# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:23:05 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: methyl (3aR,4S,7aR)-4-hydroxy-4-[(3-methylphenyl)ethynyl]octahydro-1H-indole-1-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N1CC[C@@H]2[C@H]1CCC[C@@]2(O)C#Cc3cccc(C)c3
#
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
 2U8  2U8  'methyl (3aR,4S,7aR)-4-hydroxy-4-[(3-methylphenyl)ethynyl]octahydro-1H-indole-1-carboxylate'  ligand  46  23  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2U8
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
 2U8  C1   C  CR6   0  -0.136  -3.2419  -0.3238  -0.0604
 2U8  N1   N  NT    0  -0.505   3.1158  -0.2411   0.2714
 2U8  O1   O  OH1   0  -0.662  -0.0389   3.0809   0.8946
 2U8  C2   C  CR16  0  -0.318  -3.2883  -1.4741  -0.8532
 2U8  O2   O  O     0  -0.533   3.2694  -2.3311  -0.6010
 2U8  C3   C  CR16  0  -0.346  -4.3663   0.0489   0.6784
 2U8  O3   O  O2    0  -0.480   4.8608  -1.5125   0.7648
 2U8  C4   C  CSP   0   0.084  -2.0577   0.4703  -0.0164
 2U8  C5   C  CR16  0  -0.237  -4.4491  -2.2272  -0.8957
 2U8  C6   C  CR16  0  -0.300  -5.5629  -1.8463  -0.1581
 2U8  C7   C  CR6   0   0.105  -5.5352  -0.7046   0.6398
 2U8  C8   C  CH3   0  -0.725  -6.7266  -0.3014   1.4589
 2U8  C9   C  CSP   0   0.171  -1.0584   1.1438   0.0122
 2U8  C10  C  CT    0   0.097   0.1505   1.9881   0.0223
 2U8  C11  C  CH2   0  -0.475   0.4342   2.4543  -1.4124
 2U8  C12  C  CH2   0  -0.460   0.8024   1.2903  -2.3217
 2U8  C13  C  CH2   0  -0.430   2.0380   0.5764  -1.7923
 2U8  C14  C  CH1   0  -0.057   1.8440   0.0870  -0.3561
 2U8  C15  C  CH1   0  -0.282   1.3163   1.1695   0.5935
 2U8  C16  C  CH2   0  -0.484   2.5809   1.9483   0.9519
 2U8  C17  C  CH2   0  -0.261   3.6290   0.8445   1.1050
 2U8  C19  C  CH3   0  -0.411   5.5850  -2.7320   0.6525
 2U8  H1   H  HOH1  0   0.451  -0.7361   3.6404   0.5342
 2U8  H2   H  HCR6  0   0.255  -2.4221  -1.7662  -1.4321
 2U8  H3   H  HCR6  0   0.251  -4.3235   0.9430   1.2888
 2U8  H4   H  HCR6  0   0.260  -4.4892  -3.1165  -1.5110
 2U8  H5   H  HCR6  0   0.254  -6.4660  -2.4428  -0.2052
 2U8  H6   H  HCH3  0   0.251  -6.5954  -0.5883   2.5040
 2U8  H7   H  HCH3  0   0.247  -6.8787   0.7776   1.4390
 2U8  H8   H  HCH3  0   0.246  -7.6374  -0.7787   1.1004
 2U8  H9   H  HCH2  0   0.248  -0.4434   2.9823  -1.7955
 2U8  H10  H  HCH2  0   0.243   1.2542   3.1780  -1.3866
 2U8  H11  H  HCH2  0   0.229  -0.0365   0.5922  -2.4010
 2U8  H12  H  HCH2  0   0.247   0.9910   1.6595  -3.3312
 2U8  H13  H  HCH2  0   0.247   2.2966  -0.2742  -2.4258
 2U8  H14  H  HCH2  0   0.225   2.8918   1.2608  -1.8306
 2U8  H15  H  HCH1  0   0.261   1.1856  -0.7847  -0.3524
 2U8  H16  H  HCH1  0   0.268   0.9639   0.6673   1.5011
 2U8  H17  H  HCH2  0   0.243   2.8583   2.6429   0.1572
 2U8  H18  H  HCH2  0   0.263   2.4785   2.5256   1.8685
 2U8  H19  H  HCH2  0   0.244   3.7065   0.5240   2.1464
 2U8  H20  H  HCH2  0   0.248   4.6183   1.1714   0.7822
 2U8  H21  H  HCH3  0   0.232   5.0198  -3.5763   1.0477
 2U8  H22  H  HCH3  0   0.232   5.8670  -2.9428  -0.3790
 2U8  H23  H  HCH3  0   0.246   6.4849  -2.5981   1.2466
 2U8  C18  C  C     0   0.753   3.7101  -1.4291   0.0883

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
 2U8  C8   C7   single    1.501  0.020  1.501
 2U8  C7   C6   aromatic  1.393  0.020  1.393
 2U8  C7   C3   aromatic  1.391  0.020  1.391
 2U8  C6   C5   aromatic  1.389  0.020  1.389
