# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 01:47:32 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N-(2-fluorophenyl)-4-(4-fluorophenyl)sulfonyl-3,5-dihydro-2H-1,4-benzoxazepin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)[S](=O)(=O)N2CCOc3cccc(Nc4ccccc4F)c3C2
#
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
 VYI  VYI  N-(2-fluorophenyl)-4-(4-fluorophenyl)sulfonyl-3,5-dihydro-2H-1,4-benzoxazepin-6-amine  ligand  47  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VYI
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
 VYI  C1    C  CR16  0  -0.261  -3.9450  -2.4556   1.7584
 VYI  C2    C  CR16  0  -0.270  -4.4764  -3.5085   1.0262
 VYI  C3    C  CR16  0  -0.254  -3.4559   2.9029   0.5093
 VYI  C4    C  CR16  0  -0.307  -3.2948  -1.4084   1.1237
 VYI  C5    C  CR16  0  -0.307  -3.5502   1.5857   0.0973
 VYI  C6    C  CR16  0  -0.368  -2.2966   3.6279   0.2880
 VYI  C7    C  CR16  0  -0.405  -4.3550  -3.5037  -0.3576
 VYI  C8    C  CR16  0  -0.398   5.1894  -0.8897   0.2106
 VYI  C9    C  CR16  0  -0.398   3.4651  -2.5902   0.3060
 VYI  C10   C  CR16  0  -0.224   4.2372   0.0858   0.4539
 VYI  C11   C  CR16  0  -0.223   2.5164  -1.6106   0.5488
 VYI  C12   C  CR6   0  -0.045  -1.2469   1.6652  -0.6773
 VYI  C13   C  CR6   0   0.301  -2.4510   0.9698  -0.4987
 VYI  C14   C  CR6   0   0.204  -3.1810  -1.3708  -0.2684
 VYI  C15   C  CR6   0   0.364  -1.2017   3.0168  -0.3130
 VYI  C16   C  CR6   0   0.547   4.7836  -2.2096   0.1392
 VYI  C17   C  CR6   0   0.457  -3.7245  -2.4454  -0.9731
 VYI  C18   C  CR6   0  -0.176   2.9065  -0.2790   0.6175
 VYI  C19   C  CH2   0  -0.381  -0.0310   0.9112  -1.1652
 VYI  C20   C  CH2   0  -0.299   1.8007   2.5702  -1.2979
 VYI  C21   C  CH2   0  -0.236   0.7097   3.5812  -1.6123
 VYI  N22   N  N     0  -0.586   1.2141   1.4243  -0.6262
 VYI  N23   N  NH1   0  -0.800  -2.5266  -0.3563  -0.9374
 VYI  O24   O  OS    0  -0.636   0.5439   0.3400   1.5244
 VYI  O25   O  OS    0  -0.645   2.3467   2.0986   1.5212
 VYI  O26   O  O2    0  -0.483  -0.1072   3.8042  -0.4778
 VYI  F28   F  F     0  -0.320  -3.6118  -2.4377  -2.3172
 VYI  S29   S  S     0   1.382   1.6820   0.9743   0.8819
 VYI  H1    H  HCR6  0   0.259  -4.0214  -2.4520   2.8377
 VYI  H2    H  HCR6  0   0.261  -4.9765  -4.3296   1.5206
 VYI  H4    H  HCR6  0   0.276  -2.8638  -0.6072   1.7098
 VYI  H7    H  HCR6  0   0.278  -4.7564  -4.3099  -0.9582
 VYI  H3    H  HCR6  0   0.258  -4.3079   3.3827   0.9726
 VYI  H5    H  HCR6  0   0.267  -4.4747   1.0387   0.2296
 VYI  H6    H  HCR6  0   0.260  -2.2328   4.6704   0.5721
 VYI  H8    H  HCR6  0   0.296   6.2309  -0.6267   0.0843
 VYI  H10   H  HCR6  0   0.292   4.5473   1.1197   0.5223
 VYI  H9    H  HCR6  0   0.296   3.1826  -3.6332   0.2556
 VYI  H11   H  HCR6  0   0.290   1.4846  -1.8993   0.6947
 VYI  H191  H  HCH2  0   0.286  -0.1422  -0.1421  -0.9094
 VYI  H192  H  HCH2  0   0.293   0.0587   0.9353  -2.2547
 VYI  H23   H  HNH1  0   0.401  -2.2438  -0.5410  -1.8856
 VYI  H201  H  HCH2  0   0.262   2.2897   2.2620  -2.2260
 VYI  H202  H  HCH2  0   0.274   2.5579   3.0207  -0.6612
