# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 23:35:11 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: N-({4-[(octylamino)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: CCCCCCCCNCc1ccc(CNC(=O)c2csc3N=CNC(=O)c23)cc1
#
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
 9D0  9D0  N-({4-[(octylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide  ligand  60  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_9D0
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
 9D0  CAA  C  CH3   0  -0.662  11.9736   3.8707  -0.9569
 9D0  CAJ  C  CH2   0  -0.418  11.3916   2.5614  -0.4420
 9D0  CAK  C  CH2   0  -0.406   9.8748   2.4977  -0.5734
 9D0  CAL  C  CH2   0  -0.411   9.2768   1.1912  -0.0666
 9D0  CAM  C  CH2   0  -0.411   7.7609   1.1332  -0.2063
 9D0  CAN  C  CH2   0  -0.416   7.1569  -0.1716   0.2979
 9D0  CAO  C  CH2   0  -0.441   5.6451  -0.2318   0.1212
 9D0  CAP  C  CH2   0  -0.247   5.0413  -1.5329   0.6249
 9D0  NAT  N  NH1   0  -0.596   3.6124  -1.5775   0.3778
 9D0  CAQ  C  CH2   0  -0.311   2.9887  -2.7975   0.8458
 9D0  CAY  C  CR6   0   0.074   1.5324  -2.8628   0.4655
 9D0  CAE  C  CR16  0  -0.280   1.1108  -2.4914  -0.8088
 9D0  CAG  C  CR16  0  -0.279  -0.2263  -2.5810  -1.1680
 9D0  CAD  C  CR16  0  -0.304   0.5771  -3.3208   1.3687
 9D0  CAF  C  CR16  0  -0.279  -0.7592  -3.4154   1.0074
 9D0  CAZ  C  CR6   0   0.111  -1.1779  -3.0472  -0.2674
 9D0  CAR  C  CH2   0  -0.392  -2.6349  -3.1316  -0.6467
 9D0  NAU  N  NH1   0  -0.617  -3.4434  -2.1344   0.0257
 9D0  CAX  C  C     0   0.508  -3.4235  -0.8414  -0.3263
 9D0  OAB  O  O     0  -0.464  -2.8003  -0.4052  -1.2788
 9D0  CBA  C  CR5   0   0.048  -4.2013   0.0596   0.5742
 9D0  CBD  C  CR56  0  -0.060  -5.1796   1.0118   0.1556
 9D0  CBB  C  CR6   0   0.542  -5.7995   1.1740  -1.1379
 9D0  OAC  O  O     0  -0.447  -5.6002   0.5137  -2.1390
 9D0  NAV  N  NR16  0  -0.653  -6.7256   2.2127  -1.1316
 9D0  CAH  C  CR16  0   0.162  -7.0596   2.9480  -0.0514
 9D0  NAS  N  N     0  -0.429  -6.5532   2.7843   1.1245
 9D0  CBC  C  CR56  0  -0.020  -5.6236   1.8061   1.1975
 9D0  SAW  S  S2    0   0.265  -4.8514   1.3935   2.6808
 9D0  CAI  C  CR15  0  -0.510  -3.9441   0.1544   1.9046
 9D0  H1   H  HCH3  0   0.215  11.5539   4.7248  -0.4218
 9D0  H2   H  HCH3  0   0.226  13.0570   3.9051  -0.8366
 9D0  H3   H  HCH3  0   0.216  11.7553   4.0088  -2.0175
 9D0  H4   H  HCH2  0   0.210  11.8370   1.7222  -0.9855
 9D0  H5   H  HCH2  0   0.209  11.6701   2.4234   0.6075
 9D0  H6   H  HCH2  0   0.206   9.4284   3.3368  -0.0280
 9D0  H7   H  HCH2  0   0.205   9.5972   2.6403  -1.6241
 9D0  H8   H  HCH2  0   0.206   9.7238   0.3518  -0.6109
 9D0  H9   H  HCH2  0   0.206   9.5513   1.0495   0.9849
 9D0  H10  H  HCH2  0   0.208   7.3130   1.9734   0.3358
