1.7825
 U06  C2   C  CR6   0   0.549   6.0798  -1.8994   0.6622
 U06  NAF  N  NH2   0  -0.811   7.1378  -2.5476   1.1957
 U06  NAI  N  NH2   0  -0.777   4.4372  -1.8062  -2.4075
 U06  CAK  C  CSP   0   0.078   2.9678   0.1696  -0.9889
 U06  CAL  C  CSP   0  -0.026   2.0390   0.7835  -1.4540
 U06  CAM  C  CH2   0  -0.669   0.8793   1.5266  -1.9330
 U06  CAN  C  CR6   0   0.045  -0.1923   1.6163  -0.8731
 U06  CAU  C  CR16  0  -0.194  -1.3769   0.9164  -0.9984
 U06  CAO  C  CR6   0   0.302   0.0186   2.3958   0.2739
 U06  OAP  O  O2    0  -0.483   1.1861   3.0571   0.3297
 U06  CAQ  C  CH3   0  -0.457   1.4648   3.8517   1.4617
 U06  CAR  C  CR16  0  -0.338  -0.9573   2.4434   1.2630
 U06  CAS  C  CR16  0  -0.262  -2.1342   1.7250   1.1133
 U06  CAT  C  CR6   0  -0.048  -2.3711   0.9520  -0.0168
 U06  CAV  C  CR6   0   0.062  -3.6291   0.2045  -0.1823
 U06  CAW  C  CR16  0  -0.220  -4.2420  -0.4220   0.9046
 U06  CAX  C  CR16  0  -0.303  -5.4285  -1.1125   0.7503
 U06  CAY  C  CR6   0  -0.082  -6.0378  -1.1998  -0.4985
 U06  CBB  C  C     0   0.541  -7.3100  -1.9492  -0.6074
 U06  OBD  O  O     0  -0.496  -7.8544  -2.5010   0.3129
 U06  OBC  O  OH1   0  -0.544  -7.8073  -1.9545  -1.8467
 U06  CAZ  C  CR16  0  -0.243  -5.4330  -0.5825  -1.5906
 U06  CBA  C  CR16  0  -0.280  -4.2462   0.1092  -1.4303
 U06  H1   H  HCH3  0   0.266   1.7466  -0.2034   1.5585
 U06  H2   H  HCH3  0   0.185   2.6600  -0.8632   2.9198
 U06  H3   H  HCH3  0   0.253   1.9649   0.7509   3.0205
 U06  H4   H  HCH2  0   0.273   4.4019   0.9382   2.5968
 U06  H5   H  HCH2  0   0.238   3.4923   1.5424   1.2136
 U06  H6   H  HNH2  0   0.401   7.4850  -3.3664   0.7312
 U06  H7   H  HNH2  0   0.414   7.2716  -2.5046   2.1891
 U06  H8   H  HNH2  0   0.415   3.6857  -1.3331  -2.8747
 U06  H9   H  HNH2  0   0.399   4.9456  -2.5056  -2.9152
 U06  H10  H  HCH2  0   0.273   1.1863   2.5248  -2.2573
 U06  H11  H  HCH2  0   0.300   0.4759   1.0335  -2.8200
 U06  H12  H  HCR6  0   0.256  -1.5217   0.3010  -1.8789
 U06  H13  H  HCH3  0   0.268   2.4455   4.2902   1.3002
 U06  H14  H  HCH3  0   0.215   0.7395   4.6595   1.5853
 U06  H15  H  HCH3  0   0.272   1.4928   3.2596   2.3803
 U06  H16  H  HCR6  0   0.292  -0.8290   3.0434   2.1530
 U06  H17  H  HCR6  0   0.266  -2.8839   1.8024   1.8900
 U06  H18  H  HCR6  0   0.251  -3.7731  -0.3878   1.8794
 U06  H19  H  HCR6  0   0.251  -5.8853  -1.5975   1.6022
 U06  H20  H  HOH1  0   0.512  -8.6325  -2.4562  -1.8382
