# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 09:11:53 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 4-(4-{2-[(2,2-dimethylpropanoyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(C)C(=O)NCCC1CCN(CC1)c2ncnc3cc(sc23)C(N)=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
 1NR  1NR  4-(4-{2-[(2,2-dimethylpropanoyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide  ligand  54  27  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1NR
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
 1NR  CAY  C  CH3   0  -0.629   7.8258   2.2204  -0.0421
 1NR  CAX  C  CT    0  -0.249   6.9085   1.1494   0.5417
 1NR  CAZ  C  CH3   0  -0.642   7.6936  -0.1609   0.6880
 1NR  CBA  C  CH3   0  -0.638   6.4082   1.6120   1.9163
 1NR  CAA  C  C     0   0.600   5.7108   0.9325  -0.3916
 1NR  OAC  O  O     0  -0.497   5.5613   1.5568  -1.4341
 1NR  NAB  N  NH1   0  -0.647   4.8179   0.0114   0.0068
 1NR  CAD  C  CH2   0  -0.233   3.6285  -0.3143  -0.7524
 1NR  CAE  C  CH2   0  -0.471   2.7342  -1.2496   0.0468
 1NR  CAF  C  CH1   0  -0.245   1.4883  -1.6940  -0.7142
 1NR  CAK  C  CH2   0  -0.421   0.7557  -2.7951   0.0548
 1NR  CAJ  C  CH2   0  -0.335  -0.5419  -3.2147  -0.6283
 1NR  CAG  C  CH2   0  -0.422   0.5334  -0.5360  -1.0134
 1NR  CAH  C  CH2   0  -0.355  -0.7395  -1.0569  -1.6674
 1NR  NAI  N  NT    0  -0.470  -1.3894  -2.0458  -0.8291
 1NR  C6   C  CR6   0   0.587  -2.4763  -1.8347  -0.0663
 1NR  N1   N  N     0  -0.483  -2.9711  -2.8816   0.5981
 1NR  C2   C  CR16  0   0.040  -4.0703  -2.7516   1.3278
 1NR  N3   N  N     0  -0.460  -4.7897  -1.6704   1.5151
 1NR  C4   C  CR56  0   0.317  -4.3043  -0.5798   0.8977
 1NR  CAR  C  CR15  0  -0.206  -4.8759   0.7223   1.0122
 1NR  C5   C  CR56  0  -0.329  -3.1564  -0.5934   0.0969
 1NR  SAT  S  S2    0   0.226  -2.7859   1.0017  -0.4655
 1NR  CAS  C  CR5   0  -0.278  -4.1572   1.6620   0.3533
 1NR  CAU  C  C     0   0.507  -4.5087   3.1069   0.3006
 1NR  OAV  O  O     0  -0.461  -5.6389   3.4668   0.5871
 1NR  NAW  N  NH2   0  -0.816  -3.5319   3.9413  -0.0803
 1NR  H1   H  HCH3  0   0.229   8.2180   1.9338  -1.0181
 1NR  H2   H  HCH3  0   0.229   7.3156   3.1775  -0.1503
 1NR  H3   H  HCH3  0   0.225   8.6760   2.3711   0.6247
 1NR  H4   H  HCH3  0   0.237   8.5840   0.0099   1.2952
 1NR  H5   H  HCH3  0   0.227   7.1169  -0.9461   1.1793
 1NR  H6   H  HCH3  0   0.237   8.0207  -0.5413  -0.2810
 1NR  H7   H  HCH3  0   0.236   5.8159   2.5255   1.8381
 1NR  H8   H  HCH3  0   0.227   5.7978   0.8594   2.4172
 1NR  H9   H  HCH3  0   0.236   7.2579   1.8238   2.5676
