# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 12:15:20 2020
#   Inital geometry file: a 151 line input string
#   Ligand name: 5-bromo-2-{5-[(4-methylpiperazin-1-yl)acetyl]-2-propoxyphenyl}-6-(propan-2-yl)pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCOc1ccc(cc1C2=NC(=C(Br)C(=O)N2)C(C)C)C(=O)CN3CCN(C)CC3
#
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
 5BA  5BA  5-bromo-2-{5-[(4-methylpiperazin-1-yl)acetyl]-2-propoxyphenyl}-6-(propan-2-yl)pyrimidin-4(3H)-one  ligand  62  31  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5BA
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
 5BA  CAO  C   CH2   0  -0.294   -5.9560   0.9230   1.1157
 5BA  CAM  C   CH2   0  -0.285   -7.1181   1.8963   1.0870
 5BA  NBD  N   NT    0  -0.412   -8.3665   1.1964   0.8614
 5BA  CAD  C   CH3   0  -0.517   -9.4947   2.0980   0.8766
 5BA  CAN  C   CH2   0  -0.285   -8.2989   0.4437  -0.3750
 5BA  CAP  C   CH2   0  -0.290   -7.1357  -0.5293  -0.3485
 5BA  N    N   NT    0  -0.420   -5.8875   0.1812  -0.1314
 5BA  CA   C   CH2   0  -0.403   -4.7549  -0.7021  -0.1864
 5BA  C    C   C     0   0.355   -3.4451   0.0121  -0.4546
 5BA  O    O   O     0  -0.392   -3.3983   1.2020  -0.6797
 5BA  CAV  C   CR6   0  -0.023   -2.2069  -0.8055  -0.4427
 5BA  CAJ  C   CR16  0  -0.276   -0.9735  -0.1641  -0.5526
 5BA  CAH  C   CR16  0  -0.272   -2.2140  -2.1946  -0.3431
 5BA  CAI  C   CR16  0  -0.371   -1.0400  -2.9260  -0.3724
 5BA  CAW  C   CR6   0   0.410    0.1908  -2.2792  -0.4839
 5BA  OAT  O   O2    0  -0.442    1.3576  -2.9062  -0.5626
 5BA  CAL  C   CH2   0  -0.178    1.4010  -4.3309  -0.5373
 5BA  CAK  C   CH2   0  -0.463    2.8460  -4.7593  -0.6703
 5BA  CAA  C   CH3   0  -0.671    2.9682  -6.2770  -0.6599
 5BA  CAY  C   CR6   0  -0.099    0.2152  -0.8713  -0.5522
 5BA  CAZ  C   CR6   0   0.470    1.4940  -0.1385  -0.6139
 5BA  NAR  N   N     0  -0.422    2.4330  -0.3771   0.2390
 5BA  NAS  N   NR16  0  -0.682    1.6075   0.8094  -1.5684
 5BA  CBB  C   CR6   0   0.572    2.7131   1.6285  -1.7167
 5BA  OAF  O   O     0  -0.454    2.7533   2.4788  -2.5868
 5BA  CAX  C   CR6   0  -0.374    3.7488   1.3268  -0.7556
 5BA  BR   BR  BR    0  -0.018    5.3001   2.3662  -0.9277
 5BA  CBA  C   CR6   0   0.375    3.5873   0.3413   0.1772
 5BA  CBC  C   CH1   0  -0.324    4.6274  -0.0827   1.1788
 5BA  CAC  C   CH3   0  -0.648    4.0459  -0.1421   2.5895
 5BA  CAB  C   CH3   0  -0.659    5.1929  -1.4393   0.7525
 5BA  H1   H   HCH2  0   0.244   -5.0331   1.4820   1.2667
 5BA  H2   H   HCH2  0   0.194   -6.0728   0.2423   1.9766
 5BA  H3   H   HCH2  0   0.235   -7.1678   2.4209   2.0443
 5BA  H4   H   HCH2  0   0.189   -6.9321   2.6572   0.3084
 5BA  H6   H   HCH3  0   0.191   -9.4542   2.8558   0.0787
 5BA  H7   H   HCH3  0   0.232  -10.4240   1.5384   0.7580
 5BA  H8   H   HCH3  0   0.232   -9.5412   2.6231   1.8321
