# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 02:29:17 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: 6-ethylthieno[2,3-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1sc2N=CNC(=O)c2c1
#
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
 JND  JND  6-ethylthieno[2,3-d]pyrimidin-4(3H)-one  ligand  20  12  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JND
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
 JND  C01   C  CH3   0  -0.661   3.9145  -0.5006  -0.8836
 JND  C02   C  CH2   0  -0.502   3.1246  -0.6948   0.4087
 JND  C03   C  CR5   0  -0.137   1.6702  -0.3912   0.2641
 JND  C04   C  CR15  0  -0.234   0.6129  -1.2268   0.4251
 JND  C05   C  CR56  0  -0.045  -0.6361  -0.5862   0.1878
 JND  C06   C  CR6   0   0.541  -1.9593  -1.1470   0.2664
 JND  O07   O  O     0  -0.461  -2.2523  -2.2934   0.5588
 JND  N08   N  NR16  0  -0.653  -2.9331  -0.2039  -0.0400
 JND  C09   C  CR16  0   0.154  -2.6872   1.0833  -0.3690
 JND  N10   N  N     0  -0.427  -1.5083   1.6041  -0.4408
 JND  C11   C  CR56  0  -0.035  -0.5031   0.7447  -0.1572
 JND  S12   S  S2    0   0.226   1.1552   1.2107  -0.1883
 JND  H012  H  HCH3  0   0.241   4.9591  -0.7725  -0.7339
 JND  H013  H  HCH3  0   0.233   3.5144  -1.1218  -1.6849
 JND  H011  H  HCH3  0   0.227   3.8890   0.5369  -1.2193
 JND  H021  H  HCH2  0   0.259   3.2160  -1.7285   0.7460
 JND  H022  H  HCH2  0   0.258   3.5550  -0.0727   1.1978
 JND  H041  H  HCR5  0   0.272   0.7198  -2.2660   0.7033
 JND  H081  H  HNR6  0   0.437  -3.8983  -0.5074  -0.0086
 JND  H091  H  HCR6  0   0.307  -3.5599   1.6873  -0.5791

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
 JND  C01  C02   single    1.527  0.020  1.527
 JND  C02  C03   single    1.493  0.020  1.493
 JND  C03  C04   aromatic  1.357  0.020  1.357
 JND  C03  S12   aromatic  1.742  0.020  1.742
 JND  C04  C05   aromatic  1.424  0.020  1.424
 JND  O07  C06   double    1.219  0.020  1.219
 JND  C05  C06   single    1.439  0.020  1.439
 JND  C05  C11   aromatic  1.381  0.020  1.381
 JND  S12  C11   aromatic  1.723  0.020  1.723
 JND  C06  N08   single    1.390  0.020  1.390
 JND  C11  N10   single    1.353  0.020  1.353
 JND  N08  C09   single    1.351  0.020  1.351
 JND  N10  C09   double    1.291  0.020  1.291
 JND  C01  H012  single    0.970  0.020  1.090
 JND  C01  H013  single    0.970  0.020  1.090
 JND  C01  H011  single    0.970  0.020  1.090
 JND  C02  H021  single    0.970  0.020  1.090
 JND  C02  H022  single    0.970  0.020  1.090
 JND  C04  H041  single    0.930  0.020  1.080
 JND  N08  H081  single    0.860  0.020  1.020
 JND  C09  H091  single    0.930  0.020  1.080

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
 JND  H011  C01  H013  107.89  3.000
 JND  H011  C01  H012  107.58  3.000
 JND  H013  C01  H012  108.10  3.000
 JND  H011  C01  C02   111.67  3.000
 JND  H013  C01  C02   111.09  3.000
 JND  H012  C01  C02   110.36  3.000
 JND  H022  C02  H021  106.44  3.000
 JND  H022  C02  C03   109.74  3.000
 JND  H021  C02  C03   107.71  3.000
 JND  H022  C02  C01   109.56  3.000
 JND  H021  C02  C01   109.80  3.000
 JND  C03   C02  C01   113.34  3.000
 JND  S12   C03  C04   111.50  3.000
 JND  S12   C03  C02   120.00  3.000
 JND  C04   C03  C02   128.49  3.000
 JND  H041  C04  C05   124.21  3.000
 JND  H041  C04  C03   123.05  3.000
 JND  C05   C04  C03   112.75  3.000
 JND  C11   C05  C06   118.53  3.000
 JND  C11   C05  C04   113.00  3.000
 JND  C06   C05  C04   128.47  3.000
 JND  N08   C06  O07   121.52  3.000
 JND  N08   C06  C05   111.57  3.000
 JND  O07   C06  C05   126.91  3.000
 JND  H081  N08  C09   117.82  3.000
 JND  H081  N08  C06   117.24  3.000
 JND  C09   N08  C06   124.94  3.000
 JND  H091  C09  N10   120.04  3.000
 JND  H091  C09  N08   115.61  3.000
 JND  N10   C09  N08   124.34  3.000
 JND  C11   N10  C09   114.25  3.000
 JND  S12   C11  N10   122.67  3.000
 JND  N10   C11  C05   126.37  3.000
 JND  S12   C11  C05   110.97  3.000
 JND  C11   S12  C03    91.78  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
 JND  CONST_01  C11   C05  C04  C03     0.00   0.0  0
 JND  CONST_02  C05   C11  S12  C03     0.00   0.0  0
 JND  CONST_03  C11   S12  C03  C04     0.00   0.0  0
 JND  CONST_04  S12   C11  C05  C04     0.00   0.0  0
 JND  CONST_05  S12   C03  C04  C05     0.00   0.0  0
 JND  CONST_06  C09   N08  C06  C05     0.00   0.0  0
 JND  CONST_07  N10   C09  N08  C06     0.00   0.0  0
 JND  CONST_08  C11   N10  C09  N08     0.00   0.0  0
 JND  CONST_09  C05   C04  C03  C02   180.00   0.0  0
 JND  CONST_10  C11   S12  C03  C02   180.00   0.0  0
 JND  CONST_11  C09   N08  C06  O07   180.00   0.0  0
 JND  CONST_12  H041  C04  C05  C06     0.00   0.0  0
 JND  CONST_13  H081  N08  C06  C05   180.00   0.0  0
 JND  CONST_14  H091  C09  N08  C06   180.00   0.0  0
 JND  Var_01    C04   C03  C02  C01   117.79  30.0  2
 JND  Var_02    H012  C01  C02  C03  -177.76  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
 JND  plan-1  C02   0.020
 JND  plan-1  C03   0.020
 JND  plan-1  C04   0.020
 JND  plan-1  C05   0.020
 JND  plan-1  C06   0.020
 JND  plan-1  O07   0.020
 JND  plan-1  N08   0.020
 JND  plan-1  C09   0.020
 JND  plan-1  N10   0.020
 JND  plan-1  C11   0.020
 JND  plan-1  S12   0.020
 JND  plan-1  H041  0.020
 JND  plan-1  H081  0.020
 JND  plan-1  H091  0.020