 1NR  H10  H  HNH1  0   0.394   4.9873  -0.5069   0.8530
 1NR  H11  H  HCH2  0   0.234   3.0980   0.6075  -0.9994
 1NR  H12  H  HCH2  0   0.228   3.8989  -0.7879  -1.7019
 1NR  H13  H  HCH2  0   0.239   3.3092  -2.1389   0.3271
 1NR  H14  H  HCH2  0   0.232   2.4359  -0.7630   0.9817
 1NR  H15  H  HCH1  0   0.226   1.8058  -2.1190  -1.6763
 1NR  H16  H  HCH2  0   0.243   1.4010  -3.6712   0.1549
 1NR  H17  H  HCH2  0   0.226   0.5272  -2.4491   1.0685
 1NR  H18  H  HCH2  0   0.244  -0.3304  -3.6544  -1.6075
 1NR  H19  H  HCH2  0   0.280  -1.0731  -3.9554  -0.0401
 1NR  H20  H  HCH2  0   0.227   0.2810  -0.0107  -0.0857
 1NR  H21  H  HCH2  0   0.250   0.9980   0.1927  -1.6806
 1NR  H22  H  HCH2  0   0.266  -1.4212  -0.2571  -1.9445
 1NR  H23  H  HCH2  0   0.269  -0.4870  -1.5525  -2.6100
 1NR  H24  H  HCR6  0   0.254  -4.4075  -3.6548   1.8263
 1NR  H25  H  HCR5  0   0.283  -5.7703   0.9296   1.5815
 1NR  H27  H  HNH2  0   0.415  -2.5668   3.6634  -0.1471
 1NR  H28  H  HNH2  0   0.415  -3.7131   4.9324  -0.1001

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
 1NR  CAY  CAX  single    1.526  0.020  1.526
 1NR  CAX  CAZ  single    1.535  0.020  1.535
 1NR  CAX  CBA  single    1.534  0.020  1.534
 1NR  CAX  CAA  single    1.534  0.020  1.534
 1NR  CAA  OAC  double    1.224  0.020  1.224
 1NR  CAA  NAB  single    1.343  0.020  1.343
 1NR  NAB  CAD  single    1.448  0.020  1.448
 1NR  CAD  CAE  single    1.521  0.020  1.521
 1NR  CAE  CAF  single    1.526  0.020  1.526
 1NR  CAF  CAK  single    1.530  0.020  1.530
 1NR  CAF  CAG  single    1.530  0.020  1.530
 1NR  CAK  CAJ  single    1.525  0.020  1.525
 1NR  CAJ  NAI  single    1.458  0.020  1.458
 1NR  CAG  CAH  single    1.523  0.020  1.523
 1NR  CAH  NAI  single    1.450  0.020  1.450
 1NR  NAI  C6   single    1.345  0.020  1.345
 1NR  C6   N1   aromatic  1.335  0.020  1.335
 1NR  C6   C5   aromatic  1.425  0.020  1.425
 1NR  N1   C2   aromatic  1.326  0.020  1.326
 1NR  C2   N3   aromatic  1.312  0.020  1.312
 1NR  N3   C4   aromatic  1.344  0.020  1.344
 1NR  C4   CAR  aromatic  1.427  0.020  1.427
 1NR  C4   C5   aromatic  1.400  0.020  1.400
 1NR  CAR  CAS  aromatic  1.354  0.020  1.354
 1NR  C5   SAT  aromatic  1.731  0.020  1.731
 1NR  SAT  CAS  aromatic  1.728  0.020  1.728
 1NR  CAS  CAU  single    1.488  0.020  1.488
 1NR  CAU  OAV  double    1.220  0.020  1.220
 1NR  CAU  NAW  single    1.340  0.020  1.340
 1NR  CAY  H1   single    0.970  0.020  1.090
 1NR  CAY  H2   single    0.970  0.020  1.090
 1NR  CAY  H3   single    0.970  0.020  1.090