 2U8  C3   C1   aromatic  1.396  0.020  1.396
 2U8  C5   C2   aromatic  1.384  0.020  1.384
 2U8  C1   C2   aromatic  1.398  0.020  1.398
 2U8  C1   C4   single    1.426  0.020  1.426
 2U8  C4   C9   triple    1.205  0.020  1.205
 2U8  C12  C11  single    1.522  0.020  1.522
 2U8  C12  C13  single    1.522  0.020  1.522
 2U8  C9   C10  single    1.475  0.020  1.475
 2U8  C11  C10  single    1.535  0.020  1.535
 2U8  C13  C14  single    1.530  0.020  1.530
 2U8  C10  O1   single    1.411  0.020  1.411
 2U8  C10  C15  single    1.535  0.020  1.535
 2U8  C14  C15  single    1.534  0.020  1.534
 2U8  C14  N1   single    1.456  0.020  1.456
 2U8  C15  C16  single    1.528  0.020  1.528
 2U8  O2   C18  double    1.218  0.020  1.218
 2U8  N1   C18  single    1.341  0.020  1.341
 2U8  N1   C17  single    1.462  0.020  1.462
 2U8  C16  C17  single    1.530  0.020  1.530
 2U8  C18  O3   single    1.337  0.020  1.337
 2U8  O3   C19  single    1.423  0.020  1.423
 2U8  O1   H1   single    0.850  0.020  0.980
 2U8  C2   H2   single    0.930  0.020  1.080
 2U8  C3   H3   single    0.930  0.020  1.080
 2U8  C5   H4   single    0.930  0.020  1.080
 2U8  C6   H5   single    0.930  0.020  1.080
 2U8  C8   H6   single    0.970  0.020  1.090
 2U8  C8   H7   single    0.970  0.020  1.090
 2U8  C8   H8   single    0.970  0.020  1.090
 2U8  C11  H9   single    0.970  0.020  1.090
 2U8  C11  H10  single    0.970  0.020  1.090
 2U8  C12  H11  single    0.970  0.020  1.090
 2U8  C12  H12  single    0.970  0.020  1.090
 2U8  C13  H13  single    0.970  0.020  1.090
 2U8  C13  H14  single    0.970  0.020  1.090
 2U8  C14  H15  single    0.970  0.020  1.090
 2U8  C15  H16  single    0.970  0.020  1.090
 2U8  C16  H17  single    0.970  0.020  1.090
 2U8  C16  H18  single    0.970  0.020  1.090
 2U8  C17  H19  single    0.970  0.020  1.090
 2U8  C17  H20  single    0.970  0.020  1.090
 2U8  C19  H21  single    0.970  0.020  1.090
 2U8  C19  H22  single    0.970  0.020  1.090
 2U8  C19  H23  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
 2U8  C4   C1   C3   120.24  3.000
 2U8  C4   C1   C2   120.21  3.000
 2U8  C3   C1   C2   119.54  3.000
 2U8  C18  N1   C17  125.47  3.000
 2U8  C17  N1   C14  112.66  3.000
 2U8  C18  N1   C14  121.87  3.000
 2U8  H1   O1   C10  108.39  3.000
 2U8  H2   C2   C5   120.53  3.000
 2U8  H2   C2   C1   119.93  3.000
 2U8  C5   C2   C1   119.54  3.000
 2U8  H3   C3   C7   119.73  3.000
 2U8  H3   C3   C1   119.11  3.000
 2U8  C7   C3   C1   121.16  3.000
 2U8  C19  O3   C18  116.84  3.000
 2U8  C9   C4   C1   180.00  3.000
 2U8  H4   C5   C6   119.84  3.000
 2U8  H4   C5   C2   119.71  3.000
 2U8  C6   C5   C2   120.45  3.000
 2U8  H5   C6   C7   119.52  3.000
 2U8  H5   C6   C5   119.63  3.000
 2U8  C7   C6   C5   120.86  3.000
 2U8  C8   C7   C6   121.13  3.000
 2U8  C6   C7   C3   118.45  3.000
 2U8  C8   C7   C3   120.41  3.000
 2U8  H8   C8   H7   108.13  3.000
 2U8  H8   C8   H6   107.49  3.000
 2U8  H7   C8   H6   107.12  3.000
 2U8  H8   C8   C7   111.50  3.000
 2U8  H7   C8   C7   111.52  3.000
 2U8  H6   C8   C7   110.88  3.000
 2U8  C10  C9   C4   180.00  3.000
 2U8  C15  C10  C11  111.68  3.000
 2U8  C15  C10  C9   108.66  3.000
 2U8  C11  C10  C9   108.60  3.000
 2U8  C15  C10  O1   106.56  3.000
 2U8  C11  C10  O1   111.56  3.000
 2U8  C9   C10  O1   109.73  3.000
 2U8  H10  C11  H9   106.88  3.000
 2U8  H10  C11  C12  109.79  3.000
 2U8  H9   C11  C12  110.74  3.000
