# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 10:46:12 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-({4-[(diethylamino)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(CC)Cc1ccc(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
 9D3  9D3  N-({4-[(diethylamino)methyl]phenyl}methyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide  ligand  48  26  .  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_9D3
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
 9D3  CAA  C  CH3   0  -0.664  -5.0017   3.0819   0.0961
 9D3  CAK  C  CH2   0  -0.282  -5.1762   1.8793  -0.8166
 9D3  NAZ  N  NT    0  -0.409  -5.8890   0.7865  -0.1699
 9D3  CAL  C  CH2   0  -0.284  -7.3262   1.0090  -0.1328
 9D3  CAB  C  CH3   0  -0.664  -8.0221   0.2303   0.9717
 9D3  CAN  C  CH2   0  -0.321  -5.5486  -0.4952  -0.7490
 9D3  CAU  C  CR6   0   0.074  -4.1509  -0.9414  -0.4010
 9D3  CAH  C  CR16  0  -0.301  -3.3918  -1.6703  -1.3094
 9D3  CAF  C  CR16  0  -0.278  -2.1219  -2.1240  -0.9759
 9D3  CAG  C  CR16  0  -0.268  -3.6048  -0.6710   0.8523
 9D3  CAE  C  CR16  0  -0.269  -2.3370  -1.1205   1.1842
 9D3  CAT  C  CR6   0   0.036  -1.5791  -1.8550   0.2743
 9D3  CAM  C  CH2   0  -0.321  -0.1877  -2.3019   0.6227
 9D3  NAP  N  NH1   0  -0.622   0.7352  -1.1887   0.4824
 9D3  CAS  C  C     0   0.505   2.0134  -1.2601   0.8748
 9D3  OAC  O  O     0  -0.477   2.5176  -2.2549   1.3697
 9D3  CAV  C  CR5   0   0.052   2.7820   0.0097   0.7136
 9D3  CAY  C  CR56  0  -0.060   4.0321   0.1419   0.0373
 9D3  CAW  C  CR6   0   0.541   4.7165  -0.8099  -0.8043
 9D3  OAD  O  O     0  -0.447   4.3478  -1.9300  -1.0997
 9D3  NAQ  N  NR16  0  -0.652   5.9074  -0.2872  -1.2989
 9D3  CAI  C  CR16  0   0.161   6.3548   0.9662  -1.0800
 9D3  NAO  N  N     0  -0.429   5.7323   1.8472  -0.3709
 9D3  CAX  C  CR56  0  -0.021   4.5725   1.4086   0.1667
 9D3  SAR  S  S2    0   0.265   3.5594   2.4338   1.1101
 9D3  CAJ  C  CR15  0  -0.510   2.4124   1.1679   1.3190
 9D3  H1   H  HCH3  0   0.224  -4.4494   3.8716  -0.4141
 9D3  H2   H  HCH3  0   0.223  -5.9551   3.5044   0.4157
 9D3  H3   H  HCH3  0   0.221  -4.4440   2.8001   0.9899
 9D3  H4   H  HCH2  0   0.200  -5.6708   2.1789  -1.7545
 9D3  H5   H  HCH2  0   0.231  -4.1847   1.5208  -1.1002
 9D3  H7   H  HCH2  0   0.231  -7.5003   2.0721   0.0419
 9D3  H8   H  HCH2  0   0.194  -7.7932   0.7824  -1.1054
 9D3  H9   H  HCH3  0   0.226  -9.0904   0.4493   0.9711
 9D3  H10  H  HCH3  0   0.221  -7.9157  -0.8493   0.8575
 9D3  H11  H  HCH3  0   0.222  -7.6196   0.5053   1.9468
 9D3  H12  H  HCH2  0   0.253  -6.2449  -1.2461  -0.3662
 9D3  H13  H  HCH2  0   0.213  -5.6735  -0.5077  -1.8451
 9D3  H14  H  HCR6  0   0.247  -3.7918  -1.8850  -2.2939
 9D3  H15  H  HCR6  0   0.252  -1.5477  -2.6887  -1.7010
 9D3  H16  H  HCR6  0   0.245  -4.1789  -0.0915   1.5638
 9D3  H17  H  HCR6  0   0.250  -1.9317  -0.8999   2.1654
 9D3  H18  H  HCH2  0   0.259  -0.1514  -2.6689   1.6506
