# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 16:30:19 2020
#   Inital geometry file: a 143 line input string
#   Ligand name: N-[(4-{[cyclohexyl(ethyl)amino]methyl}phenyl)methyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN(Cc1ccc(CNC(=O)c2csc3N=CNC(=O)c23)cc1)C4CCCCC4
#
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
 9D6  9D6  N-[(4-{[cyclohexyl(ethyl)amino]methyl}phenyl)methyl]-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide  ligand  58  30  .  2021-08-06  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9D6
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
 9D6  CAN  C  CH2   0  -0.424  -6.5321   1.0962   0.6450
 9D6  CAK  C  CH2   0  -0.433  -6.7641   2.4724   0.0258
 9D6  CAJ  C  CH2   0  -0.430  -7.4356   2.3667  -1.3393
 9D6  CAL  C  CH2   0  -0.429  -6.6389   1.4632  -2.2740
 9D6  CAO  C  CH2   0  -0.436  -6.4240   0.0840  -1.6563
 9D6  CBC  C  CH1   0  -0.066  -5.7346   0.1906  -0.2907
 9D6  NBD  N  NT    0  -0.415  -5.4173  -1.0874   0.3409
 9D6  CAM  C  CH2   0  -0.292  -6.5248  -2.0214   0.4560
 9D6  CAA  C  CH3   0  -0.657  -6.3879  -2.9240   1.6725
 9D6  CAQ  C  CH2   0  -0.340  -4.2227  -1.6907  -0.2054
 9D6  CAX  C  CR6   0   0.082  -2.9634  -0.9838   0.2307
 9D6  CAG  C  CR16  0  -0.268  -2.8384  -0.4771   1.5208
 9D6  CAE  C  CR16  0  -0.295  -1.6588   0.1243   1.9338
 9D6  CAF  C  CR16  0  -0.300  -1.8798  -0.8596  -0.6331
 9D6  CAD  C  CR16  0  -0.284  -0.6998  -0.2554  -0.2217
 9D6  CAW  C  CR6   0   0.095  -0.5741   0.2452   1.0700
 9D6  CAP  C  CH2   0  -0.358   0.6829   0.9424   1.5302
 9D6  NAS  N  NH1   0  -0.619   1.8917   0.2955   1.0791
 9D6  CAV  C  C     0   0.502   2.7131   0.7980   0.1435
 9D6  OAB  O  O     0  -0.468   2.5632   1.8758  -0.4061
 9D6  CAY  C  CR5   0   0.045   3.8390  -0.1077  -0.2310
 9D6  CBB  C  CR56  0  -0.058   5.2168   0.2625  -0.2822
 9D6  CAZ  C  CR6   0   0.542   5.8590   1.4550   0.2169
 9D6  OAC  O  O     0  -0.447   5.3348   2.3889   0.7919
 9D6  NAT  N  NR16  0  -0.653   7.2307   1.4287  -0.0157
 9D6  CAH  C  CR16  0   0.162   7.9035   0.4025  -0.5754
 9D6  NAR  N  N     0  -0.429   7.3540  -0.6942  -0.9776
 9D6  CBA  C  CR56  0  -0.020   6.0134  -0.7367  -0.8113
 9D6  SAU  S  S2    0   0.266   5.0858  -2.1224  -1.2423
 9D6  CAI  C  CR15  0  -0.515   3.6369  -1.3637  -0.7070
 9D6  H1   H  HCH2  0   0.226  -5.9948   1.1878   1.5924
 9D6  H2   H  HCH2  0   0.208  -7.5018   0.6418   0.8753
 9D6  H3   H  HCH2  0   0.226  -7.3676   3.0863   0.6989
 9D6  H4   H  HCH2  0   0.208  -5.8034   2.9880  -0.0834
 9D6  H5   H  HCH2  0   0.207  -8.4445   1.9577  -1.2145
 9D6  H6   H  HCH2  0   0.226  -7.5564   3.3591  -1.7809
 9D6  H7   H  HCH2  0   0.225  -7.1479   1.3670  -3.2364
 9D6  H8   H  HCH2  0   0.209  -5.6674   1.9240  -2.4839
