# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 19:28:05 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}-[[4-[(4-azanylpiperidin-1-yl)methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2,3-d]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1CCN(CC1)Cc2ccc(CNC(=O)c3csc4N=CNC(=O)c34)cc2
#
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
 BWR  BWR  ~{N}-[[4-[(4-azanylpiperidin-1-yl)methyl]phenyl]methyl]-4-oxidanylidene-3~{H}-thieno[2,3-d]pyrimidine-5-carboxamide  ligand  51  28  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BWR
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
 BWR  CAL  C  CH2   0  -0.281   4.8364  -0.9002   0.6595
 BWR  CAJ  C  CH2   0  -0.433   5.0263  -2.2513  -0.0110
 BWR  CBA  C  CH1   0  -0.068   6.4883  -2.4896  -0.3614
 BWR  NAA  N  NH2   0  -0.802   6.6356  -3.7335  -1.1030
 BWR  CAK  C  CH2   0  -0.435   6.9967  -1.3168  -1.1889
 BWR  CAM  C  CH2   0  -0.282   6.7455   0.0019  -0.4744
 BWR  NBB  N  NT    0  -0.413   5.3345   0.1716  -0.1826
 BWR  CAO  C  CH2   0  -0.311   5.0406   1.4767   0.3632
 BWR  CAV  C  CR6   0   0.073   3.5715   1.8114   0.3072
 BWR  CAG  C  CR16  0  -0.269   2.8047   1.4659  -0.8043
 BWR  CAE  C  CR16  0  -0.269   1.4653   1.8123  -0.8754
 BWR  CAF  C  CR16  0  -0.301   2.9600   2.5074   1.3430
 BWR  CAD  C  CR16  0  -0.277   1.6172   2.8572   1.2714
 BWR  CAU  C  CR6   0   0.034   0.8549   2.5164   0.1610
 BWR  CAN  C  CH2   0  -0.318  -0.6055   2.8619   0.0926
 BWR  NAQ  N  NH1   0  -0.625  -1.4068   1.7097   0.4697
 BWR  CAT  C  C     0   0.506  -2.7441   1.7164   0.4004
 BWR  OAB  O  O     0  -0.477  -3.3961   2.6639  -0.0067
 BWR  CAW  C  CR5   0   0.053  -3.4007   0.4781   0.9134
 BWR  CAZ  C  CR56  0  -0.059  -4.3996  -0.2766   0.2263
 BWR  CAX  C  CR6   0   0.540  -4.8361  -0.1776  -1.1464
 BWR  OAC  O  O     0  -0.446  -4.4208   0.5814  -2.0000
 BWR  NAR  N  NR16  0  -0.653  -5.8312  -1.1076  -1.4317
 BWR  CAH  C  CR16  0   0.163  -6.2962  -2.0365  -0.5717
 BWR  NAP  N  N     0  -0.429  -5.8790  -2.1764   0.6419
 BWR  CAY  C  CR56  0  -0.021  -4.9288  -1.2878   1.0081
 BWR  SAS  S  S2    0   0.266  -4.2092  -1.3200   2.5724
 BWR  CAI  C  CR15  0  -0.513  -3.1992   0.0151   2.1746
 BWR  H1   H  HCH2  0   0.239   3.7741  -0.7376   0.8531
 BWR  H2   H  HCH2  0   0.187   5.3390  -0.8991   1.6438
 BWR  H3   H  HCH2  0   0.228   4.6574  -3.0381   0.6532
 BWR  H4   H  HCH2  0   0.214   4.4262  -2.2891  -0.9251
 BWR  H5   H  HCH1  0   0.185   7.0598  -2.4945   0.5826
