# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 18:33:24 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (azepan-1-yl)(2H-1,3-benzodioxol-5-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(N1CCCCCC1)c2ccc3OCOc3c2
#
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
 JGP  JGP  (azepan-1-yl)(2H-1,3-benzodioxol-5-yl)methanone  ligand  35  18  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JGP
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
 JGP  C10   C  CH2   0  -0.295   1.8091   1.4489  -0.4420
 JGP  C13   C  CH2   0  -0.433   4.3445  -0.0153   1.2461
 JGP  C15   C  CH2   0  -0.323   3.2427  -0.5099  -1.0190
 JGP  C17   C  CH2   0   0.067  -4.8153  -0.1673   0.7770
 JGP  C01   C  CR16  0  -0.267  -1.0078   0.6214  -1.5193
 JGP  C02   C  CR16  0  -0.332  -2.3426   1.0390  -1.4879
 JGP  C03   C  CR56  0   0.301  -3.1304   0.5168  -0.4928
 JGP  C04   C  CR56  0   0.310  -2.6359  -0.3935   0.4303
 JGP  C05   C  CR16  0  -0.363  -1.3385  -0.8325   0.3967
 JGP  C06   C  CR6   0  -0.085  -0.5081  -0.2876  -0.5967
 JGP  O08   O  O     0  -0.501   1.0333  -2.0469  -0.7884
 JGP  N09   N  NT    0  -0.442   1.9146   0.0323  -0.7641
 JGP  C11   C  CH2   0  -0.470   2.9074   1.9506   0.4944
 JGP  C12   C  CH2   0  -0.432   3.2717   1.0007   1.6355
 JGP  C14   C  CH2   0  -0.428   3.9138  -1.0689   0.2326
 JGP  O16   O  O     0  -0.485  -3.6180  -0.7230   1.3039
 JGP  O18   O  O     0  -0.482  -4.4296   0.7730  -0.2179
 JGP  H101  H  HCH2  0   0.243   1.8189   2.0488  -1.3573
 JGP  H102  H  HCH2  0   0.259   0.8470   1.6180   0.0354
 JGP  H132  H  HCH2  0   0.213   5.2031   0.5354   0.8469
 JGP  H131  H  HCH2  0   0.228   4.7036  -0.5240   2.1445
 JGP  H152  H  HCH2  0   0.256   3.1598  -1.2919  -1.7729
 JGP  H151  H  HCH2  0   0.247   3.8499   0.2839  -1.4592
 JGP  H172  H  HCH2  0   0.249  -5.3686   0.3380   1.5677
 JGP  H011  H  HCR6  0   0.267  -0.3640   1.0144  -2.2951
 JGP  H021  H  HCR6  0   0.278  -2.7289   1.7394  -2.2154
 JGP  H051  H  HCR6  0   0.276  -0.9643  -1.5536   1.1112
 JGP  H111  H  HCH2  0   0.229   3.8124   2.1942  -0.0691
 JGP  H112  H  HCH2  0   0.250   2.5497   2.9019   0.8952
 JGP  H121  H  HCH2  0   0.218   2.3773   0.4908   2.0090
 JGP  H122  H  HCH2  0   0.234   3.6547   1.5913   2.4708
 JGP  H142  H  HCH2  0   0.230   4.7941  -1.6377  -0.0799
 JGP  H141  H  HCH2  0   0.229   3.2373  -1.7856   0.7027
 JGP  C07   C  C     0   0.520   0.8811  -0.8314  -0.7152
 JGP  H171  H  HCH2  0   0.235  -5.4251  -0.9567   0.3244

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
 JGP  C14  C15   single    1.526  0.020  1.526
 JGP  C14  C13   single    1.524  0.020  1.524
 JGP  C15  N09   single    1.457  0.020  1.457
 JGP  C11  C10   single    1.528  0.020  1.528