 1NR  CAZ  H4   single    0.970  0.020  1.090
 1NR  CAZ  H5   single    0.970  0.020  1.090
 1NR  CAZ  H6   single    0.970  0.020  1.090
 1NR  CBA  H7   single    0.970  0.020  1.090
 1NR  CBA  H8   single    0.970  0.020  1.090
 1NR  CBA  H9   single    0.970  0.020  1.090
 1NR  NAB  H10  single    0.860  0.020  1.020
 1NR  CAD  H11  single    0.970  0.020  1.090
 1NR  CAD  H12  single    0.970  0.020  1.090
 1NR  CAE  H13  single    0.970  0.020  1.090
 1NR  CAE  H14  single    0.970  0.020  1.090
 1NR  CAF  H15  single    0.970  0.020  1.090
 1NR  CAK  H16  single    0.970  0.020  1.090
 1NR  CAK  H17  single    0.970  0.020  1.090
 1NR  CAJ  H18  single    0.970  0.020  1.090
 1NR  CAJ  H19  single    0.970  0.020  1.090
 1NR  CAG  H20  single    0.970  0.020  1.090
 1NR  CAG  H21  single    0.970  0.020  1.090
 1NR  CAH  H22  single    0.970  0.020  1.090
 1NR  CAH  H23  single    0.970  0.020  1.090
 1NR  C2   H24  single    0.930  0.020  1.080
 1NR  CAR  H25  single    0.930  0.020  1.080
 1NR  NAW  H27  single    0.860  0.020  1.020
 1NR  NAW  H28  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
 1NR  H3   CAY  H2   107.70  3.000
 1NR  H3   CAY  H1   107.64  3.000
 1NR  H2   CAY  H1   108.08  3.000
 1NR  H3   CAY  CAX  109.36  3.000
 1NR  H2   CAY  CAX  111.89  3.000
 1NR  H1   CAY  CAX  111.98  3.000
 1NR  CAA  CAX  CBA  109.46  3.000
 1NR  CAA  CAX  CAZ  109.68  3.000
 1NR  CBA  CAX  CAZ  109.81  3.000
 1NR  CAA  CAX  CAY  109.62  3.000
 1NR  CBA  CAX  CAY  109.10  3.000
 1NR  CAZ  CAX  CAY  109.16  3.000
 1NR  H6   CAZ  H5   107.91  3.000
 1NR  H6   CAZ  H4   107.70  3.000
 1NR  H5   CAZ  H4   107.06  3.000
 1NR  H6   CAZ  CAX  111.49  3.000
 1NR  H5   CAZ  CAX  112.77  3.000
 1NR  H4   CAZ  CAX  109.69  3.000
 1NR  H9   CBA  H8   107.18  3.000
 1NR  H9   CBA  H7   107.63  3.000
 1NR  H8   CBA  H7   107.86  3.000
 1NR  H9   CBA  CAX  109.84  3.000
 1NR  H8   CBA  CAX  112.70  3.000
 1NR  H7   CBA  CAX  111.41  3.000
 1NR  NAB  CAA  OAC  121.40  3.000
 1NR  NAB  CAA  CAX  115.82  3.000
 1NR  OAC  CAA  CAX  122.78  3.000
 1NR  H10  NAB  CAD  117.59  3.000
 1NR  H10  NAB  CAA  119.38  3.000
 1NR  CAD  NAB  CAA  123.00  3.000
 1NR  H12  CAD  H11  106.79  3.000
 1NR  H12  CAD  CAE  109.57  3.000
 1NR  H11  CAD  CAE  110.63  3.000
 1NR  H12  CAD  NAB  110.43  3.000
 1NR  H11  CAD  NAB  109.14  3.000
 1NR  CAE  CAD  NAB  110.23  3.000
 1NR  H14  CAE  H13  106.58  3.000
 1NR  H14  CAE  CAF  109.43  3.000
 1NR  H13  CAE  CAF  108.65  3.000
 1NR  H14  CAE  CAD  109.59  3.000
 1NR  H13  CAE  CAD  108.96  3.000