 BWR  H6   H  HNH2  0   0.340   7.6160  -3.8871  -1.3081
 BWR  H7   H  HNH2  0   0.340   6.3620  -4.5096  -0.5117
 BWR  H9   H  HCH2  0   0.229   8.0680  -1.4236  -1.3826
 BWR  H10  H  HCH2  0   0.214   6.4892  -1.3117  -2.1582
 BWR  H11  H  HCH2  0   0.185   7.3594   0.0402   0.4430
 BWR  H12  H  HCH2  0   0.235   7.0746   0.8312  -1.1050
 BWR  H14  H  HCH2  0   0.209   5.3991   1.5935   1.4002
 BWR  H15  H  HCH2  0   0.251   5.5857   2.2195  -0.2286
 BWR  H16  H  HCR6  0   0.246   3.2663   0.9121  -1.6121
 BWR  H17  H  HCR6  0   0.251   0.8877   1.5350  -1.7499
 BWR  H18  H  HCR6  0   0.248   3.5353   2.7811   2.2200
 BWR  H19  H  HCR6  0   0.252   1.1594   3.3965   2.0923
 BWR  H20  H  HCH2  0   0.257  -0.8265   3.7011   0.7567
 BWR  H21  H  HCH2  0   0.258  -0.8730   3.1739  -0.9196
 BWR  H22  H  HNH1  0   0.411  -0.9342   0.8788   0.7883
 BWR  H23  H  HCR6  0   0.311  -7.0639  -2.6929  -0.9597
 BWR  H25  H  HCR5  0   0.317  -2.5266   0.4144   2.9188
 BWR  H8   H  HNR6  0   0.439  -6.2081  -1.1021  -2.3712

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
 BWR  NAA  CBA  single    1.456  0.020  1.456
 BWR  CAK  CBA  single    1.523  0.020  1.523
 BWR  CAK  CAM  single    1.521  0.020  1.521
 BWR  CBA  CAJ  single    1.522  0.020  1.522
 BWR  CAM  NBB  single    1.451  0.020  1.451
 BWR  CAJ  CAL  single    1.520  0.020  1.520
 BWR  NBB  CAL  single    1.451  0.020  1.451
 BWR  NBB  CAO  single    1.445  0.020  1.445
 BWR  CAO  CAV  single    1.508  0.020  1.508
 BWR  CAG  CAV  aromatic  1.394  0.020  1.394
 BWR  CAG  CAE  aromatic  1.385  0.020  1.385
 BWR  CAV  CAF  aromatic  1.390  0.020  1.390
 BWR  CAE  CAU  aromatic  1.394  0.020  1.394
 BWR  CAF  CAD  aromatic  1.389  0.020  1.389
 BWR  CAU  CAD  aromatic  1.389  0.020  1.389
 BWR  CAU  CAN  single    1.502  0.020  1.502
 BWR  CAN  NAQ  single    1.453  0.020  1.453
 BWR  NAQ  CAT  single    1.339  0.020  1.339
 BWR  OAB  CAT  double    1.220  0.020  1.220
 BWR  OAC  CAX  double    1.215  0.020  1.215
 BWR  CAT  CAW  single    1.493  0.020  1.493
 BWR  CAX  CAZ  single    1.444  0.020  1.444
 BWR  CAX  NAR  single    1.392  0.020  1.392
 BWR  CAW  CAZ  aromatic  1.428  0.020  1.428
 BWR  CAW  CAI  aromatic  1.358  0.020  1.358
 BWR  CAZ  CAY  aromatic  1.383  0.020  1.383
 BWR  NAR  CAH  single    1.349  0.020  1.349
 BWR  CAI  SAS  aromatic  1.721  0.020  1.721
 BWR  CAY  SAS  aromatic  1.722  0.020  1.722
 BWR  CAY  NAP  single    1.352  0.020  1.352
 BWR  CAH  NAP  double    1.291  0.020  1.291