 JGP  C11  C12   single    1.529  0.020  1.529
 JGP  C13  C12   single    1.528  0.020  1.528
 JGP  C10  N09   single    1.457  0.020  1.457
 JGP  N09  C07   single    1.348  0.020  1.348
 JGP  O16  C04   single    1.355  0.020  1.355
 JGP  O16  C17   single    1.421  0.020  1.421
 JGP  C05  C04   aromatic  1.370  0.020  1.370
 JGP  C05  C06   aromatic  1.405  0.020  1.405
 JGP  C07  C06   single    1.497  0.020  1.497
 JGP  C07  O08   double    1.227  0.020  1.227
 JGP  C04  C03   aromatic  1.388  0.020  1.388
 JGP  C06  C01   aromatic  1.388  0.020  1.388
 JGP  C17  O18   single    1.422  0.020  1.422
 JGP  C03  O18   single    1.352  0.020  1.352
 JGP  C03  C02   aromatic  1.372  0.020  1.372
 JGP  C01  C02   aromatic  1.399  0.020  1.399
 JGP  C10  H101  single    0.970  0.020  1.090
 JGP  C10  H102  single    0.970  0.020  1.090
 JGP  C13  H132  single    0.970  0.020  1.090
 JGP  C13  H131  single    0.970  0.020  1.090
 JGP  C15  H152  single    0.970  0.020  1.090
 JGP  C15  H151  single    0.970  0.020  1.090
 JGP  C17  H171  single    0.970  0.020  1.090
 JGP  C17  H172  single    0.970  0.020  1.090
 JGP  C01  H011  single    0.930  0.020  1.080
 JGP  C02  H021  single    0.930  0.020  1.080
 JGP  C05  H051  single    0.930  0.020  1.080
 JGP  C11  H111  single    0.970  0.020  1.090
 JGP  C11  H112  single    0.970  0.020  1.090
 JGP  C12  H121  single    0.970  0.020  1.090
 JGP  C12  H122  single    0.970  0.020  1.090
 JGP  C14  H142  single    0.970  0.020  1.090
 JGP  C14  H141  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
 JGP  H102  C10  H101  106.85  3.000
 JGP  H102  C10  C11   108.42  3.000
 JGP  H101  C10  C11   109.03  3.000
 JGP  H102  C10  N09   108.20  3.000
 JGP  H101  C10  N09   110.34  3.000
 JGP  C11   C10  N09   113.75  3.000
 JGP  H131  C13  H132  106.02  3.000
 JGP  H131  C13  C14   108.52  3.000
 JGP  H132  C13  C14   109.06  3.000
 JGP  H131  C13  C12   109.31  3.000
 JGP  H132  C13  C12   107.99  3.000
 JGP  C14   C13  C12   115.51  3.000
 JGP  H151  C15  H152  106.57  3.000
 JGP  H151  C15  C14   110.63  3.000
 JGP  H152  C15  C14   109.76  3.000
 JGP  H151  C15  N09   107.87  3.000
 JGP  H152  C15  N09   108.59  3.000
 JGP  C14   C15  N09   113.18  3.000
 JGP  H172  C17  H171  110.58  3.000
 JGP  H172  C17  O18   109.80  3.000
 JGP  H171  C17  O18   109.78  3.000
 JGP  H172  C17  O16   109.89  3.000
 JGP  H171  C17  O16   109.90  3.000
 JGP  O18   C17  O16   106.82  3.000
 JGP  H011  C01  C06   120.01  3.000
 JGP  H011  C01  C02   118.39  3.000
 JGP  C06   C01  C02   121.60  3.000
 JGP  H021  C02  C03   121.95  3.000
 JGP  H021  C02  C01   121.27  3.000
 JGP  C03   C02  C01   116.77  3.000
 JGP  O18   C03  C04   109.36  3.000
 JGP  O18   C03  C02   128.81  3.000
