# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 17:49:27 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (1~{R},9~{R},10~{S})-4-fluoranyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-10-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H]2C[C@H]1Nc3ccc(F)cc23
#
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
 JVN  JVN  (1~{R},9~{R},10~{S})-4-fluoranyl-12-oxa-8-azatricyclo[7.3.1.0^{2,7}]trideca-2(7),3,5-trien-10-ol  ligand  27  15  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JVN
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
 JVN  C1   C  CR6   0   0.494   2.9560  -0.2050  -0.0075
 JVN  C2   C  CR16  0  -0.409   2.8584   1.1330  -0.3406
 JVN  C3   C  CR16  0  -0.340   1.6257   1.7577  -0.2657
 JVN  C8   C  CR16  0  -0.072  -0.6274  -1.0846   0.8350
 JVN  C10  C  C     0  -0.462  -1.6138  -0.1512   1.5191
 JVN  C14  C  CH1   0   0.036  -2.5565   0.3316  -0.7426
 JVN  C15  C  CR16  0  -0.154  -1.9422   0.9525   0.5230
 JVN  O17  O  OH1   0  -0.672  -3.8315  -0.1470  -0.3745
 JVN  C4   C  CR66  0   0.346   0.4835   1.0521   0.1342
 JVN  C5   C  CR66  0   0.066   0.6081  -0.3096   0.4553
 JVN  C6   C  CR16  0  -0.477   1.8502  -0.9280   0.3849
 JVN  F7   F  F     0  -0.328   4.1593  -0.8149  -0.0702
 JVN  N9   N  NR16  0  -0.688  -0.7305   1.6855   0.2394
 JVN  O12  O  O2    0  -0.480  -1.2394  -1.6907  -0.2980
 JVN  H1   H  HCR6  0   0.274   3.7347   1.6883  -0.6496
 JVN  H2   H  HCR6  0   0.265   1.5456   2.8083  -0.5183
 JVN  H3   H  HCR6  0   0.259  -0.3550  -1.9133   1.4924
 JVN  H4   H  H     0   0.259  -2.5152  -0.6886   1.8131
 JVN  H5   H  H     0   0.253  -1.1727   0.2701   2.4253
 JVN  H8   H  HCH1  0   0.223  -2.6364   1.1086  -1.5171
 JVN  H9   H  HCR6  0   0.267  -2.6626   1.6531   0.9518
 JVN  H10  H  HOH1  0   0.453  -4.2569  -0.5152  -1.1550
 JVN  H11  H  HCR6  0   0.270   1.9463  -1.9778   0.6380
 JVN  H12  H  HNR6  0   0.382  -0.8330   2.5510  -0.2648
 JVN  C13  C  CH2   0  -0.226  -1.6519  -0.7692  -1.2851
 JVN  H6   H  HCH2  0   0.250  -2.1824  -1.3470  -2.0473
 JVN  H7   H  HCH2  0   0.214  -0.7892  -0.3122  -1.7878

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
 JVN  F7   C1   single    1.351  0.020  1.351
 JVN  C1   C6   aromatic  1.378  0.020  1.378
 JVN  C1   C2   aromatic  1.382  0.020  1.382
 JVN  C6   C5   aromatic  1.389  0.020  1.389
 JVN  C2   C3   aromatic  1.384  0.020  1.384
 JVN  C5   C8   single    1.507  0.020  1.507
 JVN  C5   C4   aromatic  1.405  0.020  1.405
 JVN  C8   O12  single    1.423  0.020  1.423
 JVN  C8   C10  single    1.521  0.020  1.521
 JVN  O12  C13  single    1.412  0.020  1.412
 JVN  C3   C4   aromatic  1.401  0.020  1.401
 JVN  C4   N9   single    1.373  0.020  1.373
 JVN  C10  C15  single    1.523  0.020  1.523
 JVN  C13  C14  single    1.525  0.020  1.525
 JVN  N9   C15  single    1.444  0.020  1.444
 JVN  C15  C14  single    1.538  0.020  1.538
 JVN  C14  O17  single    1.411  0.020  1.411
 JVN  C2   H1   single    0.930  0.020  1.080
 JVN  C3   H2   single    0.930  0.020  1.080
 JVN  C8   H3   single    0.970  0.020  1.090
 JVN  C10  H4   single    0.970  0.020  1.090
 JVN  C10  H5   single    0.970  0.020  1.090
 JVN  C13  H6   single    0.970  0.020  1.090
 JVN  C13  H7   single    0.970  0.020  1.090
 JVN  C14  H8   single    0.970  0.020  1.090