 BWR  CAL  H1   single    0.970  0.020  1.090
 BWR  CAL  H2   single    0.970  0.020  1.090
 BWR  CAJ  H3   single    0.970  0.020  1.090
 BWR  CAJ  H4   single    0.970  0.020  1.090
 BWR  CBA  H5   single    0.970  0.020  1.090
 BWR  NAA  H6   single    0.890  0.020  1.040
 BWR  NAA  H7   single    0.890  0.020  1.040
 BWR  CAK  H9   single    0.970  0.020  1.090
 BWR  CAK  H10  single    0.970  0.020  1.090
 BWR  CAM  H11  single    0.970  0.020  1.090
 BWR  CAM  H12  single    0.970  0.020  1.090
 BWR  CAO  H14  single    0.970  0.020  1.090
 BWR  CAO  H15  single    0.970  0.020  1.090
 BWR  CAG  H16  single    0.930  0.020  1.080
 BWR  CAE  H17  single    0.930  0.020  1.080
 BWR  CAF  H18  single    0.930  0.020  1.080
 BWR  CAD  H19  single    0.930  0.020  1.080
 BWR  CAN  H20  single    0.970  0.020  1.090
 BWR  CAN  H21  single    0.970  0.020  1.090
 BWR  NAQ  H22  single    0.860  0.020  1.020
 BWR  CAH  H23  single    0.930  0.020  1.080
 BWR  CAI  H25  single    0.930  0.020  1.080
 BWR  NAR  H8   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
 BWR  H2   CAL  H1   106.52  3.000
 BWR  H2   CAL  NBB  111.09  3.000
 BWR  H1   CAL  NBB  109.08  3.000
 BWR  H2   CAL  CAJ  109.69  3.000
 BWR  H1   CAL  CAJ  109.40  3.000
 BWR  NBB  CAL  CAJ  110.95  3.000
 BWR  H4   CAJ  H3   107.31  3.000
 BWR  H4   CAJ  CBA  109.21  3.000
 BWR  H3   CAJ  CBA  110.55  3.000
 BWR  H4   CAJ  CAL  109.31  3.000
 BWR  H3   CAJ  CAL  109.23  3.000
 BWR  CBA  CAJ  CAL  111.14  3.000
 BWR  H5   CBA  CAK  107.18  3.000
 BWR  H5   CBA  NAA  112.31  3.000
 BWR  CAK  CBA  NAA  110.34  3.000
 BWR  H5   CBA  CAJ  107.53  3.000
 BWR  CAK  CBA  CAJ  108.97  3.000
 BWR  NAA  CBA  CAJ  110.38  3.000
 BWR  H7   NAA  H6   105.26  3.000
 BWR  H7   NAA  CBA  109.26  3.000
 BWR  H6   NAA  CBA  109.30  3.000
 BWR  H10  CAK  H9   107.32  3.000
 BWR  H10  CAK  CAM  109.61  3.000
 BWR  H9   CAK  CAM  109.25  3.000
 BWR  H10  CAK  CBA  109.28  3.000
 BWR  H9   CAK  CBA  110.36  3.000
 BWR  CAM  CAK  CBA  110.94  3.000
 BWR  H12  CAM  H11  106.60  3.000
 BWR  H12  CAM  NBB  108.68  3.000
 BWR  H11  CAM  NBB  111.68  3.000
 BWR  H12  CAM  CAK  109.71  3.000
 BWR  H11  CAM  CAK  109.18  3.000
 BWR  NBB  CAM  CAK  110.89  3.000
 BWR  CAO  NBB  CAM  112.30  3.000
 BWR  CAO  NBB  CAL  112.21  3.000
 BWR  CAM  NBB  CAL  111.36  3.000
 BWR  H15  CAO  H14  105.93  3.000
 BWR  H15  CAO  CAV  108.32  3.000
 BWR  H14  CAO  CAV  109.15  3.000
 BWR  H15  CAO  NBB  107.90  3.000
 BWR  H14  CAO  NBB  112.62  3.000
 BWR  CAV  CAO  NBB  112.63  3.000
