# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 07:07:37 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: 6-(hydroxymethyl)-3-oxidanyl-2-(thiophen-3-ylmethyl)pyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCC1=CC(=O)C(=C(Cc2cscc2)O1)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
 JPT  JPT  6-(hydroxymethyl)-3-oxidanyl-2-(thiophen-3-ylmethyl)pyran-4-one  ligand  26  16  .  2022-07-25  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_JPT
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
 JPT  C7   C  CH2   0  -0.611  -0.6660  -0.2870  -1.6298
 JPT  C8   C  CR5   0   0.180  -1.8315   0.1132  -0.7684
 JPT  C11  C  CR15  0  -0.537  -2.4195   1.3412  -0.7860
 JPT  S2   S  S2    0   0.209  -3.7032   1.4508   0.3454
 JPT  C12  C  CR15  0  -0.460  -3.4593  -0.1655   0.8631
 JPT  C13  C  CR15  0  -0.199  -2.4359  -0.7548   0.1900
 JPT  O3   O  OH1   0  -0.662   2.8464   2.7812  -0.3792
 JPT  C5   C  C     0   0.145   1.0804  -1.6859  -0.4379
 JPT  C4   C  C     0   0.277   0.5579  -0.4971  -0.8029
 JPT  C1   C  C     0   0.391   2.2589  -1.7577   0.4151
 JPT  O2   O  O     0  -0.482   2.7223  -2.8531   0.7345
 JPT  C2   C  C1    0  -0.505   2.7831  -0.4795   0.8112
 JPT  C3   C  C     0   0.372   2.1880   0.6614   0.4086
 JPT  O1   O  O2    0  -0.414   1.1104   0.6563  -0.3716
 JPT  H7   H  HCH2  0   0.294  -0.8969  -1.2045  -2.1720
 JPT  H1   H  HCH2  0   0.292  -0.4730   0.4835  -2.3792
 JPT  H11  H  HCR5  0   0.294  -2.1633   2.1862  -1.4076
 JPT  H12  H  HCR5  0   0.296  -4.0838  -0.5952   1.6310
 JPT  H13  H  HCR5  0   0.266  -2.1167  -1.7738   0.3626
 JPT  H62  H  HCH2  0   0.233   3.5229   1.9502   1.4135
 JPT  H61  H  HCH2  0   0.243   1.8446   2.4858   1.4200
 JPT  H3   H  HOH1  0   0.466   2.8571   3.7133  -0.1431
 JPT  H4   H  HOH1  0   0.470   1.0786  -3.5597  -0.4838
 JPT  H2   H  H     0   0.289   3.6622  -0.4309   1.4390
 JPT  O4   O  OH1   0  -0.627   0.5308  -2.8425  -0.8382
 JPT  C6   C  CH2   0  -0.222   2.6252   2.0381   0.7923

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
 JPT  O3   C6   single    1.405  0.020  1.405
 JPT  C6   C3   single    1.495  0.020  1.495
 JPT  C3   O1   single    1.330  0.020  1.330
 JPT  C3   C2   double    1.348  0.020  1.348
 JPT  O1   C4   single    1.350  0.020  1.350
 JPT  C2   C1   single    1.437  0.020  1.437
 JPT  C13  C12  aromatic  1.359  0.020  1.359
 JPT  C13  C8   aromatic  1.427  0.020  1.427
 JPT  C12  S2   aromatic  1.715  0.020  1.715
 JPT  C4   C7   single    1.492  0.020  1.492
 JPT  C4   C5   double    1.349  0.020  1.349
 JPT  C1   C5   single    1.457  0.020  1.457
 JPT  C1   O2   double    1.231  0.020  1.231
 JPT  C8   C7   single    1.504  0.020  1.504
 JPT  C8   C11  aromatic  1.362  0.020  1.362
 JPT  C5   O4   single    1.342  0.020  1.342
 JPT  S2   C11  aromatic  1.715  0.020  1.715
 JPT  C7   H7   single    0.970  0.020  1.090
 JPT  C7   H1   single    0.970  0.020  1.090
 JPT  C11  H11  single    0.930  0.020  1.080
 JPT  C12  H12  single    0.930  0.020  1.080