 1NR  CAF  CAE  CAD  113.40  3.000
 1NR  H15  CAF  CAG  107.56  3.000
 1NR  H15  CAF  CAK  107.47  3.000
 1NR  CAG  CAF  CAK  110.12  3.000
 1NR  H15  CAF  CAE  108.26  3.000
 1NR  CAG  CAF  CAE  112.74  3.000
 1NR  CAK  CAF  CAE  110.48  3.000
 1NR  H17  CAK  H16  106.96  3.000
 1NR  H17  CAK  CAJ  108.90  3.000
 1NR  H16  CAK  CAJ  108.84  3.000
 1NR  H17  CAK  CAF  109.74  3.000
 1NR  H16  CAK  CAF  109.89  3.000
 1NR  CAJ  CAK  CAF  112.35  3.000
 1NR  H19  CAJ  H18  107.79  3.000
 1NR  H19  CAJ  NAI  109.73  3.000
 1NR  H18  CAJ  NAI  108.14  3.000
 1NR  H19  CAJ  CAK  111.20  3.000
 1NR  H18  CAJ  CAK  110.30  3.000
 1NR  NAI  CAJ  CAK  109.62  3.000
 1NR  H21  CAG  H20  107.19  3.000
 1NR  H21  CAG  CAH  108.76  3.000
 1NR  H20  CAG  CAH  109.58  3.000
 1NR  H21  CAG  CAF  111.03  3.000
 1NR  H20  CAG  CAF  109.93  3.000
 1NR  CAH  CAG  CAF  110.28  3.000
 1NR  H23  CAH  H22  104.97  3.000
 1NR  H23  CAH  NAI  107.00  3.000
 1NR  H22  CAH  NAI  111.60  3.000
 1NR  H23  CAH  CAG  109.38  3.000
 1NR  H22  CAH  CAG  112.46  3.000
 1NR  NAI  CAH  CAG  111.08  3.000
 1NR  C6   NAI  CAH  125.67  3.000
 1NR  C6   NAI  CAJ  121.18  3.000
 1NR  CAH  NAI  CAJ  111.46  3.000
 1NR  C5   C6   N1   116.70  3.000
 1NR  C5   C6   NAI  125.99  3.000
 1NR  N1   C6   NAI  117.31  3.000
 1NR  C2   N1   C6   120.29  3.000
 1NR  H24  C2   N3   116.73  3.000
 1NR  H24  C2   N1   115.40  3.000
 1NR  N3   C2   N1   127.88  3.000
 1NR  C4   N3   C2   113.90  3.000
 1NR  C5   C4   CAR  112.54  3.000
 1NR  C5   C4   N3   123.45  3.000
 1NR  CAR  C4   N3   123.99  3.000
 1NR  H25  CAR  CAS  124.24  3.000
 1NR  H25  CAR  C4   123.31  3.000
 1NR  CAS  CAR  C4   112.44  3.000
 1NR  SAT  C5   C4   110.64  3.000
 1NR  SAT  C5   C6   131.55  3.000
 1NR  C4   C5   C6   117.74  3.000
 1NR  CAS  SAT  C5    91.62  3.000
 1NR  CAU  CAS  SAT  122.80  3.000
 1NR  CAU  CAS  CAR  124.45  3.000
 1NR  SAT  CAS  CAR  112.74  3.000
 1NR  NAW  CAU  OAV  123.94  3.000
 1NR  NAW  CAU  CAS  116.27  3.000
 1NR  OAV  CAU  CAS  119.79  3.000
 1NR  H28  NAW  H27  116.27  3.000
 1NR  H28  NAW  CAU  119.14  3.000
 1NR  H27  NAW  CAU  123.09  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
 1NR  CONST_01  N3   C2   N1   C6      0.00   0.0  0
 1NR  CONST_02  N3   C4   C5   C6      0.00   0.0  0
 1NR  CONST_03  CAR  C4   C5   C6    180.00   0.0  0
 1NR  CONST_04  CAS  SAT  C5   C6    180.00   0.0  0
 1NR  CONST_05  C4   C5   C6   N1      0.00   0.0  0
 1NR  CONST_06  SAT  C5   C6   N1    180.00   0.0  0
 1NR  CONST_07  C4   N3   C2   N1      0.00   0.0  0