 5BA  H9   H   HCH2  0   0.236   -9.2292  -0.1148  -0.5054
 5BA  H10  H   HCH2  0   0.189   -8.1926   1.1085  -1.2506
 5BA  H11  H   HCH2  0   0.194   -7.3154  -1.2877   0.4321
 5BA  H12  H   HCH2  0   0.241   -7.0887  -1.0546  -1.3052
 5BA  H14  H   HCH2  0   0.241   -4.6469  -1.3165   0.7244
 5BA  H15  H   HCH2  0   0.286   -4.8989  -1.4174  -1.0039
 5BA  H16  H   HCR6  0   0.278   -0.9470   0.9174  -0.6096
 5BA  H17  H   HCR6  0   0.278   -3.1428  -2.7418  -0.2503
 5BA  H18  H   HCR6  0   0.297   -1.0996  -4.0033  -0.3159
 5BA  H19  H   HCH2  0   0.232    0.9746  -4.7016   0.4012
 5BA  H20  H   HCH2  0   0.231    0.8055  -4.7383  -1.3618
 5BA  H21  H   HCH2  0   0.234    3.2596  -4.3597  -1.5993
 5BA  H22  H   HCH2  0   0.238    3.4285  -4.3340   0.1506
 5BA  H23  H   HCH3  0   0.226    2.6020  -6.7017   0.2760
 5BA  H24  H   HCH3  0   0.225    2.4001  -6.7276  -1.4751
 5BA  H25  H   HCH3  0   0.240    4.0079  -6.5813  -0.7753
 5BA  H27  H   HCH1  0   0.253    5.4448   0.6383   1.1842
 5BA  H28  H   HCH3  0   0.232    3.2512  -0.8836   2.6626
 5BA  H29  H   HCH3  0   0.235    4.8308  -0.4150   3.2958
 5BA  H30  H   HCH3  0   0.234    3.6417   0.8230   2.8973
 5BA  H31  H   HCH3  0   0.236    5.6390  -1.3938  -0.2419
 5BA  H32  H   HCH3  0   0.239    5.9665  -1.7589   1.4516
 5BA  H33  H   HCH3  0   0.239    4.4109  -2.1992   0.7402
 5BA  H5   H   HNR6  0   0.438    0.8577   0.9348  -2.2389

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
 5BA  BR   CAX  single    1.875  0.020  1.875
 5BA  CAC  CBC  single    1.527  0.020  1.527
 5BA  CBC  CAB  single    1.530  0.020  1.530
 5BA  CBC  CBA  single    1.505  0.020  1.505
 5BA  CAX  CBA  double    1.366  0.020  1.366
 5BA  CAX  CBB  single    1.445  0.020  1.445
 5BA  OAF  CBB  double    1.217  0.020  1.217
 5BA  CBA  NAR  single    1.361  0.020  1.361
 5BA  CBB  NAS  single    1.384  0.020  1.384
 5BA  NAR  CAZ  double    1.291  0.020  1.291
 5BA  NAS  CAZ  single    1.350  0.020  1.350
 5BA  CAZ  CAY  single    1.475  0.020  1.475
 5BA  CAA  CAK  single    1.523  0.020  1.523
 5BA  CAK  CAL  single    1.513  0.020  1.513
 5BA  CAY  CAJ  aromatic  1.383  0.020  1.383
 5BA  CAY  CAW  aromatic  1.410  0.020  1.410
 5BA  OAT  CAW  single    1.327  0.020  1.327
 5BA  OAT  CAL  single    1.426  0.020  1.426
 5BA  CAJ  CAV  aromatic  1.395  0.020  1.395
 5BA  CAW  CAI  aromatic  1.395  0.020  1.395
 5BA  O    C    double    1.212  0.020  1.212
 5BA  CAV  C    single    1.484  0.020  1.484
 5BA  CAV  CAH  aromatic  1.393  0.020  1.393
 5BA  CAI  CAH  aromatic  1.384  0.020  1.384
 5BA  C    CA   single    1.516  0.020  1.516
 5BA  CA   N    single    1.437  0.020  1.437
 5BA  CAP  N    single    1.453  0.020  1.453
 5BA  CAP  CAN  single    1.517  0.020  1.517
 5BA  N    CAO  single    1.453  0.020  1.453
 5BA  CAN  NBD  single    1.449  0.020  1.449
 5BA  CAO  CAM  single    1.516  0.020  1.516