 2U8  H10  C11  C10  108.51  3.000
 2U8  H9   C11  C10  109.01  3.000
 2U8  C12  C11  C10  111.77  3.000
 2U8  H12  C12  H11  106.34  3.000
 2U8  H12  C12  C13  109.89  3.000
 2U8  H11  C12  C13  110.39  3.000
 2U8  H12  C12  C11  109.61  3.000
 2U8  H11  C12  C11  110.22  3.000
 2U8  C13  C12  C11  110.32  3.000
 2U8  H14  C13  H13  106.38  3.000
 2U8  H14  C13  C14  109.37  3.000
 2U8  H13  C13  C14  109.00  3.000
 2U8  H14  C13  C12  109.13  3.000
 2U8  H13  C13  C12  110.85  3.000
 2U8  C14  C13  C12  111.94  3.000
 2U8  H15  C14  C15  110.72  3.000
 2U8  H15  C14  C13  109.57  3.000
 2U8  C15  C14  C13  113.53  3.000
 2U8  H15  C14  N1   110.20  3.000
 2U8  C15  C14  N1   101.11  3.000
 2U8  C13  C14  N1   111.47  3.000
 2U8  H16  C15  C16  107.80  3.000
 2U8  H16  C15  C14  107.46  3.000
 2U8  C16  C15  C14  102.72  3.000
 2U8  H16  C15  C10  107.97  3.000
 2U8  C16  C15  C10  116.37  3.000
 2U8  C14  C15  C10  114.04  3.000
 2U8  H18  C16  H17  107.44  3.000
 2U8  H18  C16  C17  111.28  3.000
 2U8  H17  C16  C17  110.98  3.000
 2U8  H18  C16  C15  112.96  3.000
 2U8  H17  C16  C15  111.35  3.000
 2U8  C17  C16  C15  102.87  3.000
 2U8  H20  C17  H19  107.80  3.000
 2U8  H20  C17  C16  112.05  3.000
 2U8  H19  C17  C16  110.84  3.000
 2U8  H20  C17  N1   111.86  3.000
 2U8  H19  C17  N1   110.53  3.000
 2U8  C16  C17  N1   103.79  3.000
 2U8  H23  C19  H22  109.09  3.000
 2U8  H23  C19  H21  109.07  3.000
 2U8  H22  C19  H21  109.11  3.000
 2U8  H23  C19  O3   105.83  3.000
 2U8  H22  C19  O3   111.85  3.000
 2U8  H21  C19  O3   111.80  3.000
 2U8  O3   C18  O2   123.47  3.000
 2U8  O3   C18  N1   111.56  3.000
 2U8  O2   C18  N1   124.97  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
 2U8  CONST_01  C6   C7   C3   C1     0.00   0.0  0
 2U8  CONST_02  C6   C5   C2   C1     0.00   0.0  0
 2U8  CONST_03  C7   C6   C5   C2     0.00   0.0  0
 2U8  CONST_04  C7   C3   C1   C2     0.00   0.0  0
 2U8  CONST_05  C5   C6   C7   C3     0.00   0.0  0
 2U8  CONST_06  C5   C2   C1   C3     0.00   0.0  0
 2U8  CONST_07  C8   C7   C3   C1   180.00   0.0  0
 2U8  CONST_08  C7   C3   C1   C4   180.00   0.0  0
 2U8  CONST_09  C5   C2   C1   C4   180.00   0.0  0
 2U8  CONST_10  C8   C7   C6   C5   180.00   0.0  0
 2U8  CONST_11  H4   C5   C2   C1   180.00   0.0  0
 2U8  CONST_12  H5   C6   C5   C2   180.00   0.0  0
 2U8  CONST_13  H3   C3   C1   C2   180.00   0.0  0
 2U8  CONST_14  H2   C2   C1   C3   180.00   0.0  0
 2U8  Var_01    C15  C16  C17  N1    25.30  30.0  1
 2U8  Var_02    C13  C12  C11  C10  -59.18  30.0  1
 2U8  Var_03    C14  C13  C12  C11   56.77  30.0  1
 2U8  Var_04    C16  C17  N1   C14   -1.01  30.0  1
 2U8  Var_05    C14  N1   C18  O2     0.19  30.0  2
 2U8  Var_06    H6   C8   C7   C3   -78.14  30.0  2
 2U8  Var_07    H21  C19  O3   C18  -62.54  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
 2U8  chir_01  C10  C11  O1   C15  positiv
 2U8  chir_02  C14  N1   C15  C13  negativ
 2U8  chir_03  C15  C16  C14  C10  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
 2U8  plan-1  C1   0.020
 2U8  plan-1  C2   0.020
 2U8  plan-1  C3   0.020
 2U8  plan-1  C4   0.020
 2U8  plan-1  C5   0.020
 2U8  plan-1  C6   0.020
 2U8  plan-1  C7   0.020
 2U8  plan-1  C8   0.020
 2U8  plan-1  C9   0.020
 2U8  plan-1  H2   0.020
 2U8  plan-1  H3   0.020
 2U8  plan-1  H4   0.020
 2U8  plan-1  H5   0.020
 2U8  plan-2  N1   0.020
 2U8  plan-2  O2   0.020
 2U8  plan-2  O3   0.020
 2U8  plan-2  C18  0.020