 9D6  H9   H  HCH2  0   0.209  -7.3970  -0.4070  -1.5426
 9D6  H10  H  HCH2  0   0.227  -5.8359  -0.5442  -2.3324
 9D6  H11  H  HCH1  0   0.218  -4.7706   0.6896  -0.4528
 9D6  H13  H  HCH2  0   0.229  -7.4505  -1.4531   0.5570
 9D6  H14  H  HCH2  0   0.199  -6.6460  -2.6357  -0.4495
 9D6  H15  H  HCH3  0   0.222  -7.2390  -3.6026   1.7431
 9D6  H16  H  HCH3  0   0.219  -5.4862  -3.5369   1.6325
 9D6  H17  H  HCH3  0   0.221  -6.3463  -2.3301   2.5857
 9D6  H18  H  HCH2  0   0.251  -4.1652  -2.7270   0.1407
 9D6  H19  H  HCH2  0   0.217  -4.2392  -1.7540  -1.3055
 9D6  H20  H  HCR6  0   0.244  -3.6796  -0.5493   2.1987
 9D6  H21  H  HCR6  0   0.246  -1.5802   0.5047   2.9461
 9D6  H22  H  HCR6  0   0.244  -1.9587  -1.2358  -1.6469
 9D6  H23  H  HCR6  0   0.245   0.1217  -0.1729  -0.9234
 9D6  H24  H  HCH2  0   0.271   0.6970   1.9716   1.1708
 9D6  H25  H  HCH2  0   0.268   0.6955   0.9931   2.6204
 9D6  H26  H  HNH1  0   0.411   2.1236  -0.5938   1.4929
 9D6  H27  H  HCR6  0   0.311   8.9722   0.5395  -0.6725
 9D6  H29  H  HCR5  0   0.314   2.6957  -1.8832  -0.8097
 9D6  H30  H  HNR6  0   0.439   7.7644   2.2316   0.2932

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
 9D6  CAA  CAM  single    1.521  0.020  1.521
 9D6  CAM  NBD  single    1.453  0.020  1.453
 9D6  CAJ  CAL  single    1.525  0.020  1.525
 9D6  CAJ  CAK  single    1.525  0.020  1.525
 9D6  CAL  CAO  single    1.526  0.020  1.526
 9D6  CBC  CAN  single    1.527  0.020  1.527
 9D6  CBC  NBD  single    1.460  0.020  1.460
 9D6  CBC  CAO  single    1.533  0.020  1.533
 9D6  CAN  CAK  single    1.527  0.020  1.527
 9D6  NBD  CAQ  single    1.446  0.020  1.446
 9D6  CAQ  CAX  single    1.509  0.020  1.509
 9D6  CAX  CAG  aromatic  1.392  0.020  1.392
 9D6  CAX  CAF  aromatic  1.391  0.020  1.391
 9D6  CAG  CAE  aromatic  1.387  0.020  1.387
 9D6  CAF  CAD  aromatic  1.388  0.020  1.388
 9D6  CAE  CAW  aromatic  1.392  0.020  1.392
 9D6  CAD  CAW  aromatic  1.391  0.020  1.391
 9D6  CAW  CAP  single    1.509  0.020  1.509
 9D6  CAP  NAS  single    1.443  0.020  1.443
 9D6  NAS  CAV  single    1.343  0.020  1.343
 9D6  OAB  CAV  double    1.219  0.020  1.219
 9D6  OAC  CAZ  double    1.216  0.020  1.216
 9D6  CAV  CAY  single    1.493  0.020  1.493
 9D6  CAZ  CBB  single    1.444  0.020  1.444
 9D6  CAZ  NAT  single    1.391  0.020  1.391
 9D6  CAY  CBB  aromatic  1.428  0.020  1.428
 9D6  CAY  CAI  aromatic  1.358  0.020  1.358
 9D6  CBB  CBA  aromatic  1.383  0.020  1.383
 9D6  NAT  CAH  single    1.349  0.020  1.349
 9D6  CAI  SAU  aromatic  1.721  0.020  1.721
 9D6  CBA  SAU  aromatic  1.722  0.020  1.722
 9D6  CBA  NAR  single    1.351  0.020  1.351
 9D6  CAH  NAR  double    1.291  0.020  1.291
 9D6  CAN  H1   single    0.970  0.020  1.090
 9D6  CAN  H2   single    0.970  0.020  1.090
