# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:03:56 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: [(1R)-5,8-dichloro-1-propyl-1,3,4,9-tetrahydropyrano[3,4-b]indol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@]1(CC(O)=O)OCCc2c1[nH]c3c(Cl)ccc(Cl)c23
#
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
 1JE  1JE  '[(1R)-5,8-dichloro-1-propyl-1,3,4,9-tetrahydropyrano[3,4-b]indol-1-yl]acetic acid'  ligand  39  22  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_1JE
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
 1JE  C1   C   CR56  0   0.435   1.5059   0.6961   0.4828
 1JE  C2   C   CR6   0  -0.128   2.6695   1.4067   0.7535
 1JE  C3   C   CR16  0  -0.285   3.8847   0.7684   0.6373
 1JE  C4   C   CR16  0  -0.246   3.9413  -0.5761   0.2485
 1JE  C5   C   CR6   0  -0.235   2.7853  -1.2791  -0.0168
 1JE  C6   C   CR56  0   0.198   1.5356  -0.6651   0.0971
 1JE  N7   N   NR15  0  -0.753   0.2061   1.0914   0.5210
 1JE  C8   C   CR5   0   0.355  -0.5863   0.0381   0.1643
 1JE  C9   C   CR5   0   0.001   0.1755  -1.0642  -0.0880
 1JE  C10  C   CT    0   0.163  -2.0842   0.0766   0.0998
 1JE  O11  O   O2    0  -0.500  -2.5283  -1.1073  -0.5320
 1JE  C12  C   CH2   0  -0.208  -1.9235  -2.3069  -0.0814
 1JE  C13  C   CH2   0  -0.539  -0.4494  -2.3683  -0.4584
 1JE  CL1  CL  CL    0  -0.119   2.5607   3.0669   1.2236
 1JE  CL2  CL  CL    0  -0.138   2.8886  -2.9374  -0.5075
 1JE  C16  C   CH2   0  -0.575  -2.5796   1.2189  -0.8016
 1JE  C17  C   C     0   0.550  -2.1479   1.0060  -2.2288
 1JE  O18  O   O     0  -0.435  -1.0035   1.0558  -2.6033
 1JE  O19  O   OH1   0  -0.587  -3.1699   0.7626  -3.0400
 1JE  C20  C   CH2   0  -0.434  -2.6591   0.2323   1.5222
 1JE  C21  C   CH2   0  -0.432  -4.1553  -0.0311   1.6511
 1JE  C22  C   CH3   0  -0.664  -4.6504   0.2525   3.0631
 1JE  H1   H   HCR6  0   0.282   4.8022   1.3019   0.8431
 1JE  H2   H   HCR6  0   0.279   4.9051  -1.0569   0.1547
 1JE  H3   H   HNR5  0   0.409  -0.1069   2.0175   0.7632
 1JE  H4   H   HCH2  0   0.218  -2.0347  -2.4154   1.0040
 1JE  H5   H   HCH2  0   0.246  -2.4778  -3.1209  -0.5487
 1JE  H6   H   HCH2  0   0.245  -0.3330  -2.5733  -1.5265
 1JE  H7   H   HCH2  0   0.245   0.0120  -3.2022   0.0726
 1JE  H8   H   HCH2  0   0.282  -3.6645   1.2922  -0.7355
 1JE  H9   H   HCH2  0   0.282  -2.1737   2.1709  -0.4531
 1JE  H10  H   HOH1  0   0.478  -2.8481   0.6327  -3.9450
 1JE  H11  H   HCH2  0   0.245  -2.1216  -0.4343   2.2030
 1JE  H12  H   HCH2  0   0.240  -2.4325   1.2452   1.8700
 1JE  H13  H   HCH2  0   0.223  -4.7186   0.5849   0.9457
 1JE  H14  H   HCH2  0   0.230  -4.3688  -1.0698   1.3906
 1JE  H15  H   HCH3  0   0.220  -4.1328  -0.3659   3.7986
 1JE  H16  H   HCH3  0   0.220  -4.4877   1.2965   3.3374
 1JE  H17  H   HCH3  0   0.231  -5.7177   0.0499   3.1561

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
 1JE  C22  C21  single    1.523  0.020  1.523
 1JE  C21  C20  single    1.525  0.020  1.525
 1JE  C20  C10  single    1.542  0.020  1.542
 1JE  CL1  C2   single    1.729  0.020  1.729
 1JE  C2   C3   aromatic  1.378  0.020  1.378
 1JE  C2   C1   aromatic  1.390  0.020  1.390
 1JE  N7   C1   aromatic  1.359  0.020  1.359
 1JE  N7   C8   aromatic  1.366  0.020  1.366
 1JE  C3   C4   aromatic  1.401  0.020  1.401