 JGP  C04   C03  C02   121.83  3.000
 JGP  O16   C04  C05   128.63  3.000
 JGP  C05   C04  C03   122.10  3.000
 JGP  O16   C04  C03   109.27  3.000
 JGP  H051  C05  C06   121.41  3.000
 JGP  H051  C05  C04   121.66  3.000
 JGP  C06   C05  C04   116.92  3.000
 JGP  C07   C06  C05   117.63  3.000
 JGP  C07   C06  C01   121.30  3.000
 JGP  C05   C06  C01   120.75  3.000
 JGP  C07   N09  C15   117.83  3.000
 JGP  C07   N09  C10   124.04  3.000
 JGP  C15   N09  C10   117.82  3.000
 JGP  H112  C11  H111  105.43  3.000
 JGP  H112  C11  C12   110.20  3.000
 JGP  H111  C11  C12   109.01  3.000
 JGP  H112  C11  C10   105.98  3.000
 JGP  H111  C11  C10   110.62  3.000
 JGP  C12   C11  C10   115.13  3.000
 JGP  H122  C12  H121  106.09  3.000
 JGP  H122  C12  C11   108.57  3.000
 JGP  H121  C12  C11   110.44  3.000
 JGP  H122  C12  C13   107.95  3.000
 JGP  H121  C12  C13   110.53  3.000
 JGP  C11   C12  C13   112.97  3.000
 JGP  H141  C14  H142  106.28  3.000
 JGP  H141  C14  C15   108.72  3.000
 JGP  H142  C14  C15   108.07  3.000
 JGP  H141  C14  C13   110.03  3.000
 JGP  H142  C14  C13   108.79  3.000
 JGP  C15   C14  C13   114.61  3.000
 JGP  C04   O16  C17   106.05  3.000
 JGP  C03   O18  C17   106.11  3.000
 JGP  N09   C07  O08   122.51  3.000
 JGP  O08   C07  C06   118.67  3.000
 JGP  N09   C07  C06   118.80  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
 JGP  CONST_01  C04   C05  C06  C01     0.00   0.0  0
 JGP  CONST_02  C04   C03  C02  C01     0.00   0.0  0
 JGP  CONST_03  C05   C04  C03  C02     0.00   0.0  0
 JGP  CONST_04  C05   C06  C01  C02     0.00   0.0  0
 JGP  CONST_05  C06   C05  C04  C03     0.00   0.0  0
 JGP  CONST_06  C06   C01  C02  C03     0.00   0.0  0
 JGP  CONST_07  C07   C06  C01  C02   180.00   0.0  0
 JGP  CONST_08  C07   C06  C05  C04   180.00   0.0  0
 JGP  CONST_09  H051  C05  C06  C01   180.00   0.0  0
 JGP  CONST_10  H011  C01  C02  C03   180.00   0.0  0
 JGP  CONST_11  H021  C02  C03  C04   180.00   0.0  0
 JGP  Var_01    C05   C04  O16  C17  -170.89  30.0  1
 JGP  Var_02    C04   C03  O18  C17    -9.34  30.0  1
 JGP  Var_03    O16   C17  O18  C03    15.01  30.0  1
 JGP  Var_04    O18   C17  O16  C04   -15.06  30.0  1
 JGP  Var_05    N09   C07  C06  C01    56.06  30.0  2

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
 JGP  plan-1  C10   0.020
 JGP  plan-1  C15   0.020
 JGP  plan-1  C06   0.020
 JGP  plan-1  O08   0.020
 JGP  plan-1  N09   0.020
 JGP  plan-1  C07   0.020
 JGP  plan-2  C01   0.020
 JGP  plan-2  C02   0.020
 JGP  plan-2  C03   0.020
 JGP  plan-2  C04   0.020
 JGP  plan-2  C05   0.020
 JGP  plan-2  C06   0.020
 JGP  plan-2  O16   0.020
 JGP  plan-2  O18   0.020
 JGP  plan-2  H011  0.020
 JGP  plan-2  H021  0.020
 JGP  plan-2  H051  0.020
 JGP  plan-2  C07   0.020

