# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 00:27:56 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-[(carboxycarbonyl)amino]-4,7-dihydro-5H-thieno[2,3-c]pyran-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)Nc1sc2COCCc2c1C(O)=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
 OPA  OPA  '2-[(carboxycarbonyl)amino]-4,7-dihydro-5H-thieno[2,3-c]pyran-3-carboxylic acid'  ligand  27  18  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OPA
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
 OPA  O1    O  O2    0  -0.487  -1.3745   0.3711  -4.2700
 OPA  C2    C  CH2   0  -0.277  -2.0546   0.0287  -3.0925
 OPA  C3    C  CR5   0  -0.221  -1.1109  -0.0004  -1.9316
 OPA  C4    C  CR5   0   0.190   0.2376  -0.0192  -2.0447
 OPA  C5    C  CH2   0  -0.527   0.8647  -0.0413  -3.4064
 OPA  C6    C  CH2   0  -0.225  -0.1924  -0.3847  -4.4466
 OPA  S13   S  S2    0   0.232  -1.6495  -0.0024  -0.2962
 OPA  C14   C  CR5   0   0.114  -0.0228  -0.0284   0.2782
 OPA  C15   C  CR5   0  -0.064   0.8907  -0.0248  -0.7609
 OPA  C16   C  C     0   0.409   2.3433  -0.0107  -0.6220
 OPA  O17   O  OH1   0  -0.595   2.7462  -0.1258   0.6544
 OPA  O18   O  O     0  -0.428   3.1237   0.0838  -1.5199
 OPA  N19   N  NH1   0  -0.682   0.2542  -0.0531   1.6232
 OPA  C20   C  C     0   0.483  -0.6803  -0.0653   2.5972
 OPA  C21   C  C     0   0.503  -0.0512  -0.1164   3.9879
 OPA  O22   O  OH1   0  -0.550  -0.9831  -0.1381   4.9145
 OPA  O23   O  O     0  -0.470   1.1349  -0.1402   4.1789
 OPA  O24   O  O     0  -0.439  -1.8753  -0.0376   2.4142
 OPA  H21   H  HCH2  0   0.281  -2.5579  -0.9437  -3.1960
 OPA  H22A  H  HCH2  0   0.276  -2.8399   0.7738  -2.9427
 OPA  H51   H  HCH2  0   0.280   1.6632  -0.7817  -3.4580
 OPA  H52   H  HCH2  0   0.257   1.3284   0.9233  -3.6292
 OPA  H61   H  HCH2  0   0.244  -0.4129  -1.4598  -4.4019
 OPA  H62   H  HCH2  0   0.242   0.1745  -0.1691  -5.4500
 OPA  H17   H  HOH1  0   0.498   3.7152  -0.0883   0.6923
 OPA  H19   H  HNH1  0   0.430   1.2339  -0.0770   1.8843
 OPA  H22   H  HOH1  0   0.527  -0.5550  -0.1859   5.7857

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
 OPA  O1   C2    single    1.402  0.020  1.402
 OPA  O1   C6    single    1.414  0.020  1.414
 OPA  C2   C3    single    1.496  0.020  1.496
 OPA  C2   H21   single    0.970  0.020  1.090
 OPA  C2   H22A  single    0.970  0.020  1.090
 OPA  C3   C4    aromatic  1.353  0.020  1.353
 OPA  C3   S13   aromatic  1.722  0.020  1.722
 OPA  C4   C5    single    1.499  0.020  1.499
 OPA  C4   C15   aromatic  1.440  0.020  1.440
 OPA  C5   C6    single    1.522  0.020  1.522
 OPA  C5   H51   single    0.970  0.020  1.090
 OPA  C5   H52   single    0.970  0.020  1.090
 OPA  C6   H61   single    0.970  0.020  1.090
 OPA  C6   H62   single    0.970  0.020  1.090
 OPA  S13  C14   aromatic  1.725  0.020  1.725
 OPA  C14  C15   aromatic  1.384  0.020  1.384
 OPA  C14  N19   single    1.373  0.020  1.373
 OPA  C15  C16   single    1.459  0.020  1.459
 OPA  C16  O17   single    1.343  0.020  1.343
 OPA  C16  O18   double    1.193  0.020  1.193
 OPA  O17  H17   single    0.850  0.020  0.980
 OPA  N19  C20   single    1.350  0.020  1.350
 OPA  N19  H19   single    0.860  0.020  1.020
 OPA  C20  C21   single    1.527  0.020  1.527
 OPA  C20  O24   double    1.209  0.020  1.209
 OPA  C21  O22   single    1.314  0.020  1.314
 OPA  C21  O23   double    1.202  0.020  1.202
 OPA  O22  H22   single    0.850  0.020  0.980

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
 OPA  C6    O1   C2   112.32  3.000