 9D0  H11  H  HCH2  0   0.207   7.4895   1.2743  -1.2586
 9D0  H12  H  HCH2  0   0.209   7.6178  -1.0126  -0.2317
 9D0  H13  H  HCH2  0   0.209   7.4097  -0.3043   1.3556
 9D0  H14  H  HCH2  0   0.213   5.1834   0.6112   0.6476
 9D0  H15  H  HCH2  0   0.214   5.3931  -0.1105  -0.9369
 9D0  H16  H  HCH2  0   0.213   5.5033  -2.3742   0.0974
 9D0  H17  H  HCH2  0   0.185   5.2927  -1.6655   1.6901
 9D0  H18  H  HNH1  0   0.339   3.1713  -0.7868   0.8337
 9D0  H20  H  HCH2  0   0.237   3.5142  -3.6388   0.3806
 9D0  H21  H  HCH2  0   0.211   3.0885  -2.9481   1.9319
 9D0  H22  H  HCR6  0   0.242   1.8359  -2.1197  -1.5219
 9D0  H23  H  HCR6  0   0.245  -0.5342  -2.2807  -2.1621
 9D0  H24  H  HCR6  0   0.247   0.8803  -3.6110   2.3681
 9D0  H25  H  HCR6  0   0.248  -1.4820  -3.7787   1.7294
 9D0  H26  H  HCH2  0   0.264  -2.7518  -3.0277  -1.7263
 9D0  H27  H  HCH2  0   0.276  -3.0423  -4.1043  -0.3725
 9D0  H28  H  HNH1  0   0.411  -4.0107  -2.4223   0.8058
 9D0  H29  H  HCR6  0   0.311  -7.8076   3.7120  -0.2166
 9D0  H31  H  HCR5  0   0.314  -3.2326  -0.4220   2.4767
 9D0  H19  H  HNR6  0   0.439  -7.2067   2.4051  -2.0015

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
 9D0  CAH  NAS  double    1.291  0.020  1.291
 9D0  CAH  NAV  single    1.349  0.020  1.349
 9D0  NAS  CBC  single    1.351  0.020  1.351
 9D0  NAV  CBB  single    1.392  0.020  1.392
 9D0  CBC  CBD  aromatic  1.383  0.020  1.383
 9D0  CBC  SAW  aromatic  1.722  0.020  1.722
 9D0  CBB  OAC  double    1.216  0.020  1.216
 9D0  CBB  CBD  single    1.444  0.020  1.444
 9D0  CBD  CBA  aromatic  1.428  0.020  1.428
 9D0  SAW  CAI  aromatic  1.721  0.020  1.721
 9D0  CBA  CAI  aromatic  1.358  0.020  1.358
 9D0  CBA  CAX  single    1.493  0.020  1.493
 9D0  CAX  NAU  single    1.340  0.020  1.340
 9D0  CAX  OAB  double    1.219  0.020  1.219
 9D0  NAU  CAR  single    1.449  0.020  1.449
 9D0  CAF  CAD  aromatic  1.388  0.020  1.388
 9D0  CAF  CAZ  aromatic  1.391  0.020  1.391
 9D0  CAP  NAT  single    1.451  0.020  1.451
 9D0  CAP  CAO  single    1.520  0.020  1.520
 9D0  NAT  CAQ  single    1.448  0.020  1.448
 9D0  CAD  CAY  aromatic  1.392  0.020  1.392
 9D0  CAR  CAZ  single    1.508  0.020  1.508
 9D0  CAZ  CAG  aromatic  1.391  0.020  1.391
 9D0  CAO  CAN  single    1.523  0.020  1.523
 9D0  CAY  CAQ  single    1.507  0.020  1.507
 9D0  CAY  CAE  aromatic  1.393  0.020  1.393
 9D0  CAN  CAM  single    1.524  0.020  1.524
 9D0  CAG  CAE  aromatic  1.387  0.020  1.387
 9D0  CAM  CAL  single    1.523  0.020  1.523
 9D0  CAL  CAK  single    1.524  0.020  1.524
 9D0  CAK  CAJ  single    1.524  0.020  1.524
 9D0  CAJ  CAA  single    1.522  0.020  1.522
 9D0  CAA  H1   single    0.970  0.020  1.090
 9D0  CAA  H2   single    0.970  0.020  1.090
 9D0  CAA  H3   single    0.970  0.020  1.090