 VYI  H211  H  HCH2  0   0.275   1.1620   4.5368  -1.8797
 VYI  H212  H  HCH2  0   0.243   0.1043   3.2598  -2.4652
 VYI  F27   F  F     0  -0.303   5.7014  -3.1530  -0.0934

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
 VYI  C1   C2    aromatic  1.388  0.020  1.388
 VYI  C1   C4    aromatic  1.386  0.020  1.386
 VYI  C2   C7    aromatic  1.389  0.020  1.389
 VYI  C3   C5    aromatic  1.383  0.020  1.383
 VYI  C3   C6    aromatic  1.385  0.020  1.385
 VYI  C4   C14   aromatic  1.397  0.020  1.397
 VYI  C5   C13   aromatic  1.394  0.020  1.394
 VYI  C6   C15   aromatic  1.390  0.020  1.390
 VYI  C7   C17   aromatic  1.377  0.020  1.377
 VYI  C8   C10   aromatic  1.385  0.020  1.385
 VYI  C8   C16   aromatic  1.383  0.020  1.383
 VYI  C9   C11   aromatic  1.385  0.020  1.385
 VYI  C9   C16   aromatic  1.382  0.020  1.382
 VYI  C10  C18   aromatic  1.389  0.020  1.389
 VYI  C11  C18   aromatic  1.389  0.020  1.389
 VYI  C12  C13   aromatic  1.402  0.020  1.402
 VYI  C12  C15   aromatic  1.401  0.020  1.401
 VYI  C12  C19   single    1.512  0.020  1.512
 VYI  C13  N23   single    1.399  0.020  1.399
 VYI  C14  C17   aromatic  1.395  0.020  1.395
 VYI  C14  N23   single    1.380  0.020  1.380
 VYI  C15  O26   single    1.358  0.020  1.358
 VYI  C16  F27   single    1.337  0.020  1.337
 VYI  C17  F28   single    1.349  0.020  1.349
 VYI  C18  S29   single    1.772  0.020  1.772
 VYI  C19  N22   single    1.451  0.020  1.451
 VYI  C20  C21   single    1.520  0.020  1.520
 VYI  C20  N22   single    1.452  0.020  1.452
 VYI  C21  O26   single    1.416  0.020  1.416
 VYI  N22  S29   single    1.642  0.020  1.642
 VYI  O24  S29   double    1.453  0.020  1.453
 VYI  O25  S29   double    1.454  0.020  1.454
 VYI  C1   H1    single    0.930  0.020  1.080
 VYI  C2   H2    single    0.930  0.020  1.080
 VYI  C4   H4    single    0.930  0.020  1.080
 VYI  C7   H7    single    0.930  0.020  1.080
 VYI  C3   H3    single    0.930  0.020  1.080
 VYI  C5   H5    single    0.930  0.020  1.080
 VYI  C6   H6    single    0.930  0.020  1.080
 VYI  C8   H8    single    0.930  0.020  1.080
 VYI  C10  H10   single    0.930  0.020  1.080
 VYI  C9   H9    single    0.930  0.020  1.080
 VYI  C11  H11   single    0.930  0.020  1.080
 VYI  C19  H191  single    0.970  0.020  1.090
 VYI  C19  H192  single    0.970  0.020  1.090
 VYI  N23  H23   single    0.860  0.020  1.020
 VYI  C20  H201  single    0.970  0.020  1.090
 VYI  C20  H202  single    0.970  0.020  1.090
 VYI  C21  H211  single    0.970  0.020  1.090
 VYI  C21  H212  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
 VYI  H1    C1   C4    119.16  3.000
 VYI  H1    C1   C2    120.10  3.000
 VYI  C4    C1   C2    120.73  3.000
 VYI  H2    C2   C7    119.91  3.000
 VYI  H2    C2   C1    120.80  3.000
 VYI  C7    C2   C1    119.29  3.000
 VYI  H3    C3   C6    119.69  3.000
 VYI  H3    C3   C5    119.74  3.000
 VYI  C6    C3   C5    120.52  3.000
 VYI  H4    C4   C14   119.16  3.000
 VYI  H4    C4   C1    119.87  3.000
 VYI  C14   C4   C1    120.97  3.000
 VYI  H5    C5   C13   120.17  3.000
 VYI  H5    C5   C3    120.20  3.000