 9D6  CAK  H3   single    0.970  0.020  1.090
 9D6  CAK  H4   single    0.970  0.020  1.090
 9D6  CAJ  H5   single    0.970  0.020  1.090
 9D6  CAJ  H6   single    0.970  0.020  1.090
 9D6  CAL  H7   single    0.970  0.020  1.090
 9D6  CAL  H8   single    0.970  0.020  1.090
 9D6  CAO  H9   single    0.970  0.020  1.090
 9D6  CAO  H10  single    0.970  0.020  1.090
 9D6  CBC  H11  single    0.970  0.020  1.090
 9D6  CAM  H13  single    0.970  0.020  1.090
 9D6  CAM  H14  single    0.970  0.020  1.090
 9D6  CAA  H15  single    0.970  0.020  1.090
 9D6  CAA  H16  single    0.970  0.020  1.090
 9D6  CAA  H17  single    0.970  0.020  1.090
 9D6  CAQ  H18  single    0.970  0.020  1.090
 9D6  CAQ  H19  single    0.970  0.020  1.090
 9D6  CAG  H20  single    0.930  0.020  1.080
 9D6  CAE  H21  single    0.930  0.020  1.080
 9D6  CAF  H22  single    0.930  0.020  1.080
 9D6  CAD  H23  single    0.930  0.020  1.080
 9D6  CAP  H24  single    0.970  0.020  1.090
 9D6  CAP  H25  single    0.970  0.020  1.090
 9D6  NAS  H26  single    0.860  0.020  1.020
 9D6  CAH  H27  single    0.930  0.020  1.080
 9D6  CAI  H29  single    0.930  0.020  1.080
 9D6  NAT  H30  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
 9D6  H2   CAN  H1   106.72  3.000
 9D6  H2   CAN  CBC  110.19  3.000
 9D6  H1   CAN  CBC  108.91  3.000
 9D6  H2   CAN  CAK  108.95  3.000
 9D6  H1   CAN  CAK  110.53  3.000
 9D6  CBC  CAN  CAK  111.43  3.000
 9D6  H4   CAK  H3   106.33  3.000
 9D6  H4   CAK  CAJ  109.23  3.000
 9D6  H3   CAK  CAJ  110.31  3.000
 9D6  H4   CAK  CAN  109.35  3.000
 9D6  H3   CAK  CAN  109.91  3.000
 9D6  CAJ  CAK  CAN  111.56  3.000
 9D6  H6   CAJ  H5   106.45  3.000
 9D6  H6   CAJ  CAL  110.37  3.000
 9D6  H5   CAJ  CAL  109.25  3.000
 9D6  H6   CAJ  CAK  110.34  3.000
 9D6  H5   CAJ  CAK  109.23  3.000
 9D6  CAL  CAJ  CAK  111.09  3.000
 9D6  H8   CAL  H7   106.34  3.000
 9D6  H8   CAL  CAO  109.43  3.000
 9D6  H7   CAL  CAO  110.02  3.000
 9D6  H8   CAL  CAJ  109.36  3.000
 9D6  H7   CAL  CAJ  110.40  3.000
 9D6  CAO  CAL  CAJ  111.15  3.000
 9D6  H10  CAO  H9   106.50  3.000
 9D6  H10  CAO  CBC  110.39  3.000
 9D6  H9   CAO  CBC  109.75  3.000
 9D6  H10  CAO  CAL  110.14  3.000
 9D6  H9   CAO  CAL  108.78  3.000
 9D6  CBC  CAO  CAL  111.15  3.000
 9D6  H11  CBC  NBD  105.71  3.000
 9D6  H11  CBC  CAO  107.15  3.000
 9D6  NBD  CBC  CAO  114.96  3.000
 9D6  H11  CBC  CAN  106.24  3.000
 9D6  CAO  CBC  CAN  110.62  3.000
 9D6  NBD  CBC  CAN  111.56  3.000
 9D6  CAQ  NBD  CAM  113.05  3.000
 9D6  CAQ  NBD  CBC  112.42  3.000
 9D6  CAM  NBD  CBC  115.53  3.000
 9D6  H14  CAM  H13  105.86  3.000
 9D6  H14  CAM  CAA  109.67  3.000
 9D6  H13  CAM  CAA  108.15  3.000
 9D6  H14  CAM  NBD  112.17  3.000
 9D6  H13  CAM  NBD  108.61  3.000
