# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 15:21:01 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 5-(thiophen-2-yl)thieno[2,3-d]pyrimidin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N=CNc2scc(c3sccc3)c12
#
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
 54X  54X  5-(thiophen-2-yl)thieno[2,3-d]pyrimidin-4(1H)-one  ligand  21  15  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_54X
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
 54X  O15  O  O     0  -0.451  -0.0923   2.3621  -0.3702
 54X  C3   C  CR6   0   0.445   0.9154   1.6907  -0.2203
 54X  N4   N  N     0  -0.467   2.1578   2.3049  -0.1692
 54X  C5   C  CR16  0   0.154   3.2340   1.6101  -0.0423
 54X  N6   N  NR16  0  -0.650   3.2790   0.2687   0.0517
 54X  C1   C  CR56  0   0.132   2.1064  -0.4132   0.0242
 54X  S7   S  S2    0   0.295   1.9555  -2.1152   0.1008
 54X  C8   C  CR15  0  -0.570   0.2408  -1.9744  -0.0060
 54X  C9   C  CR5   0   0.241  -0.1989  -0.6897  -0.1115
 54X  C2   C  CR56  0  -0.145   0.9019   0.2400  -0.0922
 54X  C10  C  CR5   0  -0.236  -1.6272  -0.4078  -0.2324
 54X  C14  C  CR15  0  -0.224  -2.5387  -1.1847  -0.8988
 54X  C13  C  CR15  0  -0.185  -3.8772  -0.7580  -0.7153
 54X  C12  C  CR15  0  -0.471  -3.9649   0.3317   0.0985
 54X  S11  S  S2    0   0.241  -2.4258   0.8594   0.6216
 54X  H1   H  HCR6  0   0.309   4.1980   2.1030  -0.0040
 54X  H2   H  HNR6  0   0.447   4.1689  -0.1985   0.1499
 54X  H3   H  HCR5  0   0.310  -0.3600  -2.8696   0.0388
 54X  H4   H  HCR5  0   0.263  -2.2536  -2.0326  -1.5062
 54X  H5   H  HCR5  0   0.266  -4.7316  -1.2330  -1.1750
 54X  H6   H  HCR5  0   0.295  -4.8515   0.8750   0.3879

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
 54X  O15  C3   double    1.220  0.020  1.220
 54X  C12  S11  aromatic  1.709  0.020  1.709
 54X  C12  C13  aromatic  1.363  0.020  1.363
 54X  C3   N4   single    1.387  0.020  1.387
 54X  C3   C2   single    1.456  0.020  1.456
 54X  N4   C5   double    1.287  0.020  1.287
 54X  S11  C10  aromatic  1.724  0.020  1.724
 54X  C13  C14  aromatic  1.417  0.020  1.417
 54X  C10  C14  aromatic  1.371  0.020  1.371
 54X  C10  C9   single    1.461  0.020  1.461
 54X  C5   N6   single    1.345  0.020  1.345
 54X  C2   C9   aromatic  1.441  0.020  1.441
 54X  C2   C1   aromatic  1.375  0.020  1.375
 54X  C9   C8   aromatic  1.362  0.020  1.362
 54X  N6   C1   single    1.357  0.020  1.357
 54X  C1   S7   aromatic  1.710  0.020  1.710
 54X  C8   S7   aromatic  1.724  0.020  1.724
 54X  C5   H1   single    0.930  0.020  1.080
 54X  N6   H2   single    0.860  0.020  1.020
 54X  C8   H3   single    0.930  0.020  1.080
 54X  C14  H4   single    0.930  0.020  1.080
 54X  C13  H5   single    0.930  0.020  1.080
 54X  C12  H6   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
 54X  C2   C3   N4   116.51  3.000
 54X  C2   C3   O15  123.45  3.000
 54X  N4   C3   O15  120.04  3.000
 54X  C5   N4   C3   120.90  3.000