 9D0  CAJ  H4   single    0.970  0.020  1.090
 9D0  CAJ  H5   single    0.970  0.020  1.090
 9D0  CAK  H6   single    0.970  0.020  1.090
 9D0  CAK  H7   single    0.970  0.020  1.090
 9D0  CAL  H8   single    0.970  0.020  1.090
 9D0  CAL  H9   single    0.970  0.020  1.090
 9D0  CAM  H10  single    0.970  0.020  1.090
 9D0  CAM  H11  single    0.970  0.020  1.090
 9D0  CAN  H12  single    0.970  0.020  1.090
 9D0  CAN  H13  single    0.970  0.020  1.090
 9D0  CAO  H14  single    0.970  0.020  1.090
 9D0  CAO  H15  single    0.970  0.020  1.090
 9D0  CAP  H16  single    0.970  0.020  1.090
 9D0  CAP  H17  single    0.970  0.020  1.090
 9D0  NAT  H18  single    0.890  0.020  1.040
 9D0  CAQ  H20  single    0.970  0.020  1.090
 9D0  CAQ  H21  single    0.970  0.020  1.090
 9D0  CAE  H22  single    0.930  0.020  1.080
 9D0  CAG  H23  single    0.930  0.020  1.080
 9D0  CAD  H24  single    0.930  0.020  1.080
 9D0  CAF  H25  single    0.930  0.020  1.080
 9D0  CAR  H26  single    0.970  0.020  1.090
 9D0  CAR  H27  single    0.970  0.020  1.090
 9D0  NAU  H28  single    0.860  0.020  1.020
 9D0  CAH  H29  single    0.930  0.020  1.080
 9D0  CAI  H31  single    0.930  0.020  1.080
 9D0  NAV  H19  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
 9D0  H3   CAA  H2   107.57  3.000
 9D0  H3   CAA  H1   107.48  3.000
 9D0  H2   CAA  H1   107.64  3.000
 9D0  H3   CAA  CAJ  111.16  3.000
 9D0  H2   CAA  CAJ  111.69  3.000
 9D0  H1   CAA  CAJ  111.11  3.000
 9D0  H5   CAJ  H4   106.01  3.000
 9D0  H5   CAJ  CAK  109.31  3.000
 9D0  H4   CAJ  CAK  109.28  3.000
 9D0  H5   CAJ  CAA  109.59  3.000
 9D0  H4   CAJ  CAA  109.63  3.000
 9D0  CAK  CAJ  CAA  112.79  3.000
 9D0  H7   CAK  H6   105.92  3.000
 9D0  H7   CAK  CAL  109.33  3.000
 9D0  H6   CAK  CAL  109.34  3.000
 9D0  H7   CAK  CAJ  109.23  3.000
 9D0  H6   CAK  CAJ  109.30  3.000
 9D0  CAL  CAK  CAJ  113.45  3.000
 9D0  H9   CAL  H8   105.99  3.000
 9D0  H9   CAL  CAM  109.41  3.000
 9D0  H8   CAL  CAM  109.34  3.000
 9D0  H9   CAL  CAK  109.37  3.000
 9D0  H8   CAL  CAK  109.36  3.000
 9D0  CAM  CAL  CAK  113.12  3.000
 9D0  H11  CAM  H10  105.97  3.000
 9D0  H11  CAM  CAN  109.26  3.000
 9D0  H10  CAM  CAN  109.32  3.000
 9D0  H11  CAM  CAL  109.25  3.000
 9D0  H10  CAM  CAL  109.40  3.000
 9D0  CAN  CAM  CAL  113.37  3.000
 9D0  H13  CAN  H12  106.06  3.000
 9D0  H13  CAN  CAO  109.65  3.000
 9D0  H12  CAN  CAO  109.34  3.000
 9D0  H13  CAN  CAM  109.37  3.000
 9D0  H12  CAN  CAM  109.31  3.000
 9D0  CAO  CAN  CAM  112.89  3.000
 9D0  H15  CAO  H14  106.38  3.000
 9D0  H15  CAO  CAP  108.89  3.000
 9D0  H14  CAO  CAP  109.38  3.000
 9D0  H15  CAO  CAN  109.65  3.000
 9D0  H14  CAO  CAN  109.39  3.000
 9D0  CAP  CAO  CAN  112.93  3.000
 9D0  H17  CAP  H16  106.07  3.000
 9D0  H17  CAP  NAT  112.67  3.000