 1JE  C1   C6   aromatic  1.415  0.020  1.415
 1JE  O18  C17  double    1.205  0.020  1.205
 1JE  C10  C8   single    1.500  0.020  1.500
 1JE  C10  O11  single    1.413  0.020  1.413
 1JE  C10  C16  single    1.537  0.020  1.537
 1JE  C8   C9   aromatic  1.363  0.020  1.363
 1JE  C4   C5   aromatic  1.379  0.020  1.379
 1JE  C6   C9   aromatic  1.429  0.020  1.429
 1JE  C6   C5   aromatic  1.397  0.020  1.397
 1JE  O11  C12  single    1.417  0.020  1.417
 1JE  C9   C13  single    1.493  0.020  1.493
 1JE  C5   CL2  single    1.732  0.020  1.732
 1JE  C17  C16  single    1.506  0.020  1.506
 1JE  C17  O19  single    1.327  0.020  1.327
 1JE  C13  C12  single    1.523  0.020  1.523
 1JE  C3   H1   single    0.930  0.020  1.080
 1JE  C4   H2   single    0.930  0.020  1.080
 1JE  N7   H3   single    0.860  0.020  1.020
 1JE  C12  H4   single    0.970  0.020  1.090
 1JE  C12  H5   single    0.970  0.020  1.090
 1JE  C13  H6   single    0.970  0.020  1.090
 1JE  C13  H7   single    0.970  0.020  1.090
 1JE  C16  H8   single    0.970  0.020  1.090
 1JE  C16  H9   single    0.970  0.020  1.090
 1JE  O19  H10  single    0.850  0.020  0.980
 1JE  C20  H11  single    0.970  0.020  1.090
 1JE  C20  H12  single    0.970  0.020  1.090
 1JE  C21  H13  single    0.970  0.020  1.090
 1JE  C21  H14  single    0.970  0.020  1.090
 1JE  C22  H15  single    0.970  0.020  1.090
 1JE  C22  H16  single    0.970  0.020  1.090
 1JE  C22  H17  single    0.970  0.020  1.090

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
 1JE  N7   C1   C6   107.90  3.000
 1JE  C6   C1   C2   121.82  3.000
 1JE  N7   C1   C2   130.27  3.000
 1JE  CL1  C2   C3   121.56  3.000
 1JE  C3   C2   C1   119.02  3.000
 1JE  CL1  C2   C1   119.42  3.000
 1JE  H1   C3   C4   119.49  3.000
 1JE  H1   C3   C2   120.25  3.000
 1JE  C4   C3   C2   120.25  3.000
 1JE  H2   C4   C5   120.27  3.000
 1JE  H2   C4   C3   119.14  3.000
 1JE  C5   C4   C3   120.59  3.000
 1JE  CL2  C5   C6   119.81  3.000
 1JE  CL2  C5   C4   119.51  3.000
 1JE  C6   C5   C4   120.68  3.000
 1JE  C9   C6   C5   135.88  3.000
 1JE  C5   C6   C1   117.63  3.000
 1JE  C9   C6   C1   106.50  3.000
 1JE  H3   N7   C8   126.28  3.000
 1JE  H3   N7   C1   124.85  3.000
 1JE  C8   N7   C1   108.86  3.000
 1JE  C10  C8   C9   124.81  3.000
 1JE  C9   C8   N7   110.35  3.000
 1JE  C10  C8   N7   124.82  3.000
 1JE  C13  C9   C8   121.22  3.000
 1JE  C13  C9   C6   132.41  3.000
 1JE  C8   C9   C6   106.37  3.000
 1JE  C20  C10  C16  110.23  3.000
 1JE  C16  C10  O11  105.02  3.000
 1JE  C20  C10  O11  112.31  3.000
 1JE  C16  C10  C8   111.48  3.000
 1JE  O11  C10  C8   108.15  3.000
 1JE  C20  C10  C8   109.59  3.000
 1JE  C12  O11  C10  115.65  3.000
 1JE  H5   C12  H4   107.40  3.000
 1JE  H5   C12  C13  110.86  3.000
 1JE  H4   C12  C13  109.83  3.000
 1JE  H5   C12  O11  106.19  3.000
 1JE  H4   C12  O11  110.81  3.000
 1JE  C13  C12  O11  111.62  3.000
 1JE  H7   C13  H6   106.67  3.000
 1JE  H7   C13  C12  108.65  3.000
 1JE  H6   C13  C12  110.63  3.000
 1JE  H7   C13  C9   111.71  3.000
 1JE  H6   C13  C9   111.19  3.000
 1JE  C12  C13  C9   107.98  3.000
 1JE  H9   C16  H8   106.99  3.000
 1JE  H9   C16  C17  108.61  3.000
 1JE  H8   C16  C17  110.63  3.000
 1JE  H9   C16  C10  109.94  3.000
 1JE  H8   C16  C10  109.59  3.000