 9D3  H19  H  HCH2  0   0.257   0.1175  -3.1298  -0.0228
 9D3  H20  H  HNH1  0   0.411   0.4155  -0.3622   0.0025
 9D3  H21  H  HCR6  0   0.311   7.2971   1.2167  -1.5488
 9D3  H23  H  HCR5  0   0.315   1.5292   1.3423   1.9152
 9D3  H6   H  HNR6  0   0.439   6.4597  -0.8886  -1.8973

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
 9D3  CAI  NAO  double    1.291  0.020  1.291
 9D3  CAI  NAQ  single    1.349  0.020  1.349
 9D3  NAO  CAX  single    1.351  0.020  1.351
 9D3  NAQ  CAW  single    1.391  0.020  1.391
 9D3  CAX  CAY  aromatic  1.383  0.020  1.383
 9D3  CAX  SAR  aromatic  1.723  0.020  1.723
 9D3  CAW  OAD  double    1.216  0.020  1.216
 9D3  CAW  CAY  single    1.443  0.020  1.443
 9D3  CAY  CAV  aromatic  1.427  0.020  1.427
 9D3  SAR  CAJ  aromatic  1.721  0.020  1.721
 9D3  CAV  CAJ  aromatic  1.358  0.020  1.358
 9D3  CAV  CAS  single    1.493  0.020  1.493
 9D3  NAP  CAS  single    1.339  0.020  1.339
 9D3  NAP  CAM  single    1.453  0.020  1.453
 9D3  CAS  OAC  double    1.220  0.020  1.220
 9D3  CAF  CAH  aromatic  1.389  0.020  1.389
 9D3  CAF  CAT  aromatic  1.389  0.020  1.389
 9D3  CAM  CAT  single    1.502  0.020  1.502
 9D3  CAH  CAU  aromatic  1.390  0.020  1.390
 9D3  CAT  CAE  aromatic  1.394  0.020  1.394
 9D3  CAU  CAN  single    1.508  0.020  1.508
 9D3  CAU  CAG  aromatic  1.394  0.020  1.394
 9D3  CAE  CAG  aromatic  1.386  0.020  1.386
 9D3  CAN  NAZ  single    1.447  0.020  1.447
 9D3  CAK  NAZ  single    1.456  0.020  1.456
 9D3  CAK  CAA  single    1.520  0.020  1.520
 9D3  NAZ  CAL  single    1.455  0.020  1.455
 9D3  CAL  CAB  single    1.520  0.020  1.520
 9D3  CAA  H1   single    0.970  0.020  1.090
 9D3  CAA  H2   single    0.970  0.020  1.090
 9D3  CAA  H3   single    0.970  0.020  1.090
 9D3  CAK  H4   single    0.970  0.020  1.090
 9D3  CAK  H5   single    0.970  0.020  1.090
 9D3  CAL  H7   single    0.970  0.020  1.090
 9D3  CAL  H8   single    0.970  0.020  1.090
 9D3  CAB  H9   single    0.970  0.020  1.090
 9D3  CAB  H10  single    0.970  0.020  1.090
 9D3  CAB  H11  single    0.970  0.020  1.090
 9D3  CAN  H12  single    0.970  0.020  1.090
 9D3  CAN  H13  single    0.970  0.020  1.090
 9D3  CAH  H14  single    0.930  0.020  1.080
 9D3  CAF  H15  single    0.930  0.020  1.080
 9D3  CAG  H16  single    0.930  0.020  1.080
 9D3  CAE  H17  single    0.930  0.020  1.080
 9D3  CAM  H18  single    0.970  0.020  1.090
 9D3  CAM  H19  single    0.970  0.020  1.090
 9D3  NAP  H20  single    0.860  0.020  1.020
 9D3  CAI  H21  single    0.930  0.020  1.080
 9D3  CAJ  H23  single    0.930  0.020  1.080
 9D3  NAQ  H6   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
 9D3  H3   CAA  H2   107.88  3.000
 9D3  H3   CAA  H1   108.15  3.000
 9D3  H2   CAA  H1   107.42  3.000
 9D3  H3   CAA  CAK  110.27  3.000
 9D3  H2   CAA  CAK  112.47  3.000
 9D3  H1   CAA  CAK  110.50  3.000
 9D3  H5   CAK  H4   106.01  3.000