 U06  H21  H  HCR6  0   0.237  -5.8873  -0.6292  -2.5703
 U06  H22  H  HCR6  0   0.251  -3.8070   0.6086  -2.2844

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
 U06  OBD  CBB  double    1.203  0.020  1.203
 U06  NAI  C4   single    1.338  0.020  1.338
 U06  N3   C4   aromatic  1.328  0.020  1.328
 U06  N3   C2   aromatic  1.330  0.020  1.330
 U06  CBB  OBC  single    1.335  0.020  1.335
 U06  CBB  CAY  single    1.481  0.020  1.481
 U06  NAF  C2   single    1.351  0.020  1.351
 U06  C4   C5   aromatic  1.418  0.020  1.418
 U06  CAZ  CAY  aromatic  1.393  0.020  1.393
 U06  CAZ  CBA  aromatic  1.383  0.020  1.383
 U06  C2   N1   aromatic  1.336  0.020  1.336
 U06  CAY  CAX  aromatic  1.392  0.020  1.392
 U06  CBA  CAV  aromatic  1.395  0.020  1.395
 U06  C5   CAK  single    1.416  0.020  1.416
 U06  C5   C6   aromatic  1.393  0.020  1.393
 U06  N1   C6   aromatic  1.328  0.020  1.328
 U06  CAK  CAL  triple    1.207  0.020  1.207
 U06  C6   CAB  single    1.499  0.020  1.499
 U06  CAX  CAW  aromatic  1.381  0.020  1.381
 U06  CAA  CAB  single    1.528  0.020  1.528
 U06  CAV  CAW  aromatic  1.396  0.020  1.396
 U06  CAV  CAT  single    1.473  0.020  1.473
 U06  CAL  CAM  single    1.458  0.020  1.458
 U06  CAU  CAT  aromatic  1.398  0.020  1.398
 U06  CAU  CAN  aromatic  1.382  0.020  1.382
 U06  CAM  CAN  single    1.510  0.020  1.510
 U06  CAT  CAS  aromatic  1.390  0.020  1.390
 U06  CAN  CAO  aromatic  1.403  0.020  1.403
 U06  CAS  CAR  aromatic  1.387  0.020  1.387
 U06  CAO  CAR  aromatic  1.390  0.020  1.390
 U06  CAO  OAP  single    1.343  0.020  1.343
 U06  OAP  CAQ  single    1.411  0.020  1.411
 U06  CAA  H1   single    0.970  0.020  1.090
 U06  CAA  H2   single    0.970  0.020  1.090
 U06  CAA  H3   single    0.970  0.020  1.090
 U06  CAB  H4   single    0.970  0.020  1.090
 U06  CAB  H5   single    0.970  0.020  1.090
 U06  NAF  H6   single    0.890  0.020  1.040
 U06  NAF  H7   single    0.890  0.020  1.040
 U06  NAI  H8   single    0.860  0.020  1.020
 U06  NAI  H9   single    0.860  0.020  1.020
 U06  CAM  H10  single    0.970  0.020  1.090
 U06  CAM  H11  single    0.970  0.020  1.090
 U06  CAU  H12  single    0.930  0.020  1.080
 U06  CAQ  H13  single    0.970  0.020  1.090
 U06  CAQ  H14  single    0.970  0.020  1.090
 U06  CAQ  H15  single    0.970  0.020  1.090
 U06  CAR  H16  single    0.930  0.020  1.080
 U06  CAS  H17  single    0.930  0.020  1.080
 U06  CAW  H18  single    0.930  0.020  1.080