 1JE  C17  C16  C10  110.99  3.000
 1JE  O19  C17  O18  123.29  3.000
 1JE  O19  C17  C16  112.60  3.000
 1JE  O18  C17  C16  124.11  3.000
 1JE  H10  O19  C17  109.85  3.000
 1JE  H12  C20  H11  105.33  3.000
 1JE  H12  C20  C21  109.64  3.000
 1JE  H11  C20  C21  108.92  3.000
 1JE  H12  C20  C10  108.02  3.000
 1JE  H11  C20  C10  109.23  3.000
 1JE  C21  C20  C10  115.24  3.000
 1JE  H14  C21  H13  106.34  3.000
 1JE  H14  C21  C22  109.56  3.000
 1JE  H13  C21  C22  109.02  3.000
 1JE  H14  C21  C20  109.63  3.000
 1JE  H13  C21  C20  110.72  3.000
 1JE  C22  C21  C20  111.42  3.000
 1JE  H17  C22  H16  107.59  3.000
 1JE  H17  C22  H15  107.55  3.000
 1JE  H16  C22  H15  107.56  3.000
 1JE  H17  C22  C21  111.27  3.000
 1JE  H16  C22  C21  111.26  3.000
 1JE  H15  C22  C21  111.41  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
 1JE  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 1JE  CONST_02  C9   C8   N7   C1      0.00   0.0  0
 1JE  CONST_03  C8   C9   C6   C1      0.00   0.0  0
 1JE  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 1JE  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 1JE  CONST_06  C8   N7   C1   C2    180.00   0.0  0
 1JE  CONST_07  C9   C6   C1   C2    180.00   0.0  0
 1JE  CONST_08  C5   C6   C1   C2      0.00   0.0  0
 1JE  CONST_09  N7   C1   C2   C3    180.00   0.0  0
 1JE  CONST_10  C6   C1   C2   C3      0.00   0.0  0
 1JE  CONST_11  C6   C5   C4   C3      0.00   0.0  0
 1JE  CONST_12  C9   C6   C5   C4    180.00   0.0  0
 1JE  CONST_13  N7   C1   C6   C5    180.00   0.0  0
 1JE  CONST_14  C8   C9   C6   C5    180.00   0.0  0
 1JE  CONST_15  C8   N7   C1   C6      0.00   0.0  0
 1JE  CONST_16  N7   C8   C9   C6      0.00   0.0  0
 1JE  CONST_17  C9   C6   C1   N7      0.00   0.0  0
 1JE  CONST_18  CL2  C5   C6   C1    180.00   0.0  0
 1JE  CONST_19  CL2  C5   C4   C3    180.00   0.0  0
 1JE  CONST_20  CL1  C2   C3   C4    180.00   0.0  0
 1JE  CONST_21  CL1  C2   C1   C6    180.00   0.0  0
 1JE  CONST_22  CL1  C2   C1   N7      0.00   0.0  0
 1JE  CONST_23  CL2  C5   C6   C9      0.00   0.0  0
 1JE  CONST_24  H1   C3   C2   C1    180.00   0.0  0
 1JE  CONST_25  H2   C4   C3   C2    180.00   0.0  0
 1JE  CONST_26  H3   N7   C1   C2      0.00   0.0  0
 1JE  CONST_27  H10  O19  C17  C16   180.00   0.0  0
 1JE  Var_01    C12  C13  C9   C6    162.44  30.0  1
 1JE  Var_02    O11  C12  C13  C9     47.64  30.0  1
 1JE  Var_03    C13  C12  O11  C10   -67.61  30.0  1
 1JE  Var_04    C22  C21  C20  C10  -175.52  30.0  1
 1JE  Var_05    O18  C17  C16  C10   -67.65  30.0  1
 1JE  Var_06    H15  C22  C21  C20   -59.19  30.0  3

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
 1JE  chir_01  C10  C8  O11  C16  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
 1JE  plan-1  C16  0.020
 1JE  plan-1  C17  0.020
 1JE  plan-1  O18  0.020
 1JE  plan-1  O19  0.020
 1JE  plan-1  H10  0.020
 1JE  plan-2  C1   0.020
 1JE  plan-2  C2   0.020
 1JE  plan-2  C3   0.020
 1JE  plan-2  C4   0.020
 1JE  plan-2  C5   0.020
 1JE  plan-2  C6   0.020
 1JE  plan-2  N7   0.020
 1JE  plan-2  C8   0.020
 1JE  plan-2  C9   0.020
 1JE  plan-2  C10  0.020
 1JE  plan-2  C13  0.020
 1JE  plan-2  CL1  0.020
 1JE  plan-2  CL2  0.020
 1JE  plan-2  H1   0.020
 1JE  plan-2  H2   0.020
 1JE  plan-2  H3   0.020