 9D3  H5   CAK  NAZ  108.27  3.000
 9D3  H4   CAK  NAZ  111.24  3.000
 9D3  H5   CAK  CAA  108.15  3.000
 9D3  H4   CAK  CAA  110.34  3.000
 9D3  NAZ  CAK  CAA  112.54  3.000
 9D3  CAN  NAZ  CAL  112.22  3.000
 9D3  CAL  NAZ  CAK  112.34  3.000
 9D3  CAN  NAZ  CAK  111.83  3.000
 9D3  H8   CAL  H7   105.90  3.000
 9D3  H8   CAL  CAB  109.99  3.000
 9D3  H7   CAL  CAB  108.04  3.000
 9D3  H8   CAL  NAZ  111.37  3.000
 9D3  H7   CAL  NAZ  108.10  3.000
 9D3  CAB  CAL  NAZ  113.10  3.000
 9D3  H11  CAB  H10  107.90  3.000
 9D3  H11  CAB  H9   108.15  3.000
 9D3  H10  CAB  H9   107.11  3.000
 9D3  H11  CAB  CAL  110.58  3.000
 9D3  H10  CAB  CAL  112.72  3.000
 9D3  H9   CAB  CAL  110.19  3.000
 9D3  H13  CAN  H12  105.55  3.000
 9D3  H13  CAN  CAU  109.32  3.000
 9D3  H12  CAN  CAU  107.84  3.000
 9D3  H13  CAN  NAZ  112.40  3.000
 9D3  H12  CAN  NAZ  108.56  3.000
 9D3  CAU  CAN  NAZ  112.82  3.000
 9D3  CAG  CAU  CAH  118.39  3.000
 9D3  CAG  CAU  CAN  120.89  3.000
 9D3  CAH  CAU  CAN  120.69  3.000
 9D3  H14  CAH  CAF  119.38  3.000
 9D3  H14  CAH  CAU  119.72  3.000
 9D3  CAF  CAH  CAU  120.90  3.000
 9D3  H15  CAF  CAT  119.74  3.000
 9D3  H15  CAF  CAH  119.60  3.000
 9D3  CAT  CAF  CAH  120.66  3.000
 9D3  H16  CAG  CAE  120.10  3.000
 9D3  H16  CAG  CAU  119.16  3.000
 9D3  CAE  CAG  CAU  120.74  3.000
 9D3  H17  CAE  CAT  119.66  3.000
 9D3  H17  CAE  CAG  119.53  3.000
 9D3  CAT  CAE  CAG  120.81  3.000
 9D3  CAM  CAT  CAE  120.60  3.000
 9D3  CAE  CAT  CAF  118.50  3.000
 9D3  CAM  CAT  CAF  120.86  3.000
 9D3  H19  CAM  H18  106.97  3.000
 9D3  H19  CAM  NAP  110.23  3.000
 9D3  H18  CAM  NAP  109.10  3.000
 9D3  H19  CAM  CAT  110.30  3.000
 9D3  H18  CAM  CAT  110.43  3.000
 9D3  NAP  CAM  CAT  109.76  3.000
 9D3  H20  NAP  CAS  119.09  3.000
 9D3  H20  NAP  CAM  118.22  3.000
 9D3  CAS  NAP  CAM  122.49  3.000
 9D3  CAV  CAS  OAC  121.63  3.000
 9D3  OAC  CAS  NAP  123.84  3.000
 9D3  CAV  CAS  NAP  114.48  3.000
 9D3  CAJ  CAV  CAY  111.75  3.000
 9D3  CAJ  CAV  CAS  122.49  3.000
 9D3  CAY  CAV  CAS  125.50  3.000
 9D3  CAX  CAY  CAW  118.25  3.000
 9D3  CAW  CAY  CAV  129.09  3.000
 9D3  CAX  CAY  CAV  112.50  3.000
 9D3  NAQ  CAW  OAD  121.28  3.000
 9D3  OAD  CAW  CAY  127.27  3.000
 9D3  NAQ  CAW  CAY  111.44  3.000
 9D3  H6   NAQ  CAI  117.85  3.000
 9D3  H6   NAQ  CAW  117.00  3.000
 9D3  CAI  NAQ  CAW  125.12  3.000
 9D3  H21  CAI  NAO  120.00  3.000
 9D3  H21  CAI  NAQ  115.70  3.000
 9D3  NAO  CAI  NAQ  124.29  3.000
 9D3  CAX  NAO  CAI  114.26  3.000
 9D3  SAR  CAX  NAO  121.97  3.000
 9D3  SAR  CAX  CAY  111.50  3.000
 9D3  NAO  CAX  CAY  126.53  3.000
 9D3  CAJ  SAR  CAX   91.19  3.000
 9D3  H23  CAJ  SAR  119.56  3.000
 9D3  H23  CAJ  CAV  127.34  3.000
 9D3  SAR  CAJ  CAV  113.07  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
 9D3  CONST_01  CAT  CAF  CAH  CAU     0.00   0.0  0
 9D3  CONST_02  CAT  CAE  CAG  CAU     0.00   0.0  0
