# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 02:12:32 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-[(carboxycarbonyl)amino]-4,7-dihydro-5H-thieno[2,3-c]thiopyran-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C(=O)Nc1sc2CSCCc2c1C(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
 COL  COL  '2-[(carboxycarbonyl)amino]-4,7-dihydro-5H-thieno[2,3-c]thiopyran-3-carboxylic acid'  ligand  27  18  .  2021-08-07  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_COL
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
 COL  S1    S  S2    0  -0.007   1.1762  -0.5096  -4.3692
 COL  C2    C  CH2   0  -0.620   1.9261   0.0982  -2.8392
 COL  C3    C  CR5   0  -0.264   0.9471   0.0733  -1.7103
 COL  C4    C  CR5   0   0.227  -0.4109   0.0608  -1.7602
 COL  C5    C  CH2   0  -0.462  -1.1834   0.0871  -3.0495
 COL  C6    C  CH2   0  -0.588  -0.3346   0.4818  -4.2463
 COL  S13   S  S2    0   0.281   1.5521   0.0884  -0.0914
 COL  C14   C  CR5   0   0.099  -0.0410   0.0789   0.5527
 COL  C15   C  CR5   0  -0.091  -0.9974   0.0486  -0.4440
 COL  C16   C  C     0   0.531  -2.4442  -0.0410  -0.2163
 COL  O17   O  OH1   0  -0.626  -2.7918   0.1963   1.0511
 COL  O18   O  O     0  -0.429  -3.2580  -0.3061  -1.0670
 COL  N19   N  NH1   0  -0.705  -0.2560   0.0799   1.9104
 COL  C20   C  C     0   0.452   0.7187   0.0837   2.8396
 COL  C21   C  C     0   0.465   0.1578   0.0927   4.2620
 COL  O22   O  OH1   0  -0.560   1.1225   0.0955   5.1451
 COL  O23   O  O     0  -0.404  -1.0228   0.0968   4.4885
 COL  O24   O  O     0  -0.414   1.9056   0.0822   2.5998
 COL  H21   H  HCH2  0   0.294   2.3158   1.1070  -2.9968
 COL  H22A  H  HCH2  0   0.297   2.7809  -0.5474  -2.6305
 COL  H51   H  HCH2  0   0.260  -2.0061   0.8000  -2.9726
 COL  H52   H  HCH2  0   0.257  -1.6388  -0.8892  -3.2283
 COL  H61   H  HCH2  0   0.274  -0.0565   1.5367  -4.2006
 COL  H62   H  HCH2  0   0.293  -0.8927   0.3292  -5.1695
 COL  H17   H  HOH1  0   0.496  -3.7470   0.0778   1.1675
 COL  H19   H  HNH1  0   0.444  -1.2215   0.0910   2.2201
 COL  H22   H  HOH1  0   0.502   0.7626   0.1014   6.0464

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
 COL  S1   C2    single    1.809  0.020  1.809
 COL  S1   C6    single    1.811  0.020  1.811
 COL  C2   C3    single    1.495  0.020  1.495
 COL  C2   H21   single    0.970  0.020  1.090
 COL  C2   H22A  single    0.970  0.020  1.090
 COL  C3   C4    aromatic  1.359  0.020  1.359
 COL  C3   S13   aromatic  1.728  0.020  1.728
 COL  C4   C5    single    1.503  0.020  1.503
 COL  C4   C15   aromatic  1.441  0.020  1.441
 COL  C5   C6    single    1.519  0.020  1.519
 COL  C5   H51   single    0.970  0.020  1.090
 COL  C5   H52   single    0.970  0.020  1.090
 COL  C6   H61   single    0.970  0.020  1.090
 COL  C6   H62   single    0.970  0.020  1.090
 COL  S13  C14   aromatic  1.718  0.020  1.718
 COL  C14  C15   aromatic  1.382  0.020  1.382
 COL  C14  N19   single    1.375  0.020  1.375
 COL  C15  C16   single    1.467  0.020  1.467
 COL  C16  O17   single    1.335  0.020  1.335
 COL  C16  O18   double    1.207  0.020  1.207
 COL  O17  H17   single    0.850  0.020  0.980
 COL  N19  C20   single    1.347  0.020  1.347
 COL  N19  H19   single    0.860  0.020  1.020
 COL  C20  C21   single    1.529  0.020  1.529
 COL  C20  O24   double    1.211  0.020  1.211
 COL  C21  O22   single    1.308  0.020  1.308
 COL  C21  O23   double    1.202  0.020  1.202
 COL  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
 COL  C6    S1   C2    96.00  3.000