 U06  CAX  H19  single    0.930  0.020  1.080
 U06  OBC  H20  single    0.850  0.020  0.980
 U06  CAZ  H21  single    0.930  0.020  1.080
 U06  CBA  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
 U06  NAI  C4   N3   117.74  3.000
 U06  N3   C4   C5   121.49  3.000
 U06  NAI  C4   C5   120.78  3.000
 U06  CAK  C5   C6   122.42  3.000
 U06  C6   C5   C4   116.13  3.000
 U06  CAK  C5   C4   121.44  3.000
 U06  CAB  C6   N1   117.23  3.000
 U06  CAB  C6   C5   120.52  3.000
 U06  N1   C6   C5   122.23  3.000
 U06  C2   N1   C6   116.63  3.000
 U06  C2   N3   C4   116.86  3.000
 U06  H3   CAA  H2   107.69  3.000
 U06  H3   CAA  H1   107.63  3.000
 U06  H2   CAA  H1   108.32  3.000
 U06  H3   CAA  CAB  110.49  3.000
 U06  H2   CAA  CAB  111.21  3.000
 U06  H1   CAA  CAB  111.37  3.000
 U06  H5   CAB  H4   107.74  3.000
 U06  H5   CAB  CAA  109.11  3.000
 U06  H4   CAB  CAA  109.87  3.000
 U06  H5   CAB  C6   109.81  3.000
 U06  H4   CAB  C6   108.68  3.000
 U06  CAA  CAB  C6   111.54  3.000
 U06  NAF  C2   N3   116.71  3.000
 U06  NAF  C2   N1   116.61  3.000
 U06  N3   C2   N1   126.66  3.000
 U06  H7   NAF  H6   116.56  3.000
 U06  H7   NAF  C2   118.36  3.000
 U06  H6   NAF  C2   118.68  3.000
 U06  H9   NAI  H8   118.22  3.000
 U06  H9   NAI  C4   120.23  3.000
 U06  H8   NAI  C4   121.55  3.000
 U06  CAL  CAK  C5   180.00  3.000
 U06  CAM  CAL  CAK  180.00  3.000
 U06  H11  CAM  H10  105.96  3.000
 U06  H11  CAM  CAN  109.56  3.000
 U06  H10  CAM  CAN  110.69  3.000
 U06  H11  CAM  CAL  109.29  3.000
 U06  H10  CAM  CAL  109.83  3.000
 U06  CAN  CAM  CAL  111.35  3.000
 U06  CAO  CAN  CAU  118.99  3.000
 U06  CAO  CAN  CAM  120.02  3.000
 U06  CAU  CAN  CAM  120.98  3.000
 U06  H12  CAU  CAT  119.34  3.000
 U06  H12  CAU  CAN  118.41  3.000
 U06  CAT  CAU  CAN  122.23  3.000
 U06  CAR  CAO  OAP  124.32  3.000
 U06  OAP  CAO  CAN  116.00  3.000
 U06  CAR  CAO  CAN  119.68  3.000
 U06  CAQ  OAP  CAO  118.85  3.000
 U06  H15  CAQ  H14  108.80  3.000
 U06  H15  CAQ  H13  108.68  3.000
 U06  H14  CAQ  H13  108.52  3.000
 U06  H15  CAQ  OAP  111.98  3.000
 U06  H14  CAQ  OAP  112.09  3.000
 U06  H13  CAQ  OAP  106.64  3.000
 U06  H16  CAR  CAS  118.49  3.000
 U06  H16  CAR  CAO  121.43  3.000
 U06  CAS  CAR  CAO  120.07  3.000
 U06  H17  CAS  CAT  120.36  3.000
 U06  H17  CAS  CAR  118.25  3.000
 U06  CAT  CAS  CAR  121.37  3.000
 U06  CAV  CAT  CAS  121.30  3.000
 U06  CAS  CAT  CAU  117.65  3.000
 U06  CAV  CAT  CAU  121.05  3.000