 OPA  H22A  C2   H21  106.67  3.000
 OPA  H22A  C2   C3   111.10  3.000
 OPA  H21   C2   C3   110.15  3.000
 OPA  H22A  C2   O1   107.28  3.000
 OPA  H21   C2   O1   111.03  3.000
 OPA  C3    C2   O1   110.51  3.000
 OPA  S13   C3   C4   113.02  3.000
 OPA  S13   C3   C2   122.66  3.000
 OPA  C4    C3   C2   124.32  3.000
 OPA  C15   C4   C5   128.30  3.000
 OPA  C15   C4   C3   112.17  3.000
 OPA  C5    C4   C3   119.52  3.000
 OPA  H52   C5   H51  106.20  3.000
 OPA  H52   C5   C6   110.76  3.000
 OPA  H51   C5   C6   108.85  3.000
 OPA  H52   C5   C4   110.45  3.000
 OPA  H51   C5   C4   111.06  3.000
 OPA  C6    C5   C4   109.48  3.000
 OPA  H62   C6   H61  107.38  3.000
 OPA  H62   C6   C5   110.53  3.000
 OPA  H61   C6   C5   109.41  3.000
 OPA  H62   C6   O1   106.90  3.000
 OPA  H61   C6   O1   110.50  3.000
 OPA  C5    C6   O1   112.00  3.000
 OPA  C14   S13  C3    91.22  3.000
 OPA  N19   C14  C15  127.04  3.000
 OPA  N19   C14  S13  121.10  3.000
 OPA  C15   C14  S13  111.87  3.000
 OPA  C16   C15  C14  125.86  3.000
 OPA  C16   C15  C4   122.42  3.000
 OPA  C14   C15  C4   111.72  3.000
 OPA  O18   C16  O17  121.70  3.000
 OPA  O18   C16  C15  125.46  3.000
 OPA  O17   C16  C15  112.84  3.000
 OPA  H17   O17  C16  109.47  3.000
 OPA  H19   N19  C20  118.87  3.000
 OPA  H19   N19  C14  116.58  3.000
 OPA  C20   N19  C14  124.55  3.000
 OPA  O24   C20  C21  123.07  3.000
 OPA  O24   C20  N19  125.08  3.000
 OPA  C21   C20  N19  111.85  3.000
 OPA  O23   C21  O22  125.98  3.000
 OPA  O23   C21  C20  123.50  3.000
 OPA  O22   C21  C20  110.52  3.000
 OPA  H22   O22  C21  108.69  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
 OPA  CONST_01  C14  C15  C4   C3      0.00   0.0  0
 OPA  CONST_02  C15  C14  S13  C3      0.00   0.0  0
 OPA  CONST_03  C14  S13  C3   C4      0.00   0.0  0
 OPA  CONST_04  S13  C14  C15  C4      0.00   0.0  0
 OPA  CONST_05  C15  C4   C3   S13     0.00   0.0  0
 OPA  CONST_06  C16  C15  C4   C3    180.00   0.0  0
 OPA  CONST_07  N19  C14  S13  C3    180.00   0.0  0
 OPA  CONST_08  N19  C14  C15  C4    180.00   0.0  0
 OPA  CONST_09  C16  C15  C4   C5      0.00   0.0  0
 OPA  CONST_10  C16  C15  C14  S13   180.00   0.0  0
 OPA  CONST_11  C20  N19  C14  S13     0.00   0.0  0
 OPA  CONST_12  C20  N19  C14  C15   180.00   0.0  0
 OPA  CONST_13  H19  N19  C14  S13   180.00   0.0  0
 OPA  CONST_14  C21  C20  N19  C14   180.00   0.0  0
 OPA  CONST_15  O24  C20  N19  C14     0.00   0.0  0
 OPA  CONST_16  H17  O17  C16  C15   180.00   0.0  0
 OPA  CONST_17  H22  O22  C21  C20   180.00   0.0  0
 OPA  Var_01    C4   C3   C2   O1    -14.89  30.0  1
 OPA  Var_02    C4   C5   C6   O1     47.03  30.0  1
 OPA  Var_03    C5   C6   O1   C2    -67.80  30.0  1
 OPA  Var_04    C6   C5   C4   C3    -13.98  30.0  1
 OPA  Var_05    O17  C16  C15  C4   -175.05  30.0  2
 OPA  Var_06    O22  C21  C20  N19  -179.50  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
 OPA  plan-1  C14  0.020
 OPA  plan-1  N19  0.020
 OPA  plan-1  C20  0.020
 OPA  plan-1  C21  0.020
 OPA  plan-1  O24  0.020
 OPA  plan-1  H19  0.020
 OPA  plan-2  C2   0.020
 OPA  plan-2  C3   0.020
 OPA  plan-2  C4   0.020
 OPA  plan-2  C5   0.020
 OPA  plan-2  S13  0.020
 OPA  plan-2  C14  0.020
 OPA  plan-2  C15  0.020
 OPA  plan-2  C16  0.020
 OPA  plan-2  N19  0.020
 OPA  plan-3  C15  0.020
 OPA  plan-3  C16  0.020
 OPA  plan-3  O17  0.020
 OPA  plan-3  O18  0.020
 OPA  plan-3  H17  0.020
 OPA  plan-4  C20  0.020
 OPA  plan-4  C21  0.020
 OPA  plan-4  O22  0.020
 OPA  plan-4  O23  0.020
 OPA  plan-4  H22  0.020

