# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 12:06:13 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: spiro[1~{H}-2-benzofuran-3,4'-piperidine]
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC2(CCN1)OCc3ccccc23
#
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
 GF3  GF3  spiro[1~{H}-2-benzofuran-3,4'-piperidine]  ligand  29  14  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GF3
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
 GF3  C4   C  CR56  0   0.128   1.2193  -5.6526  60.6240
 GF3  C5   C  CR56  0   0.011   2.0087  -6.3846  61.4929
 GF3  C6   C  CR16  0  -0.315   2.2031  -5.9707  62.8001
 GF3  C11  C  CH2   0  -0.317  -0.2909  -7.6959  57.7153
 GF3  C7   C  CH2   0  -0.189   2.5162  -7.5910  60.7658
 GF3  C8   C  CR5   0   0.183   1.1592  -6.3567  59.2975
 GF3  C9   C  CH2   0  -0.436   1.4990  -5.4617  58.1089
 GF3  C10  C  CH2   0  -0.318   1.3539  -6.2063  56.7818
 GF3  C12  C  CH2   0  -0.430  -0.2133  -7.0049  59.0754
 GF3  N1   N  NH1   0  -0.574   0.0564  -6.8342  56.5973
 GF3  C3   C  CR16  0  -0.341   0.6026  -4.4839  61.0373
 GF3  C1   C  CR16  0  -0.257   1.5909  -4.7943  63.2204
 GF3  C2   C  CR16  0  -0.252   0.7977  -4.0562  62.3467
 GF3  O1   O  O     0  -0.525   2.1666  -7.3666  59.4129
 GF3  H4   H  HCR6  0   0.251   2.8192  -6.5423  63.4833
 GF3  H13  H  HCH2  0   0.219   0.3821  -8.5586  57.7048
 GF3  H6   H  HCH2  0   0.222   2.0561  -8.5099  61.1532
 GF3  H5   H  HCH2  0   0.237   3.6005  -7.7126  60.8445
 GF3  H7   H  HCH2  0   0.235   2.5115  -5.0643  58.2198
 GF3  H8   H  HCH2  0   0.227   0.8173  -4.6049  58.1150
 GF3  H10  H  HCH2  0   0.220   2.1244  -6.9797  56.7057
 GF3  H9   H  HCH2  0   0.235   1.5295  -5.5169  55.9536
 GF3  H15  H  HCH2  0   0.226  -0.9821  -6.2277  59.1363
 GF3  H14  H  HCH2  0   0.235  -0.4225  -7.7173  59.8791
 GF3  H11  H  HNH1  0   0.337  -0.6483  -6.1103  56.5091
 GF3  H3   H  HCR6  0   0.248  -0.0191  -3.9098  60.3605
 GF3  H1   H  HCR6  0   0.253   1.7337  -4.4481  64.2360
 GF3  H2   H  HCR6  0   0.253   0.3298  -3.1423  62.6892
 GF3  H12  H  HCH2  0   0.234  -1.2973  -8.0880  57.5561

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
 GF3  N1   C10  single    1.453  0.020  1.453
 GF3  N1   C11  single    1.454  0.020  1.454
 GF3  C10  C9   single    1.529  0.020  1.529
 GF3  C11  C12  single    1.528  0.020  1.528
 GF3  C9   C8   single    1.526  0.020  1.526
 GF3  C12  C8   single    1.534  0.020  1.534
 GF3  C8   O1   single    1.431  0.020  1.431
 GF3  C8   C4   single    1.503  0.020  1.503
 GF3  O1   C7   single    1.415  0.020  1.415
 GF3  C4   C3   aromatic  1.385  0.020  1.385
 GF3  C4   C5   aromatic  1.383  0.020  1.383
 GF3  C7   C5   single    1.497  0.020  1.497
 GF3  C3   C2   aromatic  1.391  0.020  1.391
 GF3  C5   C6   aromatic  1.385  0.020  1.385
 GF3  C2   C1   aromatic  1.392  0.020  1.392
 GF3  C6   C1   aromatic  1.391  0.020  1.391
 GF3  C6   H4   single    0.930  0.020  1.080
 GF3  C11  H12  single    0.970  0.020  1.090
 GF3  C11  H13  single    0.970  0.020  1.090
 GF3  C7   H6   single    0.970  0.020  1.090
 GF3  C7   H5   single    0.970  0.020  1.090
 GF3  C9   H7   single    0.970  0.020  1.090
 GF3  C9   H8   single    0.970  0.020  1.090
 GF3  C10  H10  single    0.970  0.020  1.090
 GF3  C10  H9   single    0.970  0.020  1.090
 GF3  C12  H15  single    0.970  0.020  1.090
 GF3  C12  H14  single    0.970  0.020  1.090
 GF3  N1   H11  single    0.890  0.020  1.040
 GF3  C3   H3   single    0.930  0.020  1.080
