# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 06:00:59 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: 3,5-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=Nc2sc(C(O)=O)c(C)c2C1=O
#
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
 68A  68A  '3,5-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carboxylic acid'  ligand  22  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_68A
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
 68A  C5   C  CR56   0  -0.040  -0.5550   1.0719  -0.0497
 68A  C7   C  CR16   0   0.151  -2.7655   1.3378  -0.0744
 68A  C10  C  CR6    0   0.573  -1.9249  -0.9277  -0.0292
 68A  C2   C  CR5    0   0.190   0.6644  -0.9423   0.0009
 68A  C3   C  CR5    0  -0.423   1.6648  -0.0110  -0.0044
 68A  S4   S  S2     0   0.218   1.0679   1.6223  -0.0412
 68A  N6   N  N      0  -0.438  -1.6118   1.9149  -0.0748
 68A  N8   N  NR6    0  -0.504  -2.9732   0.0005  -0.0530
 68A  C9   C  CH3    0  -0.514  -4.3322  -0.5224  -0.0513
 68A  O11  O  O      0  -0.471  -2.1710  -2.1222  -0.0120
 68A  C12  C  CR56   0  -0.064  -0.6243  -0.3103  -0.0266
 68A  O14  O  OC    -1  -0.596   3.7450   1.0004   0.0023
 68A  O15  O  O      0  -0.569   3.6958  -1.2326   0.0460
 68A  H1   H  HCR6   0   0.296  -3.6580   1.9509  -0.0929
 68A  H2   H  HCH3   0   0.237   0.4314  -2.8905  -0.8606
 68A  H3   H  HCH3   0   0.257   1.9020  -2.6795   0.0963
 68A  H4   H  HCH3   0   0.237   0.3300  -2.8615   0.8867
 68A  H5   H  HCH3   0   0.264  -4.5167  -1.1008   0.8511
 68A  H6   H  HCH3   0   0.260  -5.0308   0.3077  -0.0861
 68A  H7   H  HCH3   0   0.264  -4.4974  -1.1580  -0.9181
 68A  C13  C  C      0   0.411   3.1709  -0.1072   0.0171
 68A  C1   C  CH3    0  -0.741   0.8497  -2.4260   0.0333

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
 68A  O11  C10  double    1.220  0.020  1.220
 68A  C1   C2   single    1.496  0.020  1.496
 68A  C9   N8   single    1.456  0.020  1.456
 68A  C10  N8   single    1.400  0.020  1.400
 68A  C10  C12  single    1.440  0.020  1.440
 68A  O15  C13  deloc     1.242  0.020  1.242
 68A  C2   C12  aromatic  1.436  0.020  1.436
 68A  C2   C3   aromatic  1.367  0.020  1.367
 68A  N8   C7   single    1.353  0.020  1.353
 68A  C12  C5   aromatic  1.384  0.020  1.384
 68A  C3   C13  single    1.509  0.020  1.509
 68A  C3   S4   aromatic  1.739  0.020  1.739
 68A  C13  O14  deloc     1.248  0.020  1.248
 68A  C7   N6   double    1.290  0.020  1.290
 68A  C5   N6   single    1.352  0.020  1.352
 68A  C5   S4   aromatic  1.714  0.020  1.714
 68A  C7   H1   single    0.930  0.020  1.080
 68A  C1   H2   single    0.970  0.020  1.090
 68A  C1   H3   single    0.970  0.020  1.090
 68A  C1   H4   single    0.970  0.020  1.090
 68A  C9   H5   single    0.970  0.020  1.090
 68A  C9   H6   single    0.970  0.020  1.090
 68A  C9   H7   single    0.970  0.020  1.090

