# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:43:24 2021
#   Inital geometry file: a 37 line input string
#   Ligand name: 4-chloranylthieno[3,2-d]pyrimidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ncnc2ccsc12
#
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
 SWD  SWD  4-chloranylthieno[3,2-d]pyrimidine  ligand  13  10  .  2022-03-23  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SWD
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
 SWD  N1  N   N     0  -0.417  52.6633  113.7030  30.3044
 SWD  C4  C   CR15  0  -0.440  51.5170  116.7574  31.7941
 SWD  C5  C   CR56  0  -0.187  51.0669  115.4149  29.8054
 SWD  N   N   N     0  -0.391  51.3348  113.5969  28.3410
 SWD  C   C   CR6   0   0.176  50.7463  114.7184  28.6526
 SWD  C1  C   CR16  0   0.042  52.2698  113.1405  29.1855
 SWD  C2  C   CR56  0   0.300  52.0600  114.8526  30.6253
 SWD  C3  C   CR15  0  -0.179  52.3040  115.6568  31.7807
 SWD  S   S   S2    0   0.277  50.4530  116.8885  30.4390
 SWD  CL  CL  CL    0  -0.067  49.5383  115.3365  27.5955
 SWD  H1  H   HCR5  0   0.322  51.4948  117.5303  32.5474
 SWD  H2  H   HCR6  0   0.276  52.7436  112.2081  28.9044
 SWD  H3  H   HCR5  0   0.289  53.0249  115.4138  32.5468

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
 SWD  CL  C   single    1.720  0.020  1.720
 SWD  N   C   aromatic  1.304  0.020  1.304
 SWD  N   C1  aromatic  1.340  0.020  1.340
 SWD  C   C5  aromatic  1.384  0.020  1.384
 SWD  C1  N1  aromatic  1.313  0.020  1.313
 SWD  C5  S   aromatic  1.718  0.020  1.718
 SWD  C5  C2  aromatic  1.405  0.020  1.405
 SWD  N1  C2  aromatic  1.337  0.020  1.337
 SWD  S   C4  aromatic  1.728  0.020  1.728
 SWD  C2  C3  aromatic  1.429  0.020  1.429
 SWD  C4  C3  aromatic  1.353  0.020  1.353
 SWD  C4  H1  single    0.930  0.020  1.080
 SWD  C1  H2  single    0.930  0.020  1.080
 SWD  C3  H3  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
 SWD  C2  N1  C1  115.95  3.000
 SWD  H1  C4  S   118.70  3.000
 SWD  H1  C4  C3  126.96  3.000
 SWD  S   C4  C3  114.33  3.000
 SWD  S   C5  C2  112.38  3.000
 SWD  C2  C5  C   116.63  3.000
 SWD  S   C5  C   131.00  3.000
 SWD  C1  N   C   117.20  3.000
 SWD  CL  C   N   118.62  3.000
 SWD  N   C   C5  121.81  3.000
 SWD  CL  C   C5  119.57  3.000
 SWD  H2  C1  N   115.78  3.000
 SWD  H2  C1  N1  117.32  3.000
 SWD  N   C1  N1  126.90  3.000
 SWD  C3  C2  C5  111.55  3.000
 SWD  C3  C2  N1  126.93  3.000
 SWD  C5  C2  N1  121.52  3.000
 SWD  H3  C3  C2  124.14  3.000
 SWD  H3  C3  C4  124.36  3.000
 SWD  C2  C3  C4  111.50  3.000
 SWD  C5  S   C4   90.24  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
 SWD  CONST_01  C   N   C1  N1    0.00  0.0  0
 SWD  CONST_02  C   C5  C2  N1    0.00  0.0  0
 SWD  CONST_03  S   C5  C2  N1  180.00  0.0  0
 SWD  CONST_04  C4  C3  C2  N1  180.00  0.0  0
 SWD  CONST_05  C   C5  S   C4  180.00  0.0  0
 SWD  CONST_06  C2  C5  S   C4    0.00  0.0  0
 SWD  CONST_07  C5  C2  C3  C4    0.00  0.0  0
 SWD  CONST_08  C1  N   C   C5    0.00  0.0  0
 SWD  CONST_09  C3  C4  S   C5    0.00  0.0  0
 SWD  CONST_10  C1  N1  C2  C5    0.00  0.0  0
 SWD  CONST_11  S   C5  C   N   180.00  0.0  0
 SWD  CONST_12  C2  C5  C   N     0.00  0.0  0
 SWD  CONST_13  C2  N1  C1  N     0.00  0.0  0
 SWD  CONST_14  C3  C2  C5  C   180.00  0.0  0
 SWD  CONST_15  C3  C2  N1  C1  180.00  0.0  0
 SWD  CONST_16  S   C4  C3  C2    0.00  0.0  0
 SWD  CONST_17  S   C5  C2  C3    0.00  0.0  0
 SWD  CONST_18  CL  C   N   C1  180.00  0.0  0
 SWD  CONST_19  CL  C   C5  C2  180.00  0.0  0
 SWD  CONST_20  CL  C   C5  S     0.00  0.0  0
 SWD  CONST_21  H3  C3  C2  N1    0.00  0.0  0
 SWD  CONST_22  H1  C4  S   C5  180.00  0.0  0
 SWD  CONST_23  H2  C1  N   C   180.00  0.0  0

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
 SWD  plan-1  N1  0.020
 SWD  plan-1  C4  0.020
 SWD  plan-1  C5  0.020
 SWD  plan-1  N   0.020
 SWD  plan-1  C   0.020
 SWD  plan-1  C1  0.020
 SWD  plan-1  C2  0.020
 SWD  plan-1  C3  0.020
 SWD  plan-1  S   0.020
 SWD  plan-1  CL  0.020
 SWD  plan-1  H1  0.020
 SWD  plan-1  H2  0.020
 SWD  plan-1  H3  0.020

