# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:33:15 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: methyl 2-(hydroxymethyl)-6~{H}-thieno[2,3-b]pyrrole-5-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1[nH]c2sc(CO)cc2c1
#
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
 JA5  JA5  'methyl 2-(hydroxymethyl)-6~{H}-thieno[2,3-b]pyrrole-5-carboxylate'  ligand  23  14  .  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_JA5
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
 JA5  C10  C  CR15  0  -0.411   0.7928   1.5247   0.3347
 JA5  C13  C  CH3   0  -0.422   5.0286  -0.8142  -0.2929
 JA5  O01  O  OH1   0  -0.666  -4.7313  -0.3621  -0.8754
 JA5  C02  C  CH2   0  -0.206  -4.2266   0.3505   0.2308
 JA5  C03  C  CR5   0  -0.186  -2.7409   0.3798   0.1417
 JA5  C04  C  CR15  0  -0.267  -1.8939   1.4129   0.3623
 JA5  C05  C  CR55  0   0.126  -0.5220   1.0194   0.2557
 JA5  C06  C  CR55  0   0.086  -0.4059  -0.3313  -0.0560
 JA5  S07  S  S2    0   0.218  -1.9154  -1.1296  -0.2293
 JA5  N08  N  NR15  0  -0.689   0.8893  -0.6643  -0.1738
 JA5  C09  C  CR5   0   0.188   1.6397   0.4683   0.0682
 JA5  C11  C  C     0   0.550   3.0943   0.4893   0.0426
 JA5  O12  O  O2    0  -0.470   3.6065  -0.7034  -0.2359
 JA5  O14  O  O     0  -0.456   3.7554   1.4808   0.2506
 JA5  H1   H  HCR5  0   0.264   1.1016   2.5334   0.5588
 JA5  H2   H  HCH3  0   0.241   5.4444  -0.1835  -1.0782
 JA5  H3   H  HCH3  0   0.241   5.4868  -0.5521   0.6603
 JA5  H4   H  HCH3  0   0.255   5.2371  -1.8553  -0.5191
 JA5  H5   H  HOH1  0   0.461  -5.6335  -0.6277  -0.6744
 JA5  H6   H  HCH2  0   0.223  -4.5894   1.3854   0.2672
 JA5  H7   H  HCH2  0   0.231  -4.5275  -0.1239   1.1726
 JA5  H8   H  HCR5  0   0.266  -2.2348   2.4119   0.5959
 JA5  H9   H  HNR5  0   0.423   1.2534  -1.5783  -0.3908

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
 JA5  O01  C02  single    1.409  0.020  1.409
 JA5  C02  C03  single    1.489  0.020  1.489
 JA5  C03  C04  aromatic  1.354  0.020  1.354
 JA5  C03  S07  aromatic  1.760  0.020  1.760
 JA5  C04  C05  aromatic  1.431  0.020  1.431
 JA5  S07  C06  aromatic  1.716  0.020  1.716
 JA5  C05  C06  aromatic  1.391  0.020  1.391
 JA5  C05  C10  aromatic  1.411  0.020  1.411
 JA5  C06  N08  aromatic  1.343  0.020  1.343
 JA5  C10  C09  aromatic  1.380  0.020  1.380
 JA5  N08  C09  aromatic  1.380  0.020  1.380
 JA5  C09  C11  single    1.455  0.020  1.455
 JA5  C11  O14  double    1.210  0.020  1.210
 JA5  C11  O12  single    1.328  0.020  1.328
 JA5  O12  C13  single    1.428  0.020  1.428
 JA5  C10  H1   single    0.930  0.020  1.080
 JA5  C13  H2   single    0.970  0.020  1.090
 JA5  C13  H3   single    0.970  0.020  1.090
 JA5  C13  H4   single    0.970  0.020  1.090
 JA5  O01  H5   single    0.850  0.020  0.980
 JA5  C02  H6   single    0.970  0.020  1.090
 JA5  C02  H7   single    0.970  0.020  1.090
 JA5  C04  H8   single    0.930  0.020  1.080
 JA5  N08  H9   single    0.860  0.020  1.020