 JVN  C15  H9   single    0.970  0.020  1.090
 JVN  O17  H10  single    0.850  0.020  0.980
 JVN  C6   H11  single    0.930  0.020  1.080
 JVN  N9   H12  single    0.890  0.020  1.040

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
 JVN  F7   C1   C6   119.42  3.000
 JVN  C6   C1   C2   121.32  3.000
 JVN  F7   C1   C2   119.26  3.000
 JVN  H1   C2   C3   120.33  3.000
 JVN  H1   C2   C1   120.55  3.000
 JVN  C3   C2   C1   119.13  3.000
 JVN  H2   C3   C4   119.65  3.000
 JVN  H2   C3   C2   119.40  3.000
 JVN  C4   C3   C2   120.95  3.000
 JVN  H3   C8   O12  105.27  3.000
 JVN  H3   C8   C5   109.71  3.000
 JVN  O12  C8   C5   111.78  3.000
 JVN  H3   C8   C10  110.90  3.000
 JVN  O12  C8   C10  109.91  3.000
 JVN  C5   C8   C10  109.24  3.000
 JVN  H5   C10  H4   107.48  3.000
 JVN  H5   C10  C15  110.50  3.000
 JVN  H4   C10  C15  110.82  3.000
 JVN  H5   C10  C8   110.37  3.000
 JVN  H4   C10  C8   110.81  3.000
 JVN  C15  C10  C8   106.89  3.000
 JVN  H8   C14  O17  110.96  3.000
 JVN  H8   C14  C15  108.86  3.000
 JVN  O17  C14  C15  106.46  3.000
 JVN  H8   C14  C13  107.61  3.000
 JVN  O17  C14  C13  112.59  3.000
 JVN  C15  C14  C13  110.33  3.000
 JVN  H9   C15  N9   107.74  3.000
 JVN  H9   C15  C14  108.58  3.000
 JVN  N9   C15  C14  112.24  3.000
 JVN  H9   C15  C10  110.51  3.000
 JVN  C14  C15  C10  109.38  3.000
 JVN  N9   C15  C10  108.38  3.000
 JVN  H10  O17  C14  108.54  3.000
 JVN  N9   C4   C5   120.54  3.000
 JVN  N9   C4   C3   120.69  3.000
 JVN  C5   C4   C3   118.76  3.000
 JVN  C6   C5   C4   119.95  3.000
 JVN  C4   C5   C8   118.91  3.000
 JVN  C6   C5   C8   121.12  3.000
 JVN  H11  C6   C5   119.90  3.000
 JVN  H11  C6   C1   120.22  3.000
 JVN  C5   C6   C1   119.88  3.000
 JVN  H12  N9   C4   116.62  3.000
 JVN  H12  N9   C15  116.69  3.000
 JVN  C4   N9   C15  121.51  3.000
 JVN  C13  O12  C8   113.84  3.000
 JVN  H7   C13  H6   106.37  3.000
 JVN  H7   C13  O12  111.24  3.000
 JVN  H6   C13  O12  106.51  3.000
 JVN  H7   C13  C14  109.18  3.000
 JVN  H6   C13  C14  109.97  3.000
 JVN  O12  C13  C14  113.32  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
 JVN  CONST_01  C4   C5   C6   C1    0.00   0.0  0
 JVN  CONST_02  C4   C3   C2   C1    0.00   0.0  0
 JVN  CONST_03  C5   C6   C1   C2    0.00   0.0  0
 JVN  CONST_04  C5   C4   C3   C2    0.00   0.0  0
 JVN  CONST_05  C6   C1   C2   C3    0.00   0.0  0
 JVN  CONST_06  C6   C5   C4   C3    0.00   0.0  0
 JVN  CONST_07  F7   C1   C2   C3  180.00   0.0  0
 JVN  CONST_08  F7   C1   C6   C5  180.00   0.0  0
 JVN  CONST_09  H2   C3   C2   C1  180.00   0.0  0
 JVN  CONST_10  H11  C6   C1   C2  180.00   0.0  0
 JVN  CONST_11  H1   C2   C3   C4  180.00   0.0  0
 JVN  Var_01    C15  N9   C4   C3  173.90  30.0  1
 JVN  Var_02    C14  C13  O12  C8  -53.84  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
 JVN  chir_01  C8   C5   O12  C10  positiv
 JVN  chir_02  C14  O17  C15  C13  negativ
 JVN  chir_03  C15  N9   C10  C14  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
 JVN  plan-1  C1   0.020
 JVN  plan-1  C2   0.020
 JVN  plan-1  C3   0.020
 JVN  plan-1  C8   0.020
 JVN  plan-1  C4   0.020
 JVN  plan-1  C5   0.020
 JVN  plan-1  C6   0.020
 JVN  plan-1  F7   0.020
 JVN  plan-1  N9   0.020
 JVN  plan-1  H1   0.020
 JVN  plan-1  H2   0.020
 JVN  plan-1  H11  0.020