 COL  H22A  C2   H21  107.12  3.000
 COL  H22A  C2   C3   111.02  3.000
 COL  H21   C2   C3   110.97  3.000
 COL  H22A  C2   S1   106.72  3.000
 COL  H21   C2   S1   109.63  3.000
 COL  C3    C2   S1   111.21  3.000
 COL  S13   C3   C4   112.60  3.000
 COL  S13   C3   C2   118.56  3.000
 COL  C4    C3   C2   128.83  3.000
 COL  C15   C4   C5   125.05  3.000
 COL  C15   C4   C3   111.92  3.000
 COL  C5    C4   C3   123.02  3.000
 COL  H52   C5   H51  106.33  3.000
 COL  H52   C5   C6   109.65  3.000
 COL  H51   C5   C6   107.88  3.000
 COL  H52   C5   C4   109.82  3.000
 COL  H51   C5   C4   109.78  3.000
 COL  C6    C5   C4   113.14  3.000
 COL  H62   C6   H61  107.53  3.000
 COL  H62   C6   C5   110.18  3.000
 COL  H61   C6   C5   111.12  3.000
 COL  H62   C6   S1   107.05  3.000
 COL  H61   C6   S1   108.61  3.000
 COL  C5    C6   S1   112.17  3.000
 COL  C14   S13  C3    91.52  3.000
 COL  N19   C14  C15  127.17  3.000
 COL  N19   C14  S13  121.01  3.000
 COL  C15   C14  S13  111.81  3.000
 COL  C16   C15  C14  124.88  3.000
 COL  C16   C15  C4   122.93  3.000
 COL  C14   C15  C4   112.14  3.000
 COL  O18   C16  O17  122.17  3.000
 COL  O18   C16  C15  124.68  3.000
 COL  O17   C16  C15  113.14  3.000
 COL  H17   O17  C16  110.40  3.000
 COL  H19   N19  C20  118.58  3.000
 COL  H19   N19  C14  116.78  3.000
 COL  C20   N19  C14  124.63  3.000
 COL  O24   C20  C21  122.94  3.000
 COL  O24   C20  N19  124.95  3.000
 COL  C21   C20  N19  112.11  3.000
 COL  O23   C21  O22  126.66  3.000
 COL  O23   C21  C20  122.39  3.000
 COL  O22   C21  C20  110.95  3.000
 COL  H22   O22  C21  110.71  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
 COL  CONST_01  C14  C15  C4   C3      0.00   0.0  0
 COL  CONST_02  C15  C14  S13  C3      0.00   0.0  0
 COL  CONST_03  C14  S13  C3   C4      0.00   0.0  0
 COL  CONST_04  S13  C14  C15  C4      0.00   0.0  0
 COL  CONST_05  C15  C4   C3   S13     0.00   0.0  0
 COL  CONST_06  C16  C15  C4   C3    180.00   0.0  0
 COL  CONST_07  N19  C14  S13  C3    180.00   0.0  0
 COL  CONST_08  N19  C14  C15  C4    180.00   0.0  0
 COL  CONST_09  C16  C15  C4   C5      0.00   0.0  0
 COL  CONST_10  C16  C15  C14  S13   180.00   0.0  0
 COL  CONST_11  C20  N19  C14  S13     0.00   0.0  0
 COL  CONST_12  C20  N19  C14  C15   180.00   0.0  0
 COL  CONST_13  H19  N19  C14  S13   180.00   0.0  0
 COL  CONST_14  C21  C20  N19  C14   180.00   0.0  0
 COL  CONST_15  O24  C20  N19  C14     0.00   0.0  0
 COL  CONST_16  H17  O17  C16  C15   180.00   0.0  0
 COL  CONST_17  H22  O22  C21  C20   180.00   0.0  0
 COL  Var_01    C4   C3   C2   S1    -21.62  30.0  1
 COL  Var_02    C4   C5   C6   S1     51.65  30.0  1
 COL  Var_03    C5   C6   S1   C2    -65.17  30.0  1
 COL  Var_04    C6   C5   C4   C3    -14.68  30.0  1
 COL  Var_05    O17  C16  C15  C4   -169.00  30.0  2
 COL  Var_06    O22  C21  C20  N19   179.97  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
 COL  plan-1  C14  0.020
 COL  plan-1  N19  0.020
 COL  plan-1  C20  0.020
 COL  plan-1  C21  0.020
 COL  plan-1  O24  0.020
 COL  plan-1  H19  0.020
 COL  plan-2  C2   0.020
 COL  plan-2  C3   0.020
 COL  plan-2  C4   0.020
 COL  plan-2  C5   0.020
 COL  plan-2  S13  0.020
 COL  plan-2  C14  0.020
 COL  plan-2  C15  0.020
 COL  plan-2  C16  0.020
 COL  plan-2  N19  0.020
 COL  plan-3  C15  0.020
 COL  plan-3  C16  0.020
 COL  plan-3  O17  0.020
 COL  plan-3  O18  0.020
 COL  plan-3  H17  0.020
 COL  plan-4  C20  0.020
 COL  plan-4  C21  0.020
 COL  plan-4  O22  0.020
 COL  plan-4  O23  0.020
 COL  plan-4  H22  0.020