 9D0  H16  CAP  NAT  108.05  3.000
 9D0  H17  CAP  CAO  109.42  3.000
 9D0  H16  CAP  CAO  109.29  3.000
 9D0  NAT  CAP  CAO  111.17  3.000
 9D0  H18  NAT  CAQ  108.93  3.000
 9D0  H18  NAT  CAP  109.15  3.000
 9D0  CAQ  NAT  CAP  113.27  3.000
 9D0  H21  CAQ  H20  105.68  3.000
 9D0  H21  CAQ  CAY  109.31  3.000
 9D0  H20  CAQ  CAY  108.86  3.000
 9D0  H21  CAQ  NAT  113.27  3.000
 9D0  H20  CAQ  NAT  107.65  3.000
 9D0  CAY  CAQ  NAT  111.80  3.000
 9D0  CAD  CAY  CAE  118.27  3.000
 9D0  CAE  CAY  CAQ  120.80  3.000
 9D0  CAD  CAY  CAQ  120.92  3.000
 9D0  H22  CAE  CAG  119.81  3.000
 9D0  H22  CAE  CAY  119.43  3.000
 9D0  CAG  CAE  CAY  120.76  3.000
 9D0  H23  CAG  CAZ  119.52  3.000
 9D0  H23  CAG  CAE  119.58  3.000
 9D0  CAZ  CAG  CAE  120.89  3.000
 9D0  H24  CAD  CAF  119.42  3.000
 9D0  H24  CAD  CAY  119.63  3.000
 9D0  CAF  CAD  CAY  120.95  3.000
 9D0  H25  CAF  CAZ  119.88  3.000
 9D0  H25  CAF  CAD  119.43  3.000
 9D0  CAZ  CAF  CAD  120.69  3.000
 9D0  CAR  CAZ  CAF  120.42  3.000
 9D0  CAR  CAZ  CAG  121.14  3.000
 9D0  CAF  CAZ  CAG  118.43  3.000
 9D0  H27  CAR  H26  107.10  3.000
 9D0  H27  CAR  NAU  106.79  3.000
 9D0  H26  CAR  NAU  109.50  3.000
 9D0  H27  CAR  CAZ  110.36  3.000
 9D0  H26  CAR  CAZ  110.31  3.000
 9D0  NAU  CAR  CAZ  112.57  3.000
 9D0  H28  NAU  CAX  119.20  3.000
 9D0  H28  NAU  CAR  118.50  3.000
 9D0  CAX  NAU  CAR  122.26  3.000
 9D0  CBA  CAX  OAB  121.45  3.000
 9D0  OAB  CAX  NAU  123.92  3.000
 9D0  CBA  CAX  NAU  114.59  3.000
 9D0  CAI  CBA  CBD  111.73  3.000
 9D0  CAI  CBA  CAX  122.30  3.000
 9D0  CBD  CBA  CAX  125.64  3.000
 9D0  CBC  CBD  CBB  118.20  3.000
 9D0  CBB  CBD  CBA  129.18  3.000
 9D0  CBC  CBD  CBA  112.46  3.000
 9D0  NAV  CBB  OAC  121.21  3.000
 9D0  OAC  CBB  CBD  127.33  3.000
 9D0  NAV  CBB  CBD  111.45  3.000
 9D0  H19  NAV  CAH  117.83  3.000
 9D0  H19  NAV  CBB  117.01  3.000
 9D0  CAH  NAV  CBB  125.12  3.000
 9D0  H29  CAH  NAS  120.00  3.000
 9D0  H29  CAH  NAV  115.71  3.000
 9D0  NAS  CAH  NAV  124.29  3.000
 9D0  CBC  NAS  CAH  114.26  3.000
 9D0  SAW  CBC  NAS  121.89  3.000
 9D0  SAW  CBC  CBD  111.54  3.000
 9D0  NAS  CBC  CBD  126.57  3.000
 9D0  CAI  SAW  CBC   91.17  3.000
 9D0  H31  CAI  SAW  119.53  3.000
 9D0  H31  CAI  CBA  127.33  3.000
 9D0  SAW  CAI  CBA  113.09  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
 9D0  CONST_01  CAZ  CAF  CAD  CAY     0.00   0.0  0
 9D0  CONST_02  CAZ  CAG  CAE  CAY     0.00   0.0  0
 9D0  CONST_03  CAF  CAD  CAY  CAE     0.00   0.0  0
 9D0  CONST_04  CAF  CAZ  CAG  CAE     0.00   0.0  0
 9D0  CONST_05  CAD  CAF  CAZ  CAG     0.00   0.0  0
 9D0  CONST_06  CAD  CAY  CAE  CAG     0.00   0.0  0
 9D0  CONST_07  SAW  CBC  CBD  CBA     0.00   0.0  0
 9D0  CONST_08  CBC  SAW  CAI  CBA     0.00   0.0  0