 9D6  CAA  CAM  NBD  112.09  3.000
 9D6  H17  CAA  H16  107.77  3.000
 9D6  H17  CAA  H15  108.33  3.000
 9D6  H16  CAA  H15  107.33  3.000
 9D6  H17  CAA  CAM  110.49  3.000
 9D6  H16  CAA  CAM  112.24  3.000
 9D6  H15  CAA  CAM  110.53  3.000
 9D6  H19  CAQ  H18  105.20  3.000
 9D6  H19  CAQ  CAX  109.14  3.000
 9D6  H18  CAQ  CAX  107.97  3.000
 9D6  H19  CAQ  NBD  112.88  3.000
 9D6  H18  CAQ  NBD  108.61  3.000
 9D6  CAX  CAQ  NBD  112.65  3.000
 9D6  CAF  CAX  CAG  118.24  3.000
 9D6  CAF  CAX  CAQ  120.83  3.000
 9D6  CAG  CAX  CAQ  120.90  3.000
 9D6  H20  CAG  CAE  120.22  3.000
 9D6  H20  CAG  CAX  119.10  3.000
 9D6  CAE  CAG  CAX  120.68  3.000
 9D6  H21  CAE  CAW  119.50  3.000
 9D6  H21  CAE  CAG  119.46  3.000
 9D6  CAW  CAE  CAG  121.04  3.000
 9D6  H22  CAF  CAD  119.34  3.000
 9D6  H22  CAF  CAX  119.53  3.000
 9D6  CAD  CAF  CAX  121.13  3.000
 9D6  H23  CAD  CAW  120.36  3.000
 9D6  H23  CAD  CAF  119.06  3.000
 9D6  CAW  CAD  CAF  120.58  3.000
 9D6  CAP  CAW  CAD  121.65  3.000
 9D6  CAP  CAW  CAE  120.00  3.000
 9D6  CAD  CAW  CAE  118.33  3.000
 9D6  H25  CAP  H24  106.57  3.000
 9D6  H25  CAP  NAS  108.87  3.000
 9D6  H24  CAP  NAS  108.01  3.000
 9D6  H25  CAP  CAW  109.61  3.000
 9D6  H24  CAP  CAW  110.26  3.000
 9D6  NAS  CAP  CAW  113.28  3.000
 9D6  H26  NAS  CAV  118.40  3.000
 9D6  H26  NAS  CAP  117.38  3.000
 9D6  CAV  NAS  CAP  124.22  3.000
 9D6  CAY  CAV  OAB  121.07  3.000
 9D6  CAY  CAV  NAS  114.15  3.000
 9D6  OAB  CAV  NAS  124.74  3.000
 9D6  CAI  CAY  CBB  111.76  3.000
 9D6  CAI  CAY  CAV  122.46  3.000
 9D6  CBB  CAY  CAV  125.43  3.000
 9D6  CBA  CBB  CAZ  118.22  3.000
 9D6  CBA  CBB  CAY  112.47  3.000
 9D6  CAZ  CBB  CAY  129.14  3.000
 9D6  NAT  CAZ  OAC  121.25  3.000
 9D6  NAT  CAZ  CBB  111.41  3.000
 9D6  OAC  CAZ  CBB  127.33  3.000
 9D6  H30  NAT  CAH  117.85  3.000
 9D6  H30  NAT  CAZ  116.98  3.000
 9D6  CAH  NAT  CAZ  125.13  3.000
 9D6  H27  CAH  NAR  120.01  3.000
 9D6  H27  CAH  NAT  115.70  3.000
 9D6  NAR  CAH  NAT  124.29  3.000
 9D6  CBA  NAR  CAH  114.24  3.000
 9D6  SAU  CBA  NAR  121.92  3.000
 9D6  NAR  CBA  CBB  126.56  3.000
 9D6  SAU  CBA  CBB  111.52  3.000
 9D6  CAI  SAU  CBA   91.20  3.000
 9D6  H29  CAI  SAU  119.48  3.000
 9D6  H29  CAI  CAY  127.43  3.000
 9D6  SAU  CAI  CAY  113.04  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
 9D6  CONST_01  CAW  CAE  CAG  CAX     0.00   0.0  0
 9D6  CONST_02  CAW  CAD  CAF  CAX     0.00   0.0  0
 9D6  CONST_03  CAD  CAF  CAX  CAG     0.00   0.0  0
 9D6  CONST_04  CAD  CAW  CAE  CAG     0.00   0.0  0
 9D6  CONST_05  CAF  CAX  CAG  CAE     0.00   0.0  0
 9D6  CONST_06  CAF  CAD  CAW  CAE     0.00   0.0  0
 9D6  CONST_07  SAU  CBA  CBB  CAY     0.00   0.0  0
 9D6  CONST_08  CBA  SAU  CAI  CAY     0.00   0.0  0