 GF3  C1   H1   single    0.930  0.020  1.080
 GF3  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
 GF3  C3   C4   C8   129.87  3.000
 GF3  C3   C4   C5   120.88  3.000
 GF3  C8   C4   C5   109.22  3.000
 GF3  C7   C5   C6   130.67  3.000
 GF3  C6   C5   C4   120.98  3.000
 GF3  C7   C5   C4   108.34  3.000
 GF3  H4   C6   C1   120.40  3.000
 GF3  H4   C6   C5   121.17  3.000
 GF3  C1   C6   C5   118.43  3.000
 GF3  H13  C11  H12  106.40  3.000
 GF3  H13  C11  N1   108.24  3.000
 GF3  H12  C11  N1   108.72  3.000
 GF3  H13  C11  C12  109.51  3.000
 GF3  H12  C11  C12  109.82  3.000
 GF3  N1   C11  C12  113.86  3.000
 GF3  H5   C7   H6   107.27  3.000
 GF3  H5   C7   O1   109.35  3.000
 GF3  H6   C7   O1   111.50  3.000
 GF3  H5   C7   C5   112.99  3.000
 GF3  H6   C7   C5   111.15  3.000
 GF3  O1   C7   C5   104.64  3.000
 GF3  O1   C8   C12  110.08  3.000
 GF3  O1   C8   C9   108.66  3.000
 GF3  C12  C8   C9   109.53  3.000
 GF3  O1   C8   C4   103.37  3.000
 GF3  C12  C8   C4   111.19  3.000
 GF3  C9   C8   C4   113.81  3.000
 GF3  H8   C9   H7   106.96  3.000
 GF3  H8   C9   C10  109.09  3.000
 GF3  H7   C9   C10  110.67  3.000
 GF3  H8   C9   C8   108.42  3.000
 GF3  H7   C9   C8   109.90  3.000
 GF3  C10  C9   C8   111.67  3.000
 GF3  H9   C10  H10  106.28  3.000
 GF3  H9   C10  N1   108.67  3.000
 GF3  H10  C10  N1   108.33  3.000
 GF3  H9   C10  C9   109.61  3.000
 GF3  H10  C10  C9   109.74  3.000
 GF3  N1   C10  C9   113.92  3.000
 GF3  H14  C12  H15  106.68  3.000
 GF3  H14  C12  C8   109.87  3.000
 GF3  H15  C12  C8   108.68  3.000
 GF3  H14  C12  C11  110.47  3.000
 GF3  H15  C12  C11  109.56  3.000
 GF3  C8   C12  C11  111.44  3.000
 GF3  H11  N1   C10  108.85  3.000
 GF3  H11  N1   C11  108.90  3.000
 GF3  C10  N1   C11  111.83  3.000
 GF3  H3   C3   C2   120.36  3.000
 GF3  H3   C3   C4   121.08  3.000
 GF3  C2   C3   C4   118.56  3.000
 GF3  H1   C1   C2   119.64  3.000
 GF3  H1   C1   C6   119.73  3.000
 GF3  C2   C1   C6   120.63  3.000
 GF3  H2   C2   C1   119.71  3.000
 GF3  H2   C2   C3   119.79  3.000
 GF3  C1   C2   C3   120.51  3.000
 GF3  C8   O1   C7   111.28  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
 GF3  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 GF3  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 GF3  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 GF3  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 GF3  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 GF3  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 GF3  CONST_07  H2   C2   C3   C4    180.00   0.0  0
 GF3  CONST_08  H4   C6   C5   C4    180.00   0.0  0
 GF3  CONST_09  H3   C3   C4   C5    180.00   0.0  0
 GF3  CONST_10  H1   C1   C6   C5    180.00   0.0  0
 GF3  Var_01    C10  C9   C8   C4   -177.10  30.0  3
 GF3  Var_02    C11  C12  C8   C4    178.74  30.0  3
 GF3  Var_03    O1   C7   C5   C4      9.86  30.0  1
 GF3  Var_04    C9   C8   C4   C5   -128.64  30.0  1
 GF3  Var_05    C9   C10  N1   C11   -53.31  30.0  1
 GF3  Var_06    N1   C10  C9   C8     53.69  30.0  1
 GF3  Var_07    N1   C11  C12  C8    -53.97  30.0  1
 GF3  Var_08    C12  C11  N1   C10    53.56  30.0  1

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
 GF3  plan-1  C4  0.020
 GF3  plan-1  C5  0.020
 GF3  plan-1  C6  0.020
 GF3  plan-1  C7  0.020
 GF3  plan-1  C8  0.020
 GF3  plan-1  C3  0.020
 GF3  plan-1  C1  0.020
 GF3  plan-1  C2  0.020
 GF3  plan-1  H4  0.020
 GF3  plan-1  H3  0.020
 GF3  plan-1  H1  0.020
 GF3  plan-1  H2  0.020