 9D0  CONST_09  CAI  SAW  CBC  CBD     0.00   0.0  0
 9D0  CONST_10  SAW  CAI  CBA  CBD     0.00   0.0  0
 9D0  CONST_11  CAI  CBA  CBD  CBC     0.00   0.0  0
 9D0  CONST_12  CAH  NAV  CBB  CBD     0.00   0.0  0
 9D0  CONST_13  NAS  CAH  NAV  CBB     0.00   0.0  0
 9D0  CONST_14  CBC  NAS  CAH  NAV     0.00   0.0  0
 9D0  CONST_15  CAF  CAD  CAY  CAQ   180.00   0.0  0
 9D0  CONST_16  CAG  CAE  CAY  CAQ   180.00   0.0  0
 9D0  CONST_17  CAR  CAZ  CAG  CAE   180.00   0.0  0
 9D0  CONST_18  CAR  CAZ  CAF  CAD   180.00   0.0  0
 9D0  CONST_19  CBC  CBD  CBA  CAX   180.00   0.0  0
 9D0  CONST_20  CBB  CBD  CBA  CAX     0.00   0.0  0
 9D0  CONST_21  SAW  CAI  CBA  CAX   180.00   0.0  0
 9D0  CONST_22  CAH  NAV  CBB  OAC   180.00   0.0  0
 9D0  CONST_23  H25  CAF  CAD  CAY   180.00   0.0  0
 9D0  CONST_24  H23  CAG  CAE  CAY   180.00   0.0  0
 9D0  CONST_25  H24  CAD  CAY  CAE   180.00   0.0  0
 9D0  CONST_26  H22  CAE  CAY  CAD   180.00   0.0  0
 9D0  CONST_27  H31  CAI  CBA  CBD   180.00   0.0  0
 9D0  CONST_28  H19  NAV  CBB  CBD   180.00   0.0  0
 9D0  CONST_29  H29  CAH  NAV  CBB   180.00   0.0  0
 9D0  CONST_30  CBA  CAX  NAU  CAR   180.00   0.0  0
 9D0  CONST_31  H28  NAU  CAX  CBA     0.00   0.0  0
 9D0  CONST_32  OAB  CAX  NAU  CAR     0.00   0.0  0
 9D0  Var_01    CAD  CAY  CAQ  NAT  -137.97  30.0  2
 9D0  Var_02    NAU  CAR  CAZ  CAG  -108.67  30.0  2
 9D0  Var_03    CBD  CBA  CAX  NAU  -129.26  30.0  2
 9D0  Var_04    CAY  CAQ  NAT  CAP  -174.97  30.0  3
 9D0  Var_05    CAX  NAU  CAR  CAZ    74.62  30.0  1
 9D0  Var_06    CAL  CAK  CAJ  CAA   179.81  30.0  1
 9D0  Var_07    CAM  CAL  CAK  CAJ  -179.78  30.0  1
 9D0  Var_08    CAN  CAM  CAL  CAK   179.96  30.0  1
 9D0  Var_09    CAO  CAN  CAM  CAL  -178.57  30.0  1
 9D0  Var_10    CAP  CAO  CAN  CAM  -179.96  30.0  1
 9D0  Var_11    NAT  CAP  CAO  CAN  -177.14  30.0  1
 9D0  Var_12    CAQ  NAT  CAP  CAO  -179.75  30.0  3
 9D0  Var_13    H1   CAA  CAJ  CAK    58.68  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
 9D0  plan-1  CAQ  0.020
 9D0  plan-1  CAY  0.020
 9D0  plan-1  CAE  0.020
 9D0  plan-1  CAG  0.020
 9D0  plan-1  CAD  0.020
 9D0  plan-1  CAF  0.020
 9D0  plan-1  CAZ  0.020
 9D0  plan-1  CAR  0.020
 9D0  plan-1  H22  0.020
 9D0  plan-1  H23  0.020
 9D0  plan-1  H24  0.020
 9D0  plan-1  H25  0.020
 9D0  plan-2  CAX  0.020
 9D0  plan-2  CBA  0.020
 9D0  plan-2  CBD  0.020
 9D0  plan-2  CBB  0.020
 9D0  plan-2  OAC  0.020
 9D0  plan-2  NAV  0.020
 9D0  plan-2  CAH  0.020
 9D0  plan-2  NAS  0.020
 9D0  plan-2  CBC  0.020
 9D0  plan-2  SAW  0.020
 9D0  plan-2  CAI  0.020
 9D0  plan-2  H29  0.020
 9D0  plan-2  H31  0.020
 9D0  plan-2  H19  0.020
 9D0  plan-3  CAR  0.020
 9D0  plan-3  NAU  0.020
 9D0  plan-3  CAX  0.020
 9D0  plan-3  OAB  0.020
 9D0  plan-3  CBA  0.020
 9D0  plan-3  H28  0.020