 9D6  CONST_09  SAU  CAI  CAY  CBB     0.00   0.0  0
 9D6  CONST_10  CAI  SAU  CBA  CBB     0.00   0.0  0
 9D6  CONST_11  CAI  CAY  CBB  CBA     0.00   0.0  0
 9D6  CONST_12  CAH  NAT  CAZ  CBB     0.00   0.0  0
 9D6  CONST_13  NAR  CAH  NAT  CAZ     0.00   0.0  0
 9D6  CONST_14  CBA  NAR  CAH  NAT     0.00   0.0  0
 9D6  CONST_15  CAE  CAG  CAX  CAQ   180.00   0.0  0
 9D6  CONST_16  CAD  CAF  CAX  CAQ   180.00   0.0  0
 9D6  CONST_17  CAP  CAW  CAE  CAG   180.00   0.0  0
 9D6  CONST_18  CAP  CAW  CAD  CAF   180.00   0.0  0
 9D6  CONST_19  CAZ  CBB  CAY  CAV     0.00   0.0  0
 9D6  CONST_20  CBA  CBB  CAY  CAV   180.00   0.0  0
 9D6  CONST_21  SAU  CAI  CAY  CAV   180.00   0.0  0
 9D6  CONST_22  CAH  NAT  CAZ  OAC   180.00   0.0  0
 9D6  CONST_23  H21  CAE  CAG  CAX   180.00   0.0  0
 9D6  CONST_24  H23  CAD  CAF  CAX   180.00   0.0  0
 9D6  CONST_25  H22  CAF  CAX  CAG   180.00   0.0  0
 9D6  CONST_26  H20  CAG  CAX  CAF   180.00   0.0  0
 9D6  CONST_27  H29  CAI  CAY  CBB   180.00   0.0  0
 9D6  CONST_28  H30  NAT  CAZ  CBB   180.00   0.0  0
 9D6  CONST_29  H27  CAH  NAT  CAZ   180.00   0.0  0
 9D6  CONST_30  CAY  CAV  NAS  CAP   180.00   0.0  0
 9D6  CONST_31  H26  NAS  CAV  CAY     0.00   0.0  0
 9D6  CONST_32  OAB  CAV  NAS  CAP     0.00   0.0  0
 9D6  Var_01    CAL  CAJ  CAK  CAN   -55.05  30.0  1
 9D6  Var_02    CAO  CAL  CAJ  CAK    55.61  30.0  1
 9D6  Var_03    CBC  CAO  CAL  CAJ   -56.31  30.0  1
 9D6  Var_04    CBC  CAN  CAK  CAJ    55.21  30.0  1
 9D6  Var_05    CAX  CAQ  NBD  CBC    72.92  30.0  3
 9D6  Var_06    CAG  CAX  CAQ  NBD    37.78  30.0  2
 9D6  Var_07    NAS  CAP  CAW  CAE   140.08  30.0  2
 9D6  Var_08    CBB  CAY  CAV  NAS  -129.74  30.0  2
 9D6  Var_09    CAA  CAM  NBD  CBC  -149.81  30.0  2
 9D6  Var_10    CAV  NAS  CAP  CAW   109.03  30.0  3
 9D6  Var_11    H15  CAA  CAM  NBD   179.09  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
 9D6  chir_01  CBC  CAN  NBD  CAO  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
 9D6  plan-1  CAQ  0.020
 9D6  plan-1  CAX  0.020
 9D6  plan-1  CAG  0.020
 9D6  plan-1  CAE  0.020
 9D6  plan-1  CAF  0.020
 9D6  plan-1  CAD  0.020
 9D6  plan-1  CAW  0.020
 9D6  plan-1  CAP  0.020
 9D6  plan-1  H20  0.020
 9D6  plan-1  H21  0.020
 9D6  plan-1  H22  0.020
 9D6  plan-1  H23  0.020
 9D6  plan-2  CAV  0.020
 9D6  plan-2  CAY  0.020
 9D6  plan-2  CBB  0.020
 9D6  plan-2  CAZ  0.020
 9D6  plan-2  OAC  0.020
 9D6  plan-2  NAT  0.020
 9D6  plan-2  CAH  0.020
 9D6  plan-2  NAR  0.020
 9D6  plan-2  CBA  0.020
 9D6  plan-2  SAU  0.020
 9D6  plan-2  CAI  0.020
 9D6  plan-2  H27  0.020
 9D6  plan-2  H29  0.020
 9D6  plan-2  H30  0.020
 9D6  plan-3  CAP  0.020
 9D6  plan-3  NAS  0.020
 9D6  plan-3  CAV  0.020
 9D6  plan-3  OAB  0.020
 9D6  plan-3  CAY  0.020
 9D6  plan-3  H26  0.020