 U06  CBA  CAV  CAW  118.12  3.000
 U06  CAW  CAV  CAT  121.01  3.000
 U06  CBA  CAV  CAT  120.86  3.000
 U06  H18  CAW  CAX  119.23  3.000
 U06  H18  CAW  CAV  119.79  3.000
 U06  CAX  CAW  CAV  120.96  3.000
 U06  H19  CAX  CAY  119.57  3.000
 U06  H19  CAX  CAW  119.94  3.000
 U06  CAY  CAX  CAW  120.49  3.000
 U06  CAZ  CAY  CBB  122.67  3.000
 U06  CAZ  CAY  CAX  119.05  3.000
 U06  CBB  CAY  CAX  118.28  3.000
 U06  OBC  CBB  OBD  122.65  3.000
 U06  OBC  CBB  CAY  112.98  3.000
 U06  OBD  CBB  CAY  124.37  3.000
 U06  H20  OBC  CBB  108.19  3.000
 U06  H21  CAZ  CBA  119.17  3.000
 U06  H21  CAZ  CAY  120.60  3.000
 U06  CBA  CAZ  CAY  120.23  3.000
 U06  H22  CBA  CAZ  119.18  3.000
 U06  H22  CBA  CAV  119.65  3.000
 U06  CAZ  CBA  CAV  121.15  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
 U06  CONST_01  N1   C2   N3   C4      0.00   0.0  0
 U06  CONST_02  N1   C6   C5   C4      0.00   0.0  0
 U06  CONST_03  C2   N3   C4   C5      0.00   0.0  0
 U06  CONST_04  C2   N1   C6   C5      0.00   0.0  0
 U06  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 U06  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 U06  CONST_07  CAV  CAT  CAU  CAN   180.00   0.0  0
 U06  CONST_08  CAS  CAT  CAU  CAN     0.00   0.0  0
 U06  CONST_09  CAS  CAR  CAO  CAN     0.00   0.0  0
 U06  CONST_12  CAR  CAS  CAT  CAU     0.00   0.0  0
 U06  CONST_13  CAR  CAO  CAN  CAU     0.00   0.0  0
 U06  CONST_14  CAT  CAU  CAN  CAO     0.00   0.0  0
 U06  CONST_15  CAT  CAS  CAR  CAO     0.00   0.0  0
 U06  CONST_16  CAV  CAT  CAS  CAR   180.00   0.0  0
 U06  CONST_19  CAZ  CBA  CAV  CAT   180.00   0.0  0
 U06  CONST_20  CAX  CAW  CAV  CAT   180.00   0.0  0
 U06  CONST_21  CAY  CAZ  CBA  CAV     0.00   0.0  0
 U06  CONST_22  CAY  CAX  CAW  CAV     0.00   0.0  0
 U06  CONST_23  CAZ  CAY  CAX  CAW     0.00   0.0  0
 U06  CONST_24  CAZ  CBA  CAV  CAW     0.00   0.0  0
 U06  CONST_25  CBA  CAZ  CAY  CAX     0.00   0.0  0
 U06  CONST_26  CBA  CAV  CAW  CAX     0.00   0.0  0
 U06  CONST_27  NAF  C2   N3   C4    180.00   0.0  0
 U06  CONST_28  CAB  C6   C5   C4    180.00   0.0  0
 U06  CONST_29  NAI  C4   C5   C6    180.00   0.0  0
 U06  CONST_30  NAF  C2   N1   C6    180.00   0.0  0
 U06  CONST_31  CAK  C5   C6   N1    180.00   0.0  0
 U06  CONST_32  CAK  C5   C4   N3    180.00   0.0  0
 U06  CONST_33  C2   N1   C6   CAB   180.00   0.0  0
 U06  CONST_34  NAI  C4   N3   C2    180.00   0.0  0
 U06  CONST_35  CAT  CAU  CAN  CAM   180.00   0.0  0