 54X  H1   C5   N6   114.92  3.000
 54X  H1   C5   N4   120.12  3.000
 54X  N6   C5   N4   124.96  3.000
 54X  H2   N6   C1   122.08  3.000
 54X  H2   N6   C5   119.83  3.000
 54X  C1   N6   C5   118.09  3.000
 54X  C2   C1   S7   113.53  3.000
 54X  S7   C1   N6   125.13  3.000
 54X  C2   C1   N6   121.33  3.000
 54X  C8   S7   C1    90.21  3.000
 54X  H3   C8   C9   127.30  3.000
 54X  H3   C8   S7   118.92  3.000
 54X  C9   C8   S7   113.76  3.000
 54X  C10  C9   C2   128.57  3.000
 54X  C2   C9   C8   111.16  3.000
 54X  C10  C9   C8   120.27  3.000
 54X  C9   C2   C1   111.34  3.000
 54X  C1   C2   C3   118.19  3.000
 54X  C9   C2   C3   130.43  3.000
 54X  S11  C10  C14  110.45  3.000
 54X  C14  C10  C9   125.53  3.000
 54X  S11  C10  C9   123.62  3.000
 54X  H4   C14  C13  123.92  3.000
 54X  H4   C14  C10  122.84  3.000
 54X  C13  C14  C10  113.24  3.000
 54X  H5   C13  C12  123.69  3.000
 54X  H5   C13  C14  124.03  3.000
 54X  C12  C13  C14  112.27  3.000
 54X  H6   C12  S11  120.15  3.000
 54X  H6   C12  C13  127.98  3.000
 54X  S11  C12  C13  111.82  3.000
 54X  C12  S11  C10   92.21  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
 54X  CONST_01  C10  C9   C2   C1   180.00  0.0  0
 54X  CONST_02  C8   C9   C2   C1     0.00  0.0  0
 54X  CONST_03  C9   C8   S7   C1     0.00  0.0  0
 54X  CONST_04  C9   C2   C1   S7     0.00  0.0  0
 54X  CONST_05  C10  C9   C8   S7   180.00  0.0  0
 54X  CONST_06  C2   C9   C8   S7     0.00  0.0  0
 54X  CONST_09  C2   C1   S7   C8     0.00  0.0  0
 54X  CONST_10  C12  S11  C10  C9   180.00  0.0  0
 54X  CONST_11  C13  C14  C10  C9   180.00  0.0  0
 54X  CONST_14  C13  C12  S11  C10    0.00  0.0  0
 54X  CONST_15  C12  C13  C14  C10    0.00  0.0  0
 54X  CONST_16  S11  C12  C13  C14    0.00  0.0  0
 54X  CONST_17  C12  S11  C10  C14    0.00  0.0  0
 54X  CONST_18  S11  C10  C14  C13    0.00  0.0  0
 54X  CONST_19  C10  C9   C2   C3     0.00  0.0  0
 54X  CONST_20  N6   C5   N4   C3     0.00  0.0  0
 54X  CONST_21  C1   N6   C5   N4     0.00  0.0  0
 54X  CONST_22  H3   C8   S7   C1   180.00  0.0  0
 54X  CONST_23  H4   C14  C10  C9     0.00  0.0  0
 54X  CONST_24  H6   C12  S11  C10  180.00  0.0  0
 54X  CONST_25  H5   C13  C14  C10  180.00  0.0  0
 54X  CONST_26  H1   C5   N4   C3   180.00  0.0  0
 54X  CONST_27  H2   N6   C5   N4   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
 54X  plan-1  C9   0.020
 54X  plan-1  C10  0.020
 54X  plan-1  C14  0.020
 54X  plan-1  C13  0.020
 54X  plan-1  C12  0.020
 54X  plan-1  S11  0.020
 54X  plan-1  H4   0.020
 54X  plan-1  H5   0.020
 54X  plan-1  H6   0.020
 54X  plan-2  O15  0.020
 54X  plan-2  C3   0.020
 54X  plan-2  N4   0.020
 54X  plan-2  C5   0.020
 54X  plan-2  N6   0.020
 54X  plan-2  C1   0.020
 54X  plan-2  S7   0.020
 54X  plan-2  C8   0.020
 54X  plan-2  C9   0.020
 54X  plan-2  C2   0.020
 54X  plan-2  C10  0.020
 54X  plan-2  H1   0.020
 54X  plan-2  H2   0.020
 54X  plan-2  H3   0.020