 VYI  C13   C5   C3    119.62  3.000
 VYI  H6    C6   C15   119.36  3.000
 VYI  H6    C6   C3    120.77  3.000
 VYI  C15   C6   C3    119.87  3.000
 VYI  H7    C7   C17   119.62  3.000
 VYI  H7    C7   C2    121.18  3.000
 VYI  C17   C7   C2    119.20  3.000
 VYI  H8    C8   C16   120.58  3.000
 VYI  H8    C8   C10   120.75  3.000
 VYI  C16   C8   C10   118.67  3.000
 VYI  H9    C9   C16   120.59  3.000
 VYI  H9    C9   C11   120.74  3.000
 VYI  C16   C9   C11   118.66  3.000
 VYI  H10   C10  C18   121.21  3.000
 VYI  H10   C10  C8    119.17  3.000
 VYI  C18   C10  C8    119.62  3.000
 VYI  H11   C11  C18   121.15  3.000
 VYI  H11   C11  C9    119.23  3.000
 VYI  C18   C11  C9    119.62  3.000
 VYI  C19   C12  C15   122.64  3.000
 VYI  C19   C12  C13   118.98  3.000
 VYI  C15   C12  C13   118.25  3.000
 VYI  N23   C13  C12   118.47  3.000
 VYI  N23   C13  C5    120.69  3.000
 VYI  C12   C13  C5    120.84  3.000
 VYI  N23   C14  C17   120.39  3.000
 VYI  N23   C14  C4    122.77  3.000
 VYI  C17   C14  C4    116.80  3.000
 VYI  O26   C15  C12   123.63  3.000
 VYI  O26   C15  C6    115.61  3.000
 VYI  C12   C15  C6    120.74  3.000
 VYI  F27   C16  C9    118.79  3.000
 VYI  F27   C16  C8    118.76  3.000
 VYI  C9    C16  C8    122.44  3.000
 VYI  F28   C17  C14   117.80  3.000
 VYI  F28   C17  C7    119.21  3.000
 VYI  C14   C17  C7    122.99  3.000
 VYI  S29   C18  C11   119.42  3.000
 VYI  S29   C18  C10   119.58  3.000
 VYI  C11   C18  C10   120.98  3.000
 VYI  H192  C19  H191  105.29  3.000
 VYI  H192  C19  N22   106.98  3.000
 VYI  H191  C19  N22   110.02  3.000
 VYI  H192  C19  C12   112.12  3.000
 VYI  H191  C19  C12   108.93  3.000
 VYI  N22   C19  C12   113.21  3.000
 VYI  H202  C20  H201  107.60  3.000
 VYI  H202  C20  N22   109.73  3.000
 VYI  H201  C20  N22   110.54  3.000
 VYI  H202  C20  C21   110.21  3.000
 VYI  H201  C20  C21   109.45  3.000
 VYI  N22   C20  C21   109.30  3.000
 VYI  H212  C21  H211  107.21  3.000
 VYI  H212  C21  O26   110.59  3.000
 VYI  H211  C21  O26   107.33  3.000
 VYI  H212  C21  C20   111.28  3.000
 VYI  H211  C21  C20   109.62  3.000
 VYI  O26   C21  C20   110.68  3.000
 VYI  S29   N22  C20   121.74  3.000
 VYI  S29   N22  C19   119.27  3.000
 VYI  C20   N22  C19   117.00  3.000
 VYI  H23   N23  C14   117.06  3.000
 VYI  H23   N23  C13   117.02  3.000
 VYI  C14   N23  C13   124.78  3.000
 VYI  C21   O26  C15   118.09  3.000
 VYI  O25   S29  O24   120.08  3.000
 VYI  O25   S29  N22   108.79  3.000
 VYI  O24   S29  N22   107.62  3.000
 VYI  O25   S29  C18   107.26  3.000
 VYI  O24   S29  C18   107.37  3.000
 VYI  N22   S29  C18   104.70  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
 VYI  CONST_01  C17  C7   C2   C1      0.00   0.0  0
 VYI  CONST_02  C17  C14  C4   C1      0.00   0.0  0
 VYI  CONST_03  C14  C4   C1   C2      0.00   0.0  0
 VYI  CONST_04  C14  C17  C7   C2      0.00   0.0  0
 VYI  CONST_05  C12  C13  C5   C3      0.00   0.0  0
 VYI  CONST_06  C12  C15  C6   C3      0.00   0.0  0
 VYI  CONST_07  C7   C2   C1   C4      0.00   0.0  0
 VYI  CONST_08  C7   C17  C14  C4      0.00   0.0  0