 5BA  NBD  CAD  single    1.444  0.020  1.444
 5BA  NBD  CAM  single    1.449  0.020  1.449
 5BA  CAO  H1   single    0.970  0.020  1.090
 5BA  CAO  H2   single    0.970  0.020  1.090
 5BA  CAM  H3   single    0.970  0.020  1.090
 5BA  CAM  H4   single    0.970  0.020  1.090
 5BA  CAD  H6   single    0.970  0.020  1.090
 5BA  CAD  H7   single    0.970  0.020  1.090
 5BA  CAD  H8   single    0.970  0.020  1.090
 5BA  CAN  H9   single    0.970  0.020  1.090
 5BA  CAN  H10  single    0.970  0.020  1.090
 5BA  CAP  H11  single    0.970  0.020  1.090
 5BA  CAP  H12  single    0.970  0.020  1.090
 5BA  CA   H14  single    0.970  0.020  1.090
 5BA  CA   H15  single    0.970  0.020  1.090
 5BA  CAJ  H16  single    0.930  0.020  1.080
 5BA  CAH  H17  single    0.930  0.020  1.080
 5BA  CAI  H18  single    0.930  0.020  1.080
 5BA  CAL  H19  single    0.970  0.020  1.090
 5BA  CAL  H20  single    0.970  0.020  1.090
 5BA  CAK  H21  single    0.970  0.020  1.090
 5BA  CAK  H22  single    0.970  0.020  1.090
 5BA  CAA  H23  single    0.970  0.020  1.090
 5BA  CAA  H24  single    0.970  0.020  1.090
 5BA  CAA  H25  single    0.970  0.020  1.090
 5BA  CBC  H27  single    0.970  0.020  1.090
 5BA  CAC  H28  single    0.970  0.020  1.090
 5BA  CAC  H29  single    0.970  0.020  1.090
 5BA  CAC  H30  single    0.970  0.020  1.090
 5BA  CAB  H31  single    0.970  0.020  1.090
 5BA  CAB  H32  single    0.970  0.020  1.090
 5BA  CAB  H33  single    0.970  0.020  1.090
 5BA  NAS  H5   single    0.860  0.020  1.020

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
 5BA  H2   CAO  H1   107.33  3.000
 5BA  H2   CAO  N    111.08  3.000
 5BA  H1   CAO  N    109.94  3.000
 5BA  H2   CAO  CAM  109.25  3.000
 5BA  H1   CAO  CAM  108.82  3.000
 5BA  N    CAO  CAM  110.35  3.000
 5BA  H4   CAM  H3   107.13  3.000
 5BA  H4   CAM  NBD  111.60  3.000
 5BA  H3   CAM  NBD  109.21  3.000
 5BA  H4   CAM  CAO  109.06  3.000
 5BA  H3   CAM  CAO  109.05  3.000
 5BA  NBD  CAM  CAO  110.69  3.000
 5BA  CAN  NBD  CAD  111.70  3.000
 5BA  CAD  NBD  CAM  111.71  3.000
 5BA  CAN  NBD  CAM  110.09  3.000
 5BA  H8   CAD  H7   107.80  3.000
 5BA  H8   CAD  H6   107.75  3.000
 5BA  H7   CAD  H6   107.79  3.000
 5BA  H8   CAD  NBD  110.05  3.000
 5BA  H7   CAD  NBD  110.12  3.000
 5BA  H6   CAD  NBD  113.15  3.000
 5BA  H10  CAN  H9   107.15  3.000
 5BA  H10  CAN  CAP  109.03  3.000
 5BA  H9   CAN  CAP  109.09  3.000
 5BA  H10  CAN  NBD  111.61  3.000
 5BA  H9   CAN  NBD  109.12  3.000
 5BA  CAP  CAN  NBD  110.74  3.000
 5BA  H12  CAP  H11  107.22  3.000
 5BA  H12  CAP  N    109.21  3.000
 5BA  H11  CAP  N    111.75  3.000
 5BA  H12  CAP  CAN  109.04  3.000
 5BA  H11  CAP  CAN  109.18  3.000
 5BA  N    CAP  CAN  110.36  3.000
 5BA  CA   N    CAP  111.77  3.000
 5BA  CAP  N    CAO  109.72  3.000
 5BA  CA   N    CAO  112.57  3.000