 U06  CONST_36  CAR  CAO  CAN  CAM   180.00   0.0  0
 U06  CONST_37  OAP  CAO  CAN  CAU   180.00   0.0  0
 U06  CONST_38  CAS  CAR  CAO  OAP   180.00   0.0  0
 U06  CONST_39  CBB  CAY  CAX  CAW   180.00   0.0  0
 U06  CONST_40  CBA  CAZ  CAY  CBB   180.00   0.0  0
 U06  CONST_41  H16  CAR  CAO  CAN   180.00   0.0  0
 U06  CONST_42  H17  CAS  CAT  CAU   180.00   0.0  0
 U06  CONST_43  H12  CAU  CAN  CAO   180.00   0.0  0
 U06  CONST_44  H22  CBA  CAV  CAT     0.00   0.0  0
 U06  CONST_45  H18  CAW  CAV  CAT     0.00   0.0  0
 U06  CONST_46  H21  CAZ  CBA  CAV   180.00   0.0  0
 U06  CONST_47  H19  CAX  CAW  CAV   180.00   0.0  0
 U06  CONST_48  H8   NAI  C4   C5      0.00   0.0  0
 U06  CONST_49  H9   NAI  C4   C5    180.00   0.0  0
 U06  CONST_50  H6   NAF  C2   N1    180.00   0.0  0
 U06  CONST_52  H20  OBC  CBB  CAY   180.00   0.0  0
 U06  Var_01    CAA  CAB  C6   C5     79.66  30.0  2
 U06  Var_02    CAU  CAN  CAM  CAL  -109.46  30.0  2
 U06  Var_03    CAR  CAO  OAP  CAQ     0.43  30.0  1
 U06  Var_04    OBD  CBB  CAY  CAX    -0.56  30.0  2
 U06  Var_05    CAN  CAM  CAL  CAK    -8.86  30.0  3
 U06  Var_06    H1   CAA  CAB  C6    -62.90  30.0  3
 U06  Var_07    H13  CAQ  OAP  CAO  -179.93  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
 U06  plan-1  C4   0.020
 U06  plan-1  C5   0.020
 U06  plan-1  C6   0.020
 U06  plan-1  N1   0.020
 U06  plan-1  N3   0.020
 U06  plan-1  CAB  0.020
 U06  plan-1  C2   0.020
 U06  plan-1  NAF  0.020
 U06  plan-1  NAI  0.020
 U06  plan-1  CAK  0.020
 U06  plan-1  CAL  0.020
 U06  plan-2  CAM  0.020
 U06  plan-2  CAN  0.020
 U06  plan-2  CAU  0.020
 U06  plan-2  CAO  0.020
 U06  plan-2  OAP  0.020
 U06  plan-2  CAR  0.020
 U06  plan-2  CAS  0.020
 U06  plan-2  CAT  0.020
 U06  plan-2  CAV  0.020
 U06  plan-2  H12  0.020
 U06  plan-2  H16  0.020
 U06  plan-2  H17  0.020
 U06  plan-3  CAT  0.020
 U06  plan-3  CAV  0.020
 U06  plan-3  CAW  0.020
 U06  plan-3  CAX  0.020
 U06  plan-3  CAY  0.020
 U06  plan-3  CBB  0.020
 U06  plan-3  CAZ  0.020
 U06  plan-3  CBA  0.020
 U06  plan-3  H18  0.020
 U06  plan-3  H19  0.020
 U06  plan-3  H21  0.020
 U06  plan-3  H22  0.020
 U06  plan-4  C2   0.020
 U06  plan-4  NAF  0.020
 U06  plan-4  H6   0.020
 U06  plan-4  H7   0.020
 U06  plan-5  C4   0.020
 U06  plan-5  NAI  0.020
 U06  plan-5  H8   0.020
 U06  plan-5  H9   0.020
 U06  plan-6  CAY  0.020
 U06  plan-6  CBB  0.020
 U06  plan-6  OBD  0.020
 U06  plan-6  OBC  0.020
 U06  plan-6  H20  0.020