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
 JA5  H1   C10  C09  125.48  3.000
 JA5  H1   C10  C05  127.85  3.000
 JA5  C09  C10  C05  106.67  3.000
 JA5  H4   C13  H3   109.40  3.000
 JA5  H4   C13  H2   109.37  3.000
 JA5  H3   C13  H2   109.32  3.000
 JA5  H4   C13  O12  105.91  3.000
 JA5  H3   C13  O12  111.43  3.000
 JA5  H2   C13  O12  111.35  3.000
 JA5  H5   O01  C02  108.15  3.000
 JA5  H7   C02  H6   106.79  3.000
 JA5  H7   C02  C03  109.49  3.000
 JA5  H6   C02  C03  108.27  3.000
 JA5  H7   C02  O01  110.92  3.000
 JA5  H6   C02  O01  112.62  3.000
 JA5  C03  C02  O01  108.69  3.000
 JA5  S07  C03  C04  113.28  3.000
 JA5  S07  C03  C02  117.64  3.000
 JA5  C04  C03  C02  129.02  3.000
 JA5  H8   C04  C05  124.92  3.000
 JA5  H8   C04  C03  122.89  3.000
 JA5  C05  C04  C03  112.19  3.000
 JA5  C06  C05  C04  111.32  3.000
 JA5  C06  C05  C10  106.42  3.000
 JA5  C04  C05  C10  142.25  3.000
 JA5  N08  C06  S07  136.41  3.000
 JA5  N08  C06  C05  109.94  3.000
 JA5  S07  C06  C05  113.63  3.000
 JA5  C06  S07  C03   89.56  3.000
 JA5  H9   N08  C09  125.85  3.000
 JA5  H9   N08  C06  126.34  3.000
 JA5  C09  N08  C06  107.80  3.000
 JA5  C11  C09  N08  123.53  3.000
 JA5  C11  C09  C10  127.29  3.000
 JA5  N08  C09  C10  109.17  3.000
 JA5  O14  C11  O12  124.17  3.000
 JA5  O12  C11  C09  112.11  3.000
 JA5  O14  C11  C09  123.72  3.000
 JA5  C11  O12  C13  117.54  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
 JA5  CONST_01  C03  C04  C05  C10  180.00   0.0  0
 JA5  CONST_02  S07  C06  C05  C10  180.00   0.0  0
 JA5  CONST_03  N08  C06  C05  C10    0.00   0.0  0
 JA5  CONST_04  C06  N08  C09  C10    0.00   0.0  0
 JA5  CONST_05  C06  C05  C04  C03    0.00   0.0  0
 JA5  CONST_06  C05  C06  S07  C03    0.00   0.0  0
 JA5  CONST_07  N08  C06  S07  C03  180.00   0.0  0
 JA5  CONST_08  C06  S07  C03  C04    0.00   0.0  0
 JA5  CONST_09  S07  C06  C05  C04    0.00   0.0  0
 JA5  CONST_10  N08  C06  C05  C04  180.00   0.0  0
 JA5  CONST_11  C09  C10  C05  C04  180.00   0.0  0
 JA5  CONST_12  S07  C03  C04  C05    0.00   0.0  0
 JA5  CONST_13  C09  N08  C06  C05    0.00   0.0  0
 JA5  CONST_14  N08  C09  C10  C05    0.00   0.0  0
 JA5  CONST_15  C09  C10  C05  C06    0.00   0.0  0
 JA5  CONST_16  C09  N08  C06  S07  180.00   0.0  0
 JA5  CONST_17  C05  C04  C03  C02  180.00   0.0  0
 JA5  CONST_18  C06  S07  C03  C02  180.00   0.0  0
 JA5  CONST_19  C11  C09  C10  C05  180.00   0.0  0
 JA5  CONST_20  C11  C09  N08  C06  180.00   0.0  0
 JA5  CONST_21  H8   C04  C05  C10    0.00   0.0  0
 JA5  CONST_22  H9   N08  C09  C10  180.00   0.0  0
 JA5  CONST_23  H1   C10  C05  C04    0.00   0.0  0
 JA5  Var_01    O14  C11  C09  C10   -0.64  30.0  2
 JA5  Var_02    C04  C03  C02  O01  136.74  30.0  2
 JA5  Var_03    C09  C11  O12  C13  179.89  30.0  1
 JA5  Var_04    H2   C13  O12  C11  -61.82  30.0  3

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
 JA5  plan-1  C10  0.020
 JA5  plan-1  C02  0.020
 JA5  plan-1  C03  0.020
 JA5  plan-1  C04  0.020
 JA5  plan-1  C05  0.020
 JA5  plan-1  C06  0.020
 JA5  plan-1  S07  0.020
 JA5  plan-1  N08  0.020
 JA5  plan-1  C09  0.020
 JA5  plan-1  C11  0.020
 JA5  plan-1  H1   0.020
 JA5  plan-1  H8   0.020
 JA5  plan-1  H9   0.020
 JA5  plan-2  C09  0.020
 JA5  plan-2  C11  0.020
 JA5  plan-2  O12  0.020
 JA5  plan-2  O14  0.020

