# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:42:36 2020
#   Inital geometry file: a 66 line input string
#   Ligand name: 2-methyl-3,5,6,7-tetrahydro-4H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=Nc2sc3CCCc3c2C(=O)N1
#
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
 FDR  FDR  2-methyl-3,5,6,7-tetrahydro-4H-cyclopenta[4,5]thieno[2,3-d]pyrimidin-4-one  ligand  24  14  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FDR
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
 FDR  CAA   C  CH3   0  -0.748   4.2124   0.5546  -0.0255
 FDR  OAB   O  O     0  -0.461   0.8542  -2.7256   0.0400
 FDR  CAC   C  CH2   0  -0.468  -3.6376  -0.8192  -0.2289
 FDR  CAD   C  CH2   0  -0.479  -3.3574   0.6741   0.0718
 FDR  CAE   C  CH2   0  -0.494  -2.3369  -1.6017   0.0743
 FDR  NAF   N  N     0  -0.445   1.8826   1.2260  -0.0169
 FDR  NAG   N  NR16  0  -0.680   2.3893  -1.0457   0.0102
 FDR  SAH   S  S2    0   0.225  -0.7117   1.9841   0.0014
 FDR  CAI   C  CR6   0   0.462   2.7514   0.2647  -0.0120
 FDR  CAJ   C  CR55  0  -0.229  -1.8667   0.7019   0.0085
 FDR  CAK   C  CR55  0   0.192  -1.2979  -0.5260   0.0172
 FDR  CAL   C  CR6   0   0.520   1.0868  -1.5285   0.0242
 FDR  CAM   C  CR56  0  -0.050   0.5893   0.8389   0.0031
 FDR  CAN   C  CR56  0  -0.092   0.1220  -0.4643   0.0177
 FDR  HAA   H  HCH3  0   0.274   4.3770   1.6249  -0.1065
 FDR  HAAA  H  HCH3  0   0.275   4.6851   0.1947   0.8899
 FDR  HAAB  H  HCH3  0   0.273   4.7000   0.0568  -0.8646
 FDR  HAC   H  HCH2  0   0.244  -4.4886  -1.1973   0.3360
 FDR  HACA  H  HCH2  0   0.246  -3.8780  -0.9263  -1.2871
 FDR  HAD   H  HCH2  0   0.256  -3.8390   1.3365  -0.6488
 FDR  HADA  H  HCH2  0   0.254  -3.7118   0.9678   1.0638
 FDR  HAE   H  HCH2  0   0.246  -2.3584  -2.0651   1.0647
 FDR  HAEA  H  HCH2  0   0.249  -2.1650  -2.4027  -0.6451
 FDR  HNAG  H  HNR6  0   0.430   3.1247  -1.7418   0.0138

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
 FDR  CAA  CAI   single    1.490  0.020  1.490
 FDR  CAA  HAA   single    0.970  0.020  1.090
 FDR  CAA  HAAA  single    0.970  0.020  1.090
 FDR  CAA  HAAB  single    0.970  0.020  1.090
 FDR  CAL  OAB   double    1.220  0.020  1.220
 FDR  CAE  CAC   single    1.548  0.020  1.548
 FDR  CAD  CAC   single    1.549  0.020  1.549
 FDR  CAC  HAC   single    0.970  0.020  1.090
 FDR  CAC  HACA  single    0.970  0.020  1.090
 FDR  CAJ  CAD   single    1.492  0.020  1.492
 FDR  CAD  HAD   single    0.970  0.020  1.090
 FDR  CAD  HADA  single    0.970  0.020  1.090
 FDR  CAK  CAE   single    1.497  0.020  1.497
 FDR  CAE  HAE   single    0.970  0.020  1.090
 FDR  CAE  HAEA  single    0.970  0.020  1.090
 FDR  CAI  NAF   double    1.296  0.020  1.296
 FDR  NAF  CAM   single    1.350  0.020  1.350
 FDR  CAI  NAG   single    1.360  0.020  1.360
 FDR  NAG  CAL   single    1.389  0.020  1.389
 FDR  NAG  HNAG  single    0.860  0.020  1.020
 FDR  CAM  SAH   aromatic  1.733  0.020  1.733
 FDR  SAH  CAJ   aromatic  1.726  0.020  1.726
 FDR  CAK  CAJ   aromatic  1.353  0.020  1.353
 FDR  CAN  CAK   aromatic  1.421  0.020  1.421
 FDR  CAL  CAN   single    1.436  0.020  1.436
 FDR  CAM  CAN   aromatic  1.384  0.020  1.384