 VYI  CONST_09  C15  C6   C3   C5      0.00   0.0  0
 VYI  CONST_10  C15  C12  C13  C5      0.00   0.0  0
 VYI  CONST_11  C13  C5   C3   C6      0.00   0.0  0
 VYI  CONST_12  C13  C12  C15  C6      0.00   0.0  0
 VYI  CONST_13  C11  C18  C10  C8      0.00   0.0  0
 VYI  CONST_14  C11  C9   C16  C8      0.00   0.0  0
 VYI  CONST_15  C10  C18  C11  C9      0.00   0.0  0
 VYI  CONST_16  C10  C8   C16  C9      0.00   0.0  0
 VYI  CONST_17  C18  C10  C8   C16     0.00   0.0  0
 VYI  CONST_18  C18  C11  C9   C16     0.00   0.0  0
 VYI  CONST_19  N23  C14  C4   C1    180.00   0.0  0
 VYI  CONST_20  F28  C17  C7   C2    180.00   0.0  0
 VYI  CONST_21  N23  C13  C5   C3    180.00   0.0  0
 VYI  CONST_22  F28  C17  C14  C4    180.00   0.0  0
 VYI  CONST_23  N23  C14  C17  C7    180.00   0.0  0
 VYI  CONST_24  S29  C18  C10  C8    180.00   0.0  0
 VYI  CONST_25  S29  C18  C11  C9    180.00   0.0  0
 VYI  CONST_26  F27  C16  C8   C10   180.00   0.0  0
 VYI  CONST_27  F27  C16  C9   C11   180.00   0.0  0
 VYI  CONST_28  N23  C13  C12  C15   180.00   0.0  0
 VYI  CONST_29  N23  C13  C12  C19     0.00   0.0  0
 VYI  CONST_30  H7   C7   C2   C1    180.00   0.0  0
 VYI  CONST_31  H4   C4   C1   C2    180.00   0.0  0
 VYI  CONST_32  H2   C2   C1   C4    180.00   0.0  0
 VYI  CONST_33  H6   C6   C3   C5    180.00   0.0  0
 VYI  CONST_34  H5   C5   C3   C6    180.00   0.0  0
 VYI  CONST_35  H1   C1   C2   C7    180.00   0.0  0
 VYI  CONST_36  H9   C9   C16  C8    180.00   0.0  0
 VYI  CONST_37  H8   C8   C16  C9    180.00   0.0  0
 VYI  CONST_38  H11  C11  C18  C10   180.00   0.0  0
 VYI  CONST_39  H10  C10  C18  C11   180.00   0.0  0
 VYI  CONST_40  H3   C3   C5   C13   180.00   0.0  0
 VYI  Var_01    C20  N22  C19  C12   -83.10  30.0  1
 VYI  Var_02    N22  C19  C12  C13  -147.02  30.0  1
 VYI  Var_03    C20  C21  O26  C15   -90.10  30.0  1
 VYI  Var_04    C21  C20  N22  C19    43.72  30.0  1
 VYI  Var_05    O26  C21  C20  N22    47.52  30.0  1
 VYI  Var_06    C13  N23  C14  C4    -31.10  30.0  2
 VYI  Var_07    C14  N23  C13  C5    -39.18  30.0  2
 VYI  Var_08    N22  S29  C18  C10    87.79  30.0  2
 VYI  Var_09    C19  N22  S29  C18   101.17  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
 VYI  plan-1  C1   0.020
 VYI  plan-1  C2   0.020
 VYI  plan-1  C4   0.020
 VYI  plan-1  C7   0.020
 VYI  plan-1  C14  0.020
 VYI  plan-1  C17  0.020
 VYI  plan-1  N23  0.020
 VYI  plan-1  F28  0.020
 VYI  plan-1  H1   0.020
 VYI  plan-1  H2   0.020
 VYI  plan-1  H4   0.020
 VYI  plan-1  H7   0.020
 VYI  plan-2  C8   0.020
 VYI  plan-2  C9   0.020
 VYI  plan-2  C10  0.020
 VYI  plan-2  C11  0.020
 VYI  plan-2  C16  0.020
 VYI  plan-2  C18  0.020
 VYI  plan-2  S29  0.020
 VYI  plan-2  H8   0.020
 VYI  plan-2  H10  0.020
 VYI  plan-2  H9   0.020
 VYI  plan-2  H11  0.020
 VYI  plan-2  F27  0.020
 VYI  plan-3  C3   0.020
 VYI  plan-3  C5   0.020
 VYI  plan-3  C6   0.020
 VYI  plan-3  C12  0.020
 VYI  plan-3  C13  0.020
 VYI  plan-3  C15  0.020
 VYI  plan-3  C19  0.020
 VYI  plan-3  N23  0.020
 VYI  plan-3  O26  0.020
 VYI  plan-3  H3   0.020
 VYI  plan-3  H5   0.020
 VYI  plan-3  H6   0.020