 BWR  CAF  CAV  CAG  118.45  3.000
 BWR  CAF  CAV  CAO  120.81  3.000
 BWR  CAG  CAV  CAO  120.70  3.000
 BWR  H16  CAG  CAE  120.12  3.000
 BWR  H16  CAG  CAV  119.15  3.000
 BWR  CAE  CAG  CAV  120.72  3.000
 BWR  H17  CAE  CAU  119.72  3.000
 BWR  H17  CAE  CAG  119.51  3.000
 BWR  CAU  CAE  CAG  120.77  3.000
 BWR  H18  CAF  CAD  119.41  3.000
 BWR  H18  CAF  CAV  119.73  3.000
 BWR  CAD  CAF  CAV  120.86  3.000
 BWR  H19  CAD  CAU  119.71  3.000
 BWR  H19  CAD  CAF  119.64  3.000
 BWR  CAU  CAD  CAF  120.65  3.000
 BWR  CAN  CAU  CAD  120.89  3.000
 BWR  CAN  CAU  CAE  120.53  3.000
 BWR  CAD  CAU  CAE  118.55  3.000
 BWR  H21  CAN  H20  107.11  3.000
 BWR  H21  CAN  NAQ  109.38  3.000
 BWR  H20  CAN  NAQ  109.86  3.000
 BWR  H21  CAN  CAU  110.24  3.000
 BWR  H20  CAN  CAU  110.22  3.000
 BWR  NAQ  CAN  CAU  109.99  3.000
 BWR  H22  NAQ  CAT  119.27  3.000
 BWR  H22  NAQ  CAN  118.50  3.000
 BWR  CAT  NAQ  CAN  122.23  3.000
 BWR  CAW  CAT  OAB  121.60  3.000
 BWR  CAW  CAT  NAQ  114.67  3.000
 BWR  OAB  CAT  NAQ  123.70  3.000
 BWR  CAI  CAW  CAZ  111.73  3.000
 BWR  CAI  CAW  CAT  122.45  3.000
 BWR  CAZ  CAW  CAT  125.51  3.000
 BWR  CAY  CAZ  CAX  118.15  3.000
 BWR  CAY  CAZ  CAW  112.46  3.000
 BWR  CAX  CAZ  CAW  129.24  3.000
 BWR  NAR  CAX  OAC  121.17  3.000
 BWR  NAR  CAX  CAZ  111.43  3.000
 BWR  OAC  CAX  CAZ  127.39  3.000
 BWR  H8   NAR  CAH  117.86  3.000
 BWR  H8   NAR  CAX  116.93  3.000
 BWR  CAH  NAR  CAX  125.17  3.000
 BWR  H23  CAH  NAP  120.04  3.000
 BWR  H23  CAH  NAR  115.71  3.000
 BWR  NAP  CAH  NAR  124.25  3.000
 BWR  CAY  NAP  CAH  114.25  3.000
 BWR  SAS  CAY  NAP  121.84  3.000
 BWR  NAP  CAY  CAZ  126.61  3.000
 BWR  SAS  CAY  CAZ  111.54  3.000
 BWR  CAI  SAS  CAY   91.19  3.000
 BWR  H25  CAI  SAS  119.56  3.000
 BWR  H25  CAI  CAW  127.32  3.000
 BWR  SAS  CAI  CAW  113.08  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
 BWR  CONST_01  CAU  CAE  CAG  CAV     0.00   0.0  0
 BWR  CONST_02  CAU  CAD  CAF  CAV     0.00   0.0  0
 BWR  CONST_03  CAD  CAF  CAV  CAG     0.00   0.0  0
 BWR  CONST_04  CAD  CAU  CAE  CAG     0.00   0.0  0
 BWR  CONST_05  CAF  CAV  CAG  CAE     0.00   0.0  0
 BWR  CONST_06  CAF  CAD  CAU  CAE     0.00   0.0  0
 BWR  CONST_07  SAS  CAY  CAZ  CAW     0.00   0.0  0
 BWR  CONST_08  CAY  SAS  CAI  CAW     0.00   0.0  0
 BWR  CONST_09  SAS  CAI  CAW  CAZ     0.00   0.0  0
 BWR  CONST_10  CAI  SAS  CAY  CAZ     0.00   0.0  0
 BWR  CONST_11  CAI  CAW  CAZ  CAY     0.00   0.0  0