 5BA  H15  CA   H14  105.37  3.000
 5BA  H15  CA   C    106.80  3.000
 5BA  H14  CA   C    108.88  3.000
 5BA  H15  CA   N    109.03  3.000
 5BA  H14  CA   N    112.80  3.000
 5BA  C    CA   N    113.46  3.000
 5BA  CAV  C    O    120.68  3.000
 5BA  CAV  C    CA   117.39  3.000
 5BA  O    C    CA   121.93  3.000
 5BA  CAH  CAV  CAJ  117.97  3.000
 5BA  CAH  CAV  C    123.08  3.000
 5BA  CAJ  CAV  C    118.95  3.000
 5BA  H16  CAJ  CAY  119.30  3.000
 5BA  H16  CAJ  CAV  119.01  3.000
 5BA  CAY  CAJ  CAV  121.66  3.000
 5BA  H17  CAH  CAI  117.58  3.000
 5BA  H17  CAH  CAV  120.99  3.000
 5BA  CAI  CAH  CAV  121.43  3.000
 5BA  H18  CAI  CAW  121.01  3.000
 5BA  H18  CAI  CAH  118.63  3.000
 5BA  CAW  CAI  CAH  120.36  3.000
 5BA  CAY  CAW  OAT  116.99  3.000
 5BA  OAT  CAW  CAI  124.16  3.000
 5BA  CAY  CAW  CAI  118.83  3.000
 5BA  CAL  OAT  CAW  119.87  3.000
 5BA  H20  CAL  H19  107.90  3.000
 5BA  H20  CAL  CAK  110.34  3.000
 5BA  H19  CAL  CAK  110.57  3.000
 5BA  H20  CAL  OAT  109.98  3.000
 5BA  H19  CAL  OAT  109.97  3.000
 5BA  CAK  CAL  OAT  108.09  3.000
 5BA  H22  CAK  H21  107.13  3.000
 5BA  H22  CAK  CAA  109.88  3.000
 5BA  H21  CAK  CAA  109.88  3.000
 5BA  H22  CAK  CAL  109.44  3.000
 5BA  H21  CAK  CAL  109.43  3.000
 5BA  CAA  CAK  CAL  111.00  3.000
 5BA  H25  CAA  H24  107.60  3.000
 5BA  H25  CAA  H23  107.61  3.000
 5BA  H24  CAA  H23  107.78  3.000
 5BA  H25  CAA  CAK  110.75  3.000
 5BA  H24  CAA  CAK  111.39  3.000
 5BA  H23  CAA  CAK  111.52  3.000
 5BA  CAZ  CAY  CAW  120.88  3.000
 5BA  CAW  CAY  CAJ  119.72  3.000
 5BA  CAZ  CAY  CAJ  119.40  3.000
 5BA  NAS  CAZ  NAR  122.40  3.000
 5BA  NAS  CAZ  CAY  116.83  3.000
 5BA  NAR  CAZ  CAY  120.74  3.000
 5BA  CBA  NAR  CAZ  119.30  3.000
 5BA  H5   NAS  CBB  116.54  3.000
 5BA  H5   NAS  CAZ  119.49  3.000
 5BA  CBB  NAS  CAZ  123.96  3.000
 5BA  CAX  CBB  OAF  126.71  3.000
 5BA  OAF  CBB  NAS  121.09  3.000
 5BA  CAX  CBB  NAS  112.19  3.000
 5BA  CBA  CAX  BR   124.07  3.000
 5BA  CBA  CAX  CBB  121.33  3.000
 5BA  BR   CAX  CBB  114.59  3.000
 5BA  CBC  CBA  CAX  125.15  3.000
 5BA  CAX  CBA  NAR  120.79  3.000
 5BA  CBC  CBA  NAR  114.03  3.000
 5BA  H27  CBC  CAB  108.10  3.000
 5BA  H27  CBC  CAC  107.87  3.000
 5BA  CAB  CBC  CAC  111.32  3.000
 5BA  H27  CBC  CBA  109.59  3.000
 5BA  CAB  CBC  CBA  108.64  3.000
 5BA  CAC  CBC  CBA  111.26  3.000
 5BA  H30  CAC  H29  107.78  3.000
 5BA  H30  CAC  H28  108.25  3.000
 5BA  H29  CAC  H28  108.14  3.000
 5BA  H30  CAC  CBC  111.56  3.000
 5BA  H29  CAC  CBC  109.50  3.000
 5BA  H28  CAC  CBC  111.49  3.000
 5BA  H33  CAB  H32  108.16  3.000
 5BA  H33  CAB  H31  108.18  3.000
 5BA  H32  CAB  H31  107.85  3.000
 5BA  H33  CAB  CBC  110.85  3.000
 5BA  H32  CAB  CBC  110.08  3.000
 5BA  H31  CAB  CBC  111.59  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
 5BA  CONST_01  CAW  CAY  CAJ  CAV     0.00   0.0  0
