# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:14:31 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-chloro-N-[(1R,2R)-1-hydroxy-2,3-dihydro-1H-inden-2-yl]-6H-thieno[2,3-b]pyrrole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](Cc2ccccc12)NC(=O)c3[nH]c4sc(Cl)cc4c3
#
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
 2TH  2TH  2-chloro-N-[(1R,2R)-1-hydroxy-2,3-dihydro-1H-inden-2-yl]-6H-thieno[2,3-b]pyrrole-5-carboxamide  ligand  35  22  .  2022-07-22  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_2TH
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
 2TH  O1   O   OH1   0  -0.659   4.8200  -1.5712  -1.6295
 2TH  C1   C   CR15  0  -0.004   3.7244  -0.7488  -1.2890
 2TH  C2   C   CR56  0   0.047   4.1664   0.4703  -0.5183
 2TH  C3   C   CR56  0   0.107   4.1077   0.2188   0.8498
 2TH  C4   C   CR16  0  -0.326   4.5180   1.1850   1.7544
 2TH  C5   C   CR16  0  -0.251   4.9856   2.4036   1.2706
 2TH  C6   C   CR16  0  -0.261   5.0414   2.6526  -0.0968
 2TH  C7   C   CR16  0  -0.315   4.6308   1.6812  -1.0044
 2TH  C8   C   CH2   0  -0.478   3.5659  -1.1609   1.1037
 2TH  C9   C   CR15  0  -0.154   2.8944  -1.5088  -0.2402
 2TH  N1   N   NH1   0  -0.659   1.5266  -1.0342  -0.2939
 2TH  C10  C   C     0   0.534   0.5017  -1.7629   0.1958
 2TH  O2   O   O     0  -0.487   0.6464  -2.8775   0.6799
 2TH  C11  C   CR5   0   0.199  -0.8348  -1.1551   0.1131
 2TH  C12  C   CR15  0  -0.412  -1.9506  -1.5389   0.8217
 2TH  C13  C   CR55  0   0.111  -2.9960  -0.6629   0.4461
 2TH  C14  C   CR55  0   0.082  -2.4567   0.2094  -0.4883
 2TH  S1   S   S2    0   0.277  -3.5811   1.3554  -1.0981
 2TH  C15  C   CR5   0  -0.259  -4.8039   0.6473  -0.0603
 2TH  C16  C   CR15  0  -0.186  -4.3779  -0.3916   0.6931
 2TH  CL1  CL  CL    0  -0.078  -6.3756   1.3173  -0.0965
 2TH  N2   N   NR15  0  -0.708  -1.1557  -0.0739  -0.6839
 2TH  HO1  H   HOH1  0   0.454   5.4430  -1.0498  -2.1457
 2TH  H1   H   HCR5  0   0.231   3.1272  -0.4993  -2.1751
 2TH  H4   H   HCR6  0   0.251   4.4706   1.0035   2.8213
 2TH  H5   H   HCR6  0   0.257   5.3016   3.1704   1.9667
 2TH  H6   H   HCR6  0   0.256   5.4014   3.6084  -0.4545
 2TH  H7   H   HCR6  0   0.256   4.6671   1.8772  -2.0696
 2TH  H81  H   HCH2  0   0.263   2.8684  -1.2117   1.9403
 2TH  H82  H   HCH2  0   0.264   4.3779  -1.8609   1.3190
 2TH  H9   H   HCR5  0   0.274   2.8902  -2.5787  -0.4437
 2TH  HN1  H   HNH1  0   0.397   1.3927  -0.0447  -0.4384
 2TH  H12  H   HCR5  0   0.264  -1.9895  -2.3418   1.5398
 2TH  H16  H   HCR5  0   0.287  -5.0114  -0.9315   1.3809
 2TH  HN2  H   HNR5  0   0.424  -0.5707   0.3453  -1.3891

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
 2TH  O1   C1   single    1.412  0.020  1.412
 2TH  O1   HO1  single    0.850  0.020  0.980
 2TH  C1   C2   single    1.509  0.020  1.509
 2TH  C1   C9   single    1.538  0.020  1.538
 2TH  C1   H1   single    0.970  0.020  1.090
 2TH  C2   C3   aromatic  1.392  0.020  1.392
 2TH  C2   C7   aromatic  1.385  0.020  1.385
 2TH  C3   C4   aromatic  1.386  0.020  1.386
 2TH  C3   C8   single    1.504  0.020  1.504
 2TH  C4   C5   aromatic  1.392  0.020  1.392
 2TH  C4   H4   single    0.930  0.020  1.080
 2TH  C5   C6   aromatic  1.391  0.020  1.391