 BWR  CONST_12  CAH  NAR  CAX  CAZ     0.00   0.0  0
 BWR  CONST_13  NAP  CAH  NAR  CAX     0.00   0.0  0
 BWR  CONST_14  CAY  NAP  CAH  NAR     0.00   0.0  0
 BWR  CONST_15  CAE  CAG  CAV  CAO   180.00   0.0  0
 BWR  CONST_16  CAD  CAF  CAV  CAO   180.00   0.0  0
 BWR  CONST_17  CAN  CAU  CAE  CAG   180.00   0.0  0
 BWR  CONST_18  CAN  CAU  CAD  CAF   180.00   0.0  0
 BWR  CONST_19  CAX  CAZ  CAW  CAT     0.00   0.0  0
 BWR  CONST_20  CAY  CAZ  CAW  CAT   180.00   0.0  0
 BWR  CONST_21  SAS  CAI  CAW  CAT   180.00   0.0  0
 BWR  CONST_22  CAH  NAR  CAX  OAC   180.00   0.0  0
 BWR  CONST_23  H17  CAE  CAG  CAV   180.00   0.0  0
 BWR  CONST_24  H19  CAD  CAF  CAV   180.00   0.0  0
 BWR  CONST_25  H18  CAF  CAV  CAG   180.00   0.0  0
 BWR  CONST_26  H16  CAG  CAV  CAF   180.00   0.0  0
 BWR  CONST_27  H25  CAI  CAW  CAZ   180.00   0.0  0
 BWR  CONST_28  H8   NAR  CAX  CAZ   180.00   0.0  0
 BWR  CONST_29  H23  CAH  NAR  CAX   180.00   0.0  0
 BWR  CONST_30  CAW  CAT  NAQ  CAN   180.00   0.0  0
 BWR  CONST_31  H22  NAQ  CAT  CAW     0.00   0.0  0
 BWR  CONST_32  OAB  CAT  NAQ  CAN     0.00   0.0  0
 BWR  Var_01    CAK  CAM  NBB  CAL    59.55  30.0  1
 BWR  Var_02    CAM  NBB  CAL  CAJ   -59.27  30.0  1
 BWR  Var_03    NBB  CAM  CAK  CBA   -57.30  30.0  1
 BWR  Var_04    NBB  CAL  CAJ  CBA    56.83  30.0  1
 BWR  Var_05    CAV  CAO  NBB  CAL   -69.85  30.0  3
 BWR  Var_06    CAG  CAV  CAO  NBB   -39.80  30.0  2
 BWR  Var_07    NAQ  CAN  CAU  CAE    80.06  30.0  2
 BWR  Var_08    CAZ  CAW  CAT  NAQ  -130.29  30.0  2
 BWR  Var_09    CAT  NAQ  CAN  CAU  -175.05  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
 BWR  chir_01  CBA  NAA  CAK  CAJ  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
 BWR  plan-1  CAO  0.020
 BWR  plan-1  CAV  0.020
 BWR  plan-1  CAG  0.020
 BWR  plan-1  CAE  0.020
 BWR  plan-1  CAF  0.020
 BWR  plan-1  CAD  0.020
 BWR  plan-1  CAU  0.020
 BWR  plan-1  CAN  0.020
 BWR  plan-1  H16  0.020
 BWR  plan-1  H17  0.020
 BWR  plan-1  H18  0.020
 BWR  plan-1  H19  0.020
 BWR  plan-2  CAT  0.020
 BWR  plan-2  CAW  0.020
 BWR  plan-2  CAZ  0.020
 BWR  plan-2  CAX  0.020
 BWR  plan-2  OAC  0.020
 BWR  plan-2  NAR  0.020
 BWR  plan-2  CAH  0.020
 BWR  plan-2  NAP  0.020
 BWR  plan-2  CAY  0.020
 BWR  plan-2  SAS  0.020
 BWR  plan-2  CAI  0.020
 BWR  plan-2  H23  0.020
 BWR  plan-2  H25  0.020
 BWR  plan-2  H8   0.020
 BWR  plan-3  CAN  0.020
 BWR  plan-3  NAQ  0.020
 BWR  plan-3  CAT  0.020
 BWR  plan-3  OAB  0.020
 BWR  plan-3  CAW  0.020
 BWR  plan-3  H22  0.020

