# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 18:25:37 2021
#   Inital geometry file: a 77 line input string
#   Ligand name: ~{N}-[(3~{R})-2-oxidanylideneazepan-3-yl]furan-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NCCCC[C@H]1NC(=O)c2occc2
#
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
 RYG  RYG  ~{N}-[(3~{R})-2-oxidanylideneazepan-3-yl]furan-2-carboxamide  ligand  30  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RYG
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
 RYG  N1   N  NH1   0  -0.673   8.6770  23.2662   1.1688
 RYG  C4   C  CR15  0   0.010   4.4577  21.6793   0.6120
 RYG  C5   C  C     0   0.472   7.5962  22.7951   1.8084
 RYG  C6   C  CH1   0  -0.191   9.8636  23.6939   1.8643
 RYG  C7   C  CH2   0  -0.419   9.7068  25.1095   2.4723
 RYG  C8   C  CH2   0  -0.476  10.9873  25.9325   2.5951
 RYG  C10  C  CH2   0  -0.330  12.4823  23.8719   2.8752
 RYG  C1   C  CR15  0  -0.326   4.9931  21.8357  -0.6246
 RYG  C11  C  C     0   0.520  11.0342  23.6283   0.8881
 RYG  C2   C  CR15  0  -0.353   6.3180  22.3058  -0.4153
 RYG  C3   C  CR5   0   0.277   6.4806  22.3969   0.9325
 RYG  C9   C  CH2   0  -0.428  12.1235  25.2791   3.3740
 RYG  N2   N  NH1   0  -0.608  12.2463  23.6806   1.4564
 RYG  O1   O  O     0  -0.395   5.3479  22.0146   1.5566
 RYG  O2   O  O     0  -0.491   7.5184  22.6850   3.0242
 RYG  O3   O  O     0  -0.486  10.8604  23.5415  -0.3209
 RYG  H1   H  HNH1  0   0.400   8.6773  23.3809   0.1660
 RYG  H3   H  HCH1  0   0.285  10.0485  22.9801   2.6706
 RYG  H4   H  HCH2  0   0.246   9.0092  25.6624   1.8400
 RYG  H5   H  HCH2  0   0.245   9.2318  25.0052   3.4496
 RYG  H6   H  HCH2  0   0.231  11.3434  26.1987   1.5965
 RYG  H7   H  HCH2  0   0.251  10.7345  26.8802   3.0745
 RYG  H8   H  HCH2  0   0.250  11.9283  23.1166   3.4354
 RYG  H9   H  HCH2  0   0.280  13.5343  23.6612   3.0558
 RYG  H10  H  HCR5  0   0.274   4.5074  21.6399  -1.5661
 RYG  H11  H  HCR5  0   0.275   7.0453  22.5341  -1.1785
 RYG  H12  H  HCH2  0   0.239  12.9994  25.9279   3.3111
 RYG  H13  H  HCH2  0   0.234  11.8639  25.2100   4.4330
 RYG  H14  H  HNH1  0   0.400  13.0379  23.7118   0.8315
 RYG  H2   H  HCR5  0   0.289   3.4900  21.3491   0.9531

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
 RYG  C1   C2   aromatic  1.421  0.020  1.421
 RYG  C1   C4   aromatic  1.357  0.020  1.357
 RYG  C2   C3   aromatic  1.361  0.020  1.361
 RYG  O3   C11  double    1.225  0.020  1.225
 RYG  C4   O1   aromatic  1.341  0.020  1.341
 RYG  C11  N2   single    1.340  0.020  1.340
 RYG  C11  C6   single    1.526  0.020  1.526
 RYG  C3   O1   aromatic  1.349  0.020  1.349
 RYG  C3   C5   single    1.473  0.020  1.473
 RYG  N1   C5   single    1.341  0.020  1.341
 RYG  N1   C6   single    1.440  0.020  1.440
 RYG  N2   C10  single    1.451  0.020  1.451
 RYG  C5   O2   double    1.223  0.020  1.223
 RYG  C6   C7   single    1.549  0.020  1.549
 RYG  C7   C8   single    1.527  0.020  1.527
 RYG  C8   C9   single    1.525  0.020  1.525
 RYG  C10  C9   single    1.535  0.020  1.535
 RYG  N1   H1   single    0.860  0.020  1.020
 RYG  C4   H2   single    0.930  0.020  1.080
 RYG  C6   H3   single    0.970  0.020  1.090
 RYG  C7   H4   single    0.970  0.020  1.090
 RYG  C7   H5   single    0.970  0.020  1.090
 RYG  C8   H6   single    0.970  0.020  1.090
 RYG  C8   H7   single    0.970  0.020  1.090
 RYG  C10  H8   single    0.970  0.020  1.090
 RYG  C10  H9   single    0.970  0.020  1.090
 RYG  C1   H10  single    0.930  0.020  1.080
 RYG  C2   H11  single    0.930  0.020  1.080
 RYG  C9   H12  single    0.970  0.020  1.090
 RYG  C9   H13  single    0.970  0.020  1.090
 RYG  N2   H14  single    0.860  0.020  1.020