 9D3  CONST_03  CAE  CAT  CAF  CAH     0.00   0.0  0
 9D3  CONST_04  CAE  CAG  CAU  CAH     0.00   0.0  0
 9D3  CONST_05  CAG  CAU  CAH  CAF     0.00   0.0  0
 9D3  CONST_06  CAG  CAE  CAT  CAF     0.00   0.0  0
 9D3  CONST_07  SAR  CAX  CAY  CAV     0.00   0.0  0
 9D3  CONST_08  CAX  SAR  CAJ  CAV     0.00   0.0  0
 9D3  CONST_09  CAJ  SAR  CAX  CAY     0.00   0.0  0
 9D3  CONST_10  SAR  CAJ  CAV  CAY     0.00   0.0  0
 9D3  CONST_11  CAJ  CAV  CAY  CAX     0.00   0.0  0
 9D3  CONST_12  CAI  NAQ  CAW  CAY     0.00   0.0  0
 9D3  CONST_13  NAO  CAI  NAQ  CAW     0.00   0.0  0
 9D3  CONST_14  CAX  NAO  CAI  NAQ     0.00   0.0  0
 9D3  CONST_15  CAF  CAH  CAU  CAN   180.00   0.0  0
 9D3  CONST_16  CAE  CAG  CAU  CAN   180.00   0.0  0
 9D3  CONST_17  CAM  CAT  CAF  CAH   180.00   0.0  0
 9D3  CONST_18  CAM  CAT  CAE  CAG   180.00   0.0  0
 9D3  CONST_19  CAX  CAY  CAV  CAS   180.00   0.0  0
 9D3  CONST_20  CAW  CAY  CAV  CAS     0.00   0.0  0
 9D3  CONST_21  SAR  CAJ  CAV  CAS   180.00   0.0  0
 9D3  CONST_22  CAI  NAQ  CAW  OAD   180.00   0.0  0
 9D3  CONST_23  H15  CAF  CAH  CAU   180.00   0.0  0
 9D3  CONST_24  H17  CAE  CAG  CAU   180.00   0.0  0
 9D3  CONST_25  H16  CAG  CAU  CAH   180.00   0.0  0
 9D3  CONST_26  H14  CAH  CAU  CAG   180.00   0.0  0
 9D3  CONST_27  H23  CAJ  CAV  CAY   180.00   0.0  0
 9D3  CONST_28  H6   NAQ  CAW  CAY   180.00   0.0  0
 9D3  CONST_29  H21  CAI  NAQ  CAW   180.00   0.0  0
 9D3  CONST_30  CAV  CAS  NAP  CAM   180.00   0.0  0
 9D3  CONST_31  H20  NAP  CAS  CAV     0.00   0.0  0
 9D3  CONST_32  OAC  CAS  NAP  CAM     0.00   0.0  0
 9D3  Var_01    CAH  CAU  CAN  NAZ  -145.91  30.0  3
 9D3  Var_02    NAP  CAM  CAT  CAF    99.71  30.0  2
 9D3  Var_03    CAY  CAV  CAS  NAP  -127.55  30.0  3
 9D3  Var_04    CAU  CAN  NAZ  CAK    71.37  30.0  1
 9D3  Var_05    CAS  NAP  CAM  CAT   172.15  30.0  1
 9D3  Var_06    CAN  NAZ  CAK  CAA  -154.16  30.0  3
 9D3  Var_07    CAB  CAL  NAZ  CAK  -156.82  30.0  3
 9D3  Var_08    H1   CAA  CAK  NAZ   178.96  30.0  3
 9D3  Var_09    H9   CAB  CAL  NAZ   178.69  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
 9D3  plan-1  CAN  0.020
 9D3  plan-1  CAU  0.020
 9D3  plan-1  CAH  0.020
 9D3  plan-1  CAF  0.020
 9D3  plan-1  CAG  0.020
 9D3  plan-1  CAE  0.020
 9D3  plan-1  CAT  0.020
 9D3  plan-1  CAM  0.020
 9D3  plan-1  H14  0.020
 9D3  plan-1  H15  0.020
 9D3  plan-1  H16  0.020
 9D3  plan-1  H17  0.020
 9D3  plan-2  CAS  0.020
 9D3  plan-2  CAV  0.020
 9D3  plan-2  CAY  0.020
 9D3  plan-2  CAW  0.020
 9D3  plan-2  OAD  0.020
 9D3  plan-2  NAQ  0.020
 9D3  plan-2  CAI  0.020
 9D3  plan-2  NAO  0.020
 9D3  plan-2  CAX  0.020
 9D3  plan-2  SAR  0.020
 9D3  plan-2  CAJ  0.020
 9D3  plan-2  H21  0.020
 9D3  plan-2  H23  0.020
 9D3  plan-2  H6   0.020
 9D3  plan-3  CAM  0.020
 9D3  plan-3  NAP  0.020
 9D3  plan-3  CAS  0.020
 9D3  plan-3  OAC  0.020
 9D3  plan-3  CAV  0.020
 9D3  plan-3  H20  0.020