 5BA  CONST_02  CAW  CAI  CAH  CAV     0.00   0.0  0
 5BA  CONST_03  CAI  CAW  CAY  CAJ     0.00   0.0  0
 5BA  CONST_04  CAI  CAH  CAV  CAJ     0.00   0.0  0
 5BA  CONST_05  CAY  CAJ  CAV  CAH     0.00   0.0  0
 5BA  CONST_06  CAY  CAW  CAI  CAH     0.00   0.0  0
 5BA  CONST_07  CAZ  CAY  CAJ  CAV   180.00   0.0  0
 5BA  CONST_08  CAZ  CAY  CAW  CAI   180.00   0.0  0
 5BA  CONST_09  CBA  NAR  CAZ  CAY   180.00   0.0  0
 5BA  CONST_10  CBB  NAS  CAZ  CAY   180.00   0.0  0
 5BA  CONST_11  CAX  CBB  NAS  CAZ     0.00   0.0  0
 5BA  CONST_12  CBB  NAS  CAZ  NAR     0.00   0.0  0
 5BA  CONST_13  CBA  NAR  CAZ  NAS     0.00   0.0  0
 5BA  CONST_14  CAY  CAJ  CAV  C     180.00   0.0  0
 5BA  CONST_15  CAI  CAH  CAV  C     180.00   0.0  0
 5BA  CONST_16  OAT  CAW  CAY  CAJ   180.00   0.0  0
 5BA  CONST_17  OAT  CAW  CAI  CAH   180.00   0.0  0
 5BA  CONST_18  CAZ  CAY  CAW  OAT     0.00   0.0  0
 5BA  CONST_19  OAF  CBB  NAS  CAZ   180.00   0.0  0
 5BA  CONST_20  H18  CAI  CAH  CAV   180.00   0.0  0
 5BA  CONST_21  H17  CAH  CAV  CAJ   180.00   0.0  0
 5BA  CONST_22  H16  CAJ  CAV  CAH   180.00   0.0  0
 5BA  CONST_23  H5   NAS  CAZ  CAY     0.00   0.0  0
 5BA  Var_01    CAN  CAP  N    CAO    58.11  30.0  1
 5BA  Var_02    CAN  NBD  CAM  CAO   -57.32  30.0  1
 5BA  Var_03    CAP  N    CAO  CAM   -58.22  30.0  1
 5BA  Var_04    CAP  CAN  NBD  CAM    57.23  30.0  1
 5BA  Var_05    N    CAP  CAN  NBD   -58.00  30.0  1
 5BA  Var_06    N    CAO  CAM  NBD    58.18  30.0  1
 5BA  Var_07    NAR  CAZ  CAY  CAJ   128.78  30.0  3
 5BA  Var_08    C    CA   N    CAO   -76.29  30.0  2
 5BA  Var_09    CAV  C    CA   N     176.17  30.0  2
 5BA  Var_10    CAJ  CAV  C    CA   -173.69  30.0  2
 5BA  Var_11    CAY  CAW  OAT  CAL  -178.27  30.0  2
 5BA  Var_12    CAC  CBC  CBA  NAR   -51.21  30.0  2
 5BA  Var_13    H6   CAD  NBD  CAM    62.33  30.0  3
 5BA  Var_14    CAK  CAL  OAT  CAW   178.86  30.0  3
 5BA  Var_15    H28  CAC  CBC  CBA    62.49  30.0  3
 5BA  Var_16    H31  CAB  CBC  CBA    59.02  30.0  3
 5BA  Var_17    CAA  CAK  CAL  OAT  -179.64  30.0  1
 5BA  Var_18    H23  CAA  CAK  CAL   -61.28  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
 5BA  plan-1  C    0.020
 5BA  plan-1  CAV  0.020
 5BA  plan-1  CAJ  0.020
 5BA  plan-1  CAH  0.020
 5BA  plan-1  CAI  0.020
 5BA  plan-1  CAW  0.020
 5BA  plan-1  OAT  0.020
 5BA  plan-1  CAY  0.020
 5BA  plan-1  CAZ  0.020
 5BA  plan-1  H16  0.020
 5BA  plan-1  H17  0.020
 5BA  plan-1  H18  0.020
 5BA  plan-2  CAY  0.020
 5BA  plan-2  CAZ  0.020
 5BA  plan-2  NAR  0.020
 5BA  plan-2  NAS  0.020
 5BA  plan-2  CBB  0.020
 5BA  plan-2  OAF  0.020
 5BA  plan-2  CAX  0.020
 5BA  plan-2  BR   0.020
 5BA  plan-2  CBA  0.020
 5BA  plan-2  CBC  0.020
 5BA  plan-2  H5   0.020
 5BA  plan-3  CA   0.020
 5BA  plan-3  C    0.020
 5BA  plan-3  O    0.020
 5BA  plan-3  CAV  0.020