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
 RYG  H1   N1   C6   116.47  3.000
 RYG  H1   N1   C5   120.93  3.000
 RYG  C6   N1   C5   122.53  3.000
 RYG  H2   C4   O1   116.73  3.000
 RYG  H2   C4   C1   132.70  3.000
 RYG  O1   C4   C1   110.57  3.000
 RYG  O2   C5   C3   121.23  3.000
 RYG  O2   C5   N1   123.84  3.000
 RYG  C3   C5   N1   114.93  3.000
 RYG  H3   C6   C11  108.32  3.000
 RYG  H3   C6   C7   108.94  3.000
 RYG  C11  C6   C7   111.60  3.000
 RYG  H3   C6   N1   107.56  3.000
 RYG  C7   C6   N1   112.18  3.000
 RYG  C11  C6   N1   108.08  3.000
 RYG  H5   C7   H4   106.79  3.000
 RYG  H5   C7   C8   110.14  3.000
 RYG  H4   C7   C8   108.03  3.000
 RYG  H5   C7   C6   107.95  3.000
 RYG  H4   C7   C6   107.47  3.000
 RYG  C8   C7   C6   116.06  3.000
 RYG  H7   C8   H6   105.38  3.000
 RYG  H7   C8   C9   108.68  3.000
 RYG  H6   C8   C9   109.16  3.000
 RYG  H7   C8   C7   107.99  3.000
 RYG  H6   C8   C7   109.33  3.000
 RYG  C9   C8   C7   115.79  3.000
 RYG  H9   C10  H8   105.76  3.000
 RYG  H9   C10  N2   107.10  3.000
 RYG  H8   C10  N2   109.16  3.000
 RYG  H9   C10  C9   110.46  3.000
 RYG  H8   C10  C9   110.42  3.000
 RYG  N2   C10  C9   113.61  3.000
 RYG  H10  C1   C2   127.52  3.000
 RYG  H10  C1   C4   126.71  3.000
 RYG  C2   C1   C4   105.77  3.000
 RYG  O3   C11  N2   123.36  3.000
 RYG  N2   C11  C6   114.91  3.000
 RYG  O3   C11  C6   121.73  3.000
 RYG  H11  C2   C3   127.31  3.000
 RYG  H11  C2   C1   126.46  3.000
 RYG  C3   C2   C1   106.23  3.000
 RYG  O1   C3   C2   109.82  3.000
 RYG  O1   C3   C5   115.95  3.000
 RYG  C2   C3   C5   134.23  3.000
 RYG  H13  C9   H12  106.50  3.000
 RYG  H13  C9   C10  108.21  3.000
 RYG  H12  C9   C10  109.78  3.000
 RYG  H13  C9   C8   110.19  3.000
 RYG  H12  C9   C8   108.28  3.000
 RYG  C10  C9   C8   113.63  3.000
 RYG  H14  N2   C11  116.64  3.000
 RYG  H14  N2   C10  118.29  3.000
 RYG  C11  N2   C10  124.54  3.000
 RYG  C3   O1   C4   107.61  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
 RYG  CONST_01  C3   C2  C1  C4    0.00   0.0  0
 RYG  CONST_02  C2   C3  O1  C4    0.00   0.0  0
 RYG  CONST_03  O1   C3  C2  C1    0.00   0.0  0
 RYG  CONST_04  C3   O1  C4  C1    0.00   0.0  0
 RYG  CONST_05  O1   C4  C1  C2    0.00   0.0  0
 RYG  CONST_06  C5   C3  O1  C4  180.00   0.0  0
 RYG  CONST_07  C1   C2  C3  C5  180.00   0.0  0
 RYG  CONST_08  H11  C2  C1  C4  180.00   0.0  0
 RYG  CONST_09  H2   C4  C1  C2  180.00   0.0  0
 RYG  CONST_10  H10  C1  C2  C3  180.00   0.0  0
 RYG  CONST_11  C3   C5  N1  C6  180.00   0.0  0
 RYG  CONST_12  O2   C5  N1  C6    0.00   0.0  0
 RYG  CONST_13  H1   N1  C5  C3    0.00   0.0  0
 RYG  Var_01    C2   C3  C5  N1    5.62  30.0  2

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
 RYG  chir_01  C6  C11  N1  C7  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
 RYG  plan-1  C4   0.020
 RYG  plan-1  C5   0.020
 RYG  plan-1  C1   0.020
 RYG  plan-1  C2   0.020
 RYG  plan-1  C3   0.020
 RYG  plan-1  O1   0.020
 RYG  plan-1  H10  0.020
 RYG  plan-1  H11  0.020
 RYG  plan-1  H2   0.020
 RYG  plan-2  N1   0.020
 RYG  plan-2  C5   0.020
 RYG  plan-2  C6   0.020
 RYG  plan-2  C3   0.020
 RYG  plan-2  O2   0.020
 RYG  plan-2  H1   0.020
 RYG  plan-3  C6   0.020
 RYG  plan-3  C10  0.020
 RYG  plan-3  C11  0.020
 RYG  plan-3  N2   0.020
 RYG  plan-3  O3   0.020
 RYG  plan-3  H14  0.020