 2TH  C5   H5   single    0.930  0.020  1.080
 2TH  C6   C7   aromatic  1.391  0.020  1.391
 2TH  C6   H6   single    0.930  0.020  1.080
 2TH  C7   H7   single    0.930  0.020  1.080
 2TH  C8   C9   single    1.542  0.020  1.542
 2TH  C8   H81  single    0.970  0.020  1.090
 2TH  C8   H82  single    0.970  0.020  1.090
 2TH  C9   N1   single    1.449  0.020  1.449
 2TH  C9   H9   single    0.970  0.020  1.090
 2TH  N1   C10  single    1.350  0.020  1.350
 2TH  N1   HN1  single    0.860  0.020  1.020
 2TH  C10  O2   double    1.224  0.020  1.224
 2TH  C10  C11  single    1.471  0.020  1.471
 2TH  C11  C12  aromatic  1.376  0.020  1.376
 2TH  C11  N2   aromatic  1.381  0.020  1.381
 2TH  C12  C13  aromatic  1.415  0.020  1.415
 2TH  C12  H12  single    0.930  0.020  1.080
 2TH  C13  C14  aromatic  1.387  0.020  1.387
 2TH  C13  C16  aromatic  1.430  0.020  1.430
 2TH  C14  S1   aromatic  1.717  0.020  1.717
 2TH  C14  N2   aromatic  1.346  0.020  1.346
 2TH  S1   C15  aromatic  1.753  0.020  1.753
 2TH  C15  C16  aromatic  1.352  0.020  1.352
 2TH  C15  CL1  single    1.709  0.020  1.709
 2TH  C16  H16  single    0.930  0.020  1.080
 2TH  N2   HN2  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
 2TH  HO1  O1   C1   108.43  3.000
 2TH  H1   C1   C9   111.68  3.000
 2TH  H1   C1   C2   112.85  3.000
 2TH  C9   C1   C2   102.07  3.000
 2TH  H1   C1   O1   111.10  3.000
 2TH  C9   C1   O1   107.18  3.000
 2TH  C2   C1   O1   111.51  3.000
 2TH  C7   C2   C3   121.13  3.000
 2TH  C7   C2   C1   128.72  3.000
 2TH  C3   C2   C1   110.10  3.000
 2TH  C8   C3   C4   129.50  3.000
 2TH  C8   C3   C2   110.30  3.000
 2TH  C4   C3   C2   120.20  3.000
 2TH  H4   C4   C5   120.24  3.000
 2TH  H4   C4   C3   120.88  3.000
 2TH  C5   C4   C3   118.88  3.000
 2TH  H5   C5   C6   119.57  3.000
 2TH  H5   C5   C4   119.64  3.000
 2TH  C6   C5   C4   120.78  3.000
 2TH  H6   C6   C7   119.95  3.000
 2TH  H6   C6   C5   119.76  3.000
 2TH  C7   C6   C5   120.29  3.000
 2TH  H7   C7   C6   120.33  3.000
 2TH  H7   C7   C2   120.96  3.000
 2TH  C6   C7   C2   118.71  3.000
 2TH  H82  C8   H81  107.11  3.000
 2TH  H82  C8   C9   110.52  3.000
 2TH  H81  C8   C9   112.31  3.000
 2TH  H82  C8   C3   110.67  3.000
 2TH  H81  C8   C3   113.75  3.000
 2TH  C9   C8   C3   102.51  3.000
 2TH  H9   C9   N1   108.13  3.000
 2TH  H9   C9   C8   112.72  3.000
 2TH  N1   C9   C8   111.69  3.000
 2TH  H9   C9   C1   111.10  3.000
 2TH  N1   C9   C1   108.80  3.000
 2TH  C8   C9   C1   104.35  3.000
 2TH  HN1  N1   C10  118.73  3.000
 2TH  HN1  N1   C9   116.86  3.000
 2TH  C10  N1   C9   121.78  3.000
 2TH  C11  C10  O2   120.40  3.000
 2TH  C11  C10  N1   116.53  3.000
 2TH  O2   C10  N1   123.06  3.000
 2TH  N2   C11  C12  109.09  3.000
 2TH  N2   C11  C10  124.56  3.000
 2TH  C12  C11  C10  126.34  3.000
 2TH  H12  C12  C13  127.70  3.000
 2TH  H12  C12  C11  125.44  3.000
 2TH  C13  C12  C11  106.84  3.000
 2TH  C16  C13  C14  111.89  3.000
 2TH  C16  C13  C12  141.80  3.000
 2TH  C14  C13  C12  106.31  3.000
 2TH  N2   C14  S1   136.20  3.000
 2TH  N2   C14  C13  109.96  3.000
 2TH  S1   C14  C13  113.84  3.000
 2TH  C15  S1   C14   88.68  3.000
 2TH  CL1  C15  C16  127.07  3.000
 2TH  CL1  C15  S1   118.07  3.000