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
 68A  C12  C5   N6   125.72  3.000
 68A  N6   C5   S4   122.68  3.000
 68A  C12  C5   S4   111.60  3.000
 68A  H1   C7   N8   115.67  3.000
 68A  H1   C7   N6   118.93  3.000
 68A  N8   C7   N6   125.40  3.000
 68A  C12  C10  O11  127.03  3.000
 68A  C12  C10  N8   113.08  3.000
 68A  O11  C10  N8   119.88  3.000
 68A  C12  C2   C3   110.92  3.000
 68A  C3   C2   C1   125.83  3.000
 68A  C12  C2   C1   123.25  3.000
 68A  S4   C3   C2   112.88  3.000
 68A  S4   C3   C13  113.74  3.000
 68A  C2   C3   C13  133.39  3.000
 68A  C3   S4   C5    91.34  3.000
 68A  C7   N6   C5   114.84  3.000
 68A  C9   N8   C10  117.43  3.000
 68A  C10  N8   C7   122.70  3.000
 68A  C9   N8   C7   119.87  3.000
 68A  H7   C9   H6   108.88  3.000
 68A  H7   C9   H5   108.95  3.000
 68A  H6   C9   H5   108.91  3.000
 68A  H7   C9   N8   110.53  3.000
 68A  H6   C9   N8   109.03  3.000
 68A  H5   C9   N8   110.50  3.000
 68A  C2   C12  C10  128.48  3.000
 68A  C2   C12  C5   113.26  3.000
 68A  C10  C12  C5   118.26  3.000
 68A  O15  C13  O14  127.60  3.000
 68A  O14  C13  C3   113.73  3.000
 68A  O15  C13  C3   118.67  3.000
 68A  H4   C1   H3   108.89  3.000
 68A  H4   C1   H2   106.78  3.000
 68A  H3   C1   H2   108.68  3.000
 68A  H4   C1   C2   110.75  3.000
 68A  H3   C1   C2   110.69  3.000
 68A  H2   C1   C2   110.93  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
 68A  CONST_01  C3   C2   C12  C5      0.00   0.0  0
 68A  CONST_02  C2   C3   S4   C5      0.00   0.0  0
 68A  CONST_03  S4   C5   C12  C2      0.00   0.0  0
 68A  CONST_04  C12  C5   S4   C3      0.00   0.0  0
 68A  CONST_05  C12  C2   C3   S4      0.00   0.0  0
 68A  CONST_06  N8   C7   N6   C5      0.00   0.0  0
 68A  CONST_07  C12  C10  N8   C7      0.00   0.0  0
 68A  CONST_08  N6   C7   N8   C10     0.00   0.0  0
 68A  CONST_09  C1   C2   C12  C5    180.00   0.0  0
 68A  CONST_10  C13  C3   S4   C5    180.00   0.0  0
 68A  CONST_11  C1   C2   C12  C10     0.00   0.0  0
 68A  CONST_12  C12  C2   C3   C13   180.00   0.0  0
 68A  CONST_13  S4   C3   C2   C1    180.00   0.0  0
 68A  CONST_14  O11  C10  N8   C7    180.00   0.0  0
 68A  CONST_15  C9   N8   C7   N6    180.00   0.0  0
 68A  CONST_16  C12  C10  N8   C9    180.00   0.0  0
 68A  CONST_17  H1   C7   N6   C5    180.00   0.0  0
 68A  CONST_18  O11  C10  N8   C9      0.00   0.0  0
 68A  Var_01    O15  C13  C3   C2     -0.00  30.0  2
 68A  Var_02    H5   C9   N8   C7   -118.71  30.0  3
 68A  Var_03    H2   C1   C2   C3   -118.27  30.0  2

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
 68A  plan-1  C5   0.020
 68A  plan-1  C7   0.020
 68A  plan-1  C10  0.020
 68A  plan-1  C2   0.020
 68A  plan-1  C3   0.020
 68A  plan-1  S4   0.020
 68A  plan-1  N6   0.020
 68A  plan-1  N8   0.020
 68A  plan-1  C9   0.020
 68A  plan-1  O11  0.020
 68A  plan-1  C12  0.020
 68A  plan-1  H1   0.020
 68A  plan-1  C13  0.020
 68A  plan-1  C1   0.020
 68A  plan-2  C3   0.020
 68A  plan-2  O14  0.020
 68A  plan-2  O15  0.020
 68A  plan-2  C13  0.020