 1NR  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 1NR  CONST_09  CAR  C4   N3   C2    180.00   0.0  0
 1NR  CONST_10  C5   C4   N3   C2      0.00   0.0  0
 1NR  CONST_11  CAS  CAR  C4   N3    180.00   0.0  0
 1NR  CONST_12  SAT  C5   C4   N3    180.00   0.0  0
 1NR  CONST_13  SAT  CAS  CAR  C4      0.00   0.0  0
 1NR  CONST_14  CAS  SAT  C5   C4      0.00   0.0  0
 1NR  CONST_15  SAT  C5   C4   CAR     0.00   0.0  0
 1NR  CONST_16  C5   SAT  CAS  CAR     0.00   0.0  0
 1NR  CONST_17  CAS  CAR  C4   C5      0.00   0.0  0
 1NR  CONST_18  C2   N1   C6   NAI   180.00   0.0  0
 1NR  CONST_19  C4   C5   C6   NAI   180.00   0.0  0
 1NR  CONST_20  SAT  C5   C6   NAI     0.00   0.0  0
 1NR  CONST_21  CAU  CAS  CAR  C4    180.00   0.0  0
 1NR  CONST_22  CAU  CAS  SAT  C5    180.00   0.0  0
 1NR  CONST_23  H24  C2   N1   C6    180.00   0.0  0
 1NR  CONST_24  H25  CAR  C4   N3      0.00   0.0  0
 1NR  CONST_25  H27  NAW  CAU  CAS     0.00   0.0  0
 1NR  CONST_26  H28  NAW  CAU  CAS   180.00   0.0  0
 1NR  CONST_27  CAD  NAB  CAA  CAX   180.00   0.0  0
 1NR  CONST_28  CAD  NAB  CAA  OAC     0.00   0.0  0
 1NR  CONST_29  H10  NAB  CAA  CAX     0.00   0.0  0
 1NR  Var_01    NAI  CAJ  CAK  CAF   -55.33  30.0  1
 1NR  Var_02    NAI  CAH  CAG  CAF    57.21  30.0  1
 1NR  Var_03    CAH  NAI  CAJ  CAK    60.41  30.0  1
 1NR  Var_04    CAG  CAH  NAI  CAJ   -62.39  30.0  1
 1NR  Var_05    N1   C6   NAI  CAJ   -18.84  30.0  2
 1NR  Var_06    OAV  CAU  CAS  CAR   -17.57  30.0  2
 1NR  Var_07    CAF  CAE  CAD  NAB  -177.22  30.0  3
 1NR  Var_08    OAC  CAA  CAX  CAY    -0.25  30.0  3
 1NR  Var_09    CAE  CAD  NAB  CAA  -172.41  30.0  3
 1NR  Var_10    H4   CAZ  CAX  CAY    55.95  30.0  3
 1NR  Var_11    H7   CBA  CAX  CAY    62.37  30.0  3
 1NR  Var_12    H1   CAY  CAX  CAZ    59.39  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
 1NR  chir_01  CAF  CAE  CAK  CAG  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
 1NR  plan-1  NAI  0.020
 1NR  plan-1  C6   0.020
 1NR  plan-1  N1   0.020
 1NR  plan-1  C2   0.020
 1NR  plan-1  N3   0.020
 1NR  plan-1  C4   0.020
 1NR  plan-1  CAR  0.020
 1NR  plan-1  C5   0.020
 1NR  plan-1  SAT  0.020
 1NR  plan-1  CAS  0.020
 1NR  plan-1  CAU  0.020
 1NR  plan-1  H24  0.020
 1NR  plan-1  H25  0.020
 1NR  plan-2  CAS  0.020
 1NR  plan-2  CAU  0.020
 1NR  plan-2  OAV  0.020
 1NR  plan-2  NAW  0.020
 1NR  plan-2  H27  0.020
 1NR  plan-2  H28  0.020
 1NR  plan-3  CAX  0.020
 1NR  plan-3  CAA  0.020
 1NR  plan-3  OAC  0.020
 1NR  plan-3  NAB  0.020
 1NR  plan-3  CAD  0.020
 1NR  plan-3  H10  0.020