 2TH  C16  C15  S1   114.86  3.000
 2TH  H16  C16  C15  123.66  3.000
 2TH  H16  C16  C13  125.61  3.000
 2TH  C15  C16  C13  110.74  3.000
 2TH  HN2  N2   C14  125.13  3.000
 2TH  HN2  N2   C11  126.49  3.000
 2TH  C14  N2   C11  107.79  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
 2TH  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 2TH  CONST_02  C5   C6   C7   C2      0.00   0.0  0
 2TH  CONST_03  C6   C7   C2   C3      0.00   0.0  0
 2TH  CONST_04  C6   C5   C4   C3      0.00   0.0  0
 2TH  CONST_05  C7   C2   C3   C4      0.00   0.0  0
 2TH  CONST_06  C7   C6   C5   C4      0.00   0.0  0
 2TH  CONST_07  C14  C13  C12  C11     0.00   0.0  0
 2TH  CONST_08  C16  C13  C12  C11   180.00   0.0  0
 2TH  CONST_09  C13  C14  N2   C11     0.00   0.0  0
 2TH  CONST_10  S1   C14  N2   C11   180.00   0.0  0
 2TH  CONST_11  C14  N2   C11  C12     0.00   0.0  0
 2TH  CONST_12  S1   C14  C13  C12   180.00   0.0  0
 2TH  CONST_13  N2   C14  C13  C12     0.00   0.0  0
 2TH  CONST_14  C15  C16  C13  C12   180.00   0.0  0
 2TH  CONST_15  N2   C11  C12  C13     0.00   0.0  0
 2TH  CONST_16  C15  S1   C14  C13     0.00   0.0  0
 2TH  CONST_17  S1   C15  C16  C13     0.00   0.0  0
 2TH  CONST_18  C15  C16  C13  C14     0.00   0.0  0
 2TH  CONST_19  C16  C15  S1   C14     0.00   0.0  0
 2TH  CONST_20  C16  C13  C14  S1      0.00   0.0  0
 2TH  CONST_21  N2   C14  S1   C15   180.00   0.0  0
 2TH  CONST_22  N2   C14  C13  C16   180.00   0.0  0
 2TH  CONST_23  C13  C12  C11  C10   180.00   0.0  0
 2TH  CONST_24  C14  N2   C11  C10   180.00   0.0  0
 2TH  CONST_25  CL1  C15  C16  C13   180.00   0.0  0
 2TH  CONST_26  CL1  C15  S1   C14   180.00   0.0  0
 2TH  CONST_27  H7   C7   C2   C1      0.00   0.0  0
 2TH  CONST_28  H4   C4   C3   C2    180.00   0.0  0
 2TH  CONST_29  H6   C6   C7   C2    180.00   0.0  0
 2TH  CONST_30  H5   C5   C4   C3    180.00   0.0  0
 2TH  CONST_31  HN2  N2   C11  C12   180.00   0.0  0
 2TH  CONST_32  H16  C16  C13  C12     0.00   0.0  0
 2TH  CONST_33  H12  C12  C13  C14   180.00   0.0  0
 2TH  CONST_34  C11  C10  N1   C9    180.00   0.0  0
 2TH  CONST_35  O2   C10  N1   C9      0.00   0.0  0
 2TH  Var_01    C9   C8   C3   C2    -17.68  30.0  1
 2TH  Var_02    C12  C11  C10  N1   -162.78  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 2TH  chir_01  C1  O1  C2  C9  positiv
 2TH  chir_02  C9  N1  C8  C1  positiv

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
 2TH  plan-1  C10  0.020
 2TH  plan-1  C11  0.020
 2TH  plan-1  C12  0.020
 2TH  plan-1  C13  0.020
 2TH  plan-1  C14  0.020
 2TH  plan-1  S1   0.020
 2TH  plan-1  C15  0.020
 2TH  plan-1  C16  0.020
 2TH  plan-1  CL1  0.020
 2TH  plan-1  N2   0.020
 2TH  plan-1  H12  0.020
 2TH  plan-1  H16  0.020
 2TH  plan-1  HN2  0.020
 2TH  plan-2  C1   0.020
 2TH  plan-2  C2   0.020
 2TH  plan-2  C3   0.020
 2TH  plan-2  C4   0.020
 2TH  plan-2  C5   0.020
 2TH  plan-2  C6   0.020
 2TH  plan-2  C7   0.020
 2TH  plan-2  C8   0.020
 2TH  plan-2  H4   0.020
 2TH  plan-2  H5   0.020
 2TH  plan-2  H6   0.020
 2TH  plan-2  H7   0.020
 2TH  plan-3  C9   0.020
 2TH  plan-3  N1   0.020
 2TH  plan-3  C10  0.020
 2TH  plan-3  O2   0.020
 2TH  plan-3  C11  0.020
 2TH  plan-3  HN1  0.020