 JPT  C13  H13  single    0.930  0.020  1.080
 JPT  C6   H62  single    0.970  0.020  1.090
 JPT  C6   H61  single    0.970  0.020  1.090
 JPT  O3   H3   single    0.850  0.020  0.980
 JPT  O4   H4   single    0.850  0.020  0.980
 JPT  C2   H2   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
 JPT  H1   C7   H7   106.85  3.000
 JPT  H1   C7   C4   109.56  3.000
 JPT  H7   C7   C4   109.32  3.000
 JPT  H1   C7   C8   110.02  3.000
 JPT  H7   C7   C8   110.16  3.000
 JPT  C4   C7   C8   110.84  3.000
 JPT  C13  C8   C11  111.98  3.000
 JPT  C11  C8   C7   124.57  3.000
 JPT  C13  C8   C7   123.44  3.000
 JPT  H11  C11  S2   120.50  3.000
 JPT  H11  C11  C8   127.64  3.000
 JPT  S2   C11  C8   111.86  3.000
 JPT  C12  S2   C11   91.86  3.000
 JPT  H12  C12  C13  127.99  3.000
 JPT  H12  C12  S2   120.52  3.000
 JPT  C13  C12  S2   111.48  3.000
 JPT  H13  C13  C12  123.47  3.000
 JPT  H13  C13  C8   123.72  3.000
 JPT  C12  C13  C8   112.81  3.000
 JPT  H3   O3   C6   108.04  3.000
 JPT  C1   C5   O4   117.62  3.000
 JPT  O4   C5   C4   121.35  3.000
 JPT  C1   C5   C4   121.02  3.000
 JPT  O1   C4   C5   120.53  3.000
 JPT  C5   C4   C7   126.29  3.000
 JPT  O1   C4   C7   113.12  3.000
 JPT  C2   C1   O2   125.61  3.000
 JPT  O2   C1   C5   120.02  3.000
 JPT  C2   C1   C5   114.37  3.000
 JPT  H2   C2   C3   119.61  3.000
 JPT  H2   C2   C1   119.77  3.000
 JPT  C3   C2   C1   120.62  3.000
 JPT  O1   C3   C2   121.96  3.000
 JPT  C2   C3   C6   125.01  3.000
 JPT  O1   C3   C6   113.02  3.000
 JPT  C3   O1   C4   121.49  3.000
 JPT  H4   O4   C5   107.28  3.000
 JPT  H61  C6   H62  106.94  3.000
 JPT  H61  C6   C3   108.33  3.000
 JPT  H62  C6   C3   108.15  3.000
 JPT  H61  C6   O3   111.92  3.000
 JPT  H62  C6   O3   112.73  3.000
 JPT  C3   C6   O3   108.62  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
 JPT  CONST_01  S2   C12  C13  C8     0.00   0.0  0
 JPT  CONST_02  C12  S2   C11  C8     0.00   0.0  0
 JPT  CONST_03  C12  C13  C8   C11    0.00   0.0  0
 JPT  CONST_04  C13  C12  S2   C11    0.00   0.0  0
 JPT  CONST_05  C13  C8   C11  S2     0.00   0.0  0
 JPT  CONST_06  C12  C13  C8   C7   180.00   0.0  0
 JPT  CONST_07  S2   C11  C8   C7   180.00   0.0  0
 JPT  CONST_08  H12  C12  C13  C8   180.00   0.0  0
 JPT  CONST_09  H13  C13  C8   C11  180.00   0.0  0
 JPT  CONST_10  H11  C11  S2   C12  180.00   0.0  0
 JPT  Var_01    C3   C2   C1   C5     0.57  30.0  1
 JPT  Var_02    C2   C3   O1   C4    -0.11  30.0  1
 JPT  Var_03    C2   C1   C5   C4     0.06  30.0  1
 JPT  Var_04    O1   C3   C2   C1    -0.57  30.0  1
 JPT  Var_05    O1   C4   C5   C1    -0.71  30.0  1
 JPT  Var_06    C4   C7   C8   C11  111.86  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
 JPT  plan-1  C7   0.020
 JPT  plan-1  C8   0.020
 JPT  plan-1  C11  0.020
 JPT  plan-1  S2   0.020
 JPT  plan-1  C12  0.020
 JPT  plan-1  C13  0.020
 JPT  plan-1  H11  0.020
 JPT  plan-1  H12  0.020
 JPT  plan-1  H13  0.020
 JPT  plan-2  C5   0.020
 JPT  plan-2  C1   0.020
 JPT  plan-2  O2   0.020
 JPT  plan-2  C2   0.020