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
 FDR  HAAB  CAA  HAAA  107.53  3.000
 FDR  HAAB  CAA  HAA   108.95  3.000
 FDR  HAAA  CAA  HAA   108.78  3.000
 FDR  HAAB  CAA  CAI   110.90  3.000
 FDR  HAAA  CAA  CAI   110.67  3.000
 FDR  HAA   CAA  CAI   109.95  3.000
 FDR  HACA  CAC  HAC   107.28  3.000
 FDR  HACA  CAC  CAE   109.00  3.000
 FDR  HAC   CAC  CAE   112.30  3.000
 FDR  HACA  CAC  CAD   108.84  3.000
 FDR  HAC   CAC  CAD   112.04  3.000
 FDR  CAE   CAC  CAD   107.30  3.000
 FDR  HADA  CAD  HAD   107.05  3.000
 FDR  HADA  CAD  CAJ   110.93  3.000
 FDR  HAD   CAD  CAJ   113.68  3.000
 FDR  HADA  CAD  CAC   112.11  3.000
 FDR  HAD   CAD  CAC   112.17  3.000
 FDR  CAJ   CAD  CAC   100.98  3.000
 FDR  HAEA  CAE  HAE   106.82  3.000
 FDR  HAEA  CAE  CAK   113.17  3.000
 FDR  HAE   CAE  CAK   110.65  3.000
 FDR  HAEA  CAE  CAC   112.00  3.000
 FDR  HAE   CAE  CAC   112.03  3.000
 FDR  CAK   CAE  CAC   102.27  3.000
 FDR  CAM   NAF  CAI   115.44  3.000
 FDR  HNAG  NAG  CAL   116.24  3.000
 FDR  HNAG  NAG  CAI   117.97  3.000
 FDR  CAL   NAG  CAI   125.79  3.000
 FDR  CAM   SAH  CAJ    90.66  3.000
 FDR  NAG   CAI  NAF   122.44  3.000
 FDR  NAG   CAI  CAA   116.68  3.000
 FDR  NAF   CAI  CAA   120.88  3.000
 FDR  CAK   CAJ  SAH   113.13  3.000
 FDR  CAK   CAJ  CAD   113.75  3.000
 FDR  SAH   CAJ  CAD   133.05  3.000
 FDR  CAN   CAK  CAJ   112.37  3.000
 FDR  CAN   CAK  CAE   136.45  3.000
 FDR  CAJ   CAK  CAE   111.14  3.000
 FDR  CAN   CAL  NAG   111.85  3.000
 FDR  CAN   CAL  OAB   126.81  3.000
 FDR  NAG   CAL  OAB   121.34  3.000
 FDR  CAN   CAM  SAH   111.63  3.000
 FDR  CAN   CAM  NAF   126.40  3.000
 FDR  SAH   CAM  NAF   121.97  3.000
 FDR  CAM   CAN  CAL   118.08  3.000
 FDR  CAM   CAN  CAK   112.21  3.000
 FDR  CAL   CAN  CAK   129.70  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
 FDR  CONST_01  CAK   CAN  CAM  SAH    0.00   0.0  0
 FDR  CONST_02  CAN   CAK  CAJ  SAH    0.00   0.0  0
 FDR  CONST_03  CAN   CAM  SAH  CAJ    0.00   0.0  0
 FDR  CONST_04  CAM   CAN  CAK  CAJ    0.00   0.0  0
 FDR  CONST_05  CAM   SAH  CAJ  CAK    0.00   0.0  0
 FDR  CONST_06  CAL   NAG  CAI  NAF    0.00   0.0  0
 FDR  CONST_07  CAM   NAF  CAI  NAG    0.00   0.0  0
 FDR  CONST_08  CAN   CAL  NAG  CAI    0.00   0.0  0
 FDR  CONST_09  CAM   NAF  CAI  CAA  180.00   0.0  0
 FDR  CONST_10  CAL   NAG  CAI  CAA  180.00   0.0  0
 FDR  CONST_11  CAI   NAG  CAL  OAB  180.00   0.0  0
 FDR  CONST_12  HNAG  NAG  CAI  NAF  180.00   0.0  0
 FDR  Var_01    CAJ   CAK  CAE  CAC   12.51  30.0  1
 FDR  Var_02    SAH   CAJ  CAD  CAC  170.05  30.0  1
 FDR  Var_03    CAK   CAE  CAC  CAD  -20.41  30.0  1
 FDR  Var_04    CAJ   CAD  CAC  CAE   20.44  30.0  1
 FDR  Var_05    HAA   CAA  CAI  NAF   -3.80  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
 FDR  plan-1  CAA   0.020
 FDR  plan-1  OAB   0.020
 FDR  plan-1  CAD   0.020
 FDR  plan-1  CAE   0.020
 FDR  plan-1  NAF   0.020
 FDR  plan-1  NAG   0.020
 FDR  plan-1  SAH   0.020
 FDR  plan-1  CAI   0.020
 FDR  plan-1  CAJ   0.020
 FDR  plan-1  CAK   0.020
 FDR  plan-1  CAL   0.020
 FDR  plan-1  CAM   0.020
 FDR  plan-1  CAN   0.020
 FDR  plan-1  HNAG  0.020

