# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 03:51:12 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (4R,4aS,7aS,9S)-3,10-dimethyl-5,6,7,7a,8,9-hexahydro-4H-4a,9-epiminopyrrolo[3',4':5,6]cyclohepta[1,2-d][1,2]oxazol-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@H]2C[C@H]3CNC[C@@]13[C@H](O)c4c(C)noc24
#
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
 RGY  RGY  (4R,4aS,7aS,9S)-3,10-dimethyl-5,6,7,7a,8,9-hexahydro-4H-4a,9-epiminopyrrolo[3',4':5,6]cyclohepta[1,2-d][1,2]oxazol-4-ol  ligand  34  17  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RGY
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
 RGY  N1   N  NT    0  -0.403  -0.8761  -1.0147   1.0309
 RGY  N3   N  N     0  -0.191   3.2857  -0.4173  -0.5828
 RGY  C4   C  CR15  0  -0.250  -1.4848  -0.2435  -1.0814
 RGY  C5   C  CH2   0  -0.263  -3.0079  -0.1654  -1.1168
 RGY  C6   C  CH2   0  -0.282  -2.4387   0.9290   0.8497
 RGY  C7   C  CR5   0   0.061  -1.1508   0.2529   0.3521
 RGY  C8   C  CH1   0  -0.029   0.0778   1.1911   0.3964
 RGY  C10  C  CR5   0   0.431   1.2168  -0.9717  -0.0945
 RGY  C1   C  CH3   0  -0.540  -0.4275  -0.9725   2.4033
 RGY  C11  C  CR5   0   0.230   2.6252   0.6723  -0.3014
 RGY  C12  C  CH3   0  -0.749   3.2846   2.0036  -0.3465
 RGY  C2   C  CH1   0  -0.234  -0.0441  -1.7548   0.0963
 RGY  C3   C  CH2   0  -0.414  -0.8810  -1.6547  -1.1857
 RGY  C9   C  CR5   0  -0.163   1.2748   0.3722   0.0202
 RGY  N2   N  NR15  0  -0.607  -3.2792   1.0274  -0.3364
 RGY  O1   O  OH1   0  -0.659  -0.1339   2.2761  -0.4768
 RGY  O2   O  O     0  -0.347   2.3988  -1.4599  -0.4524
 RGY  H2   H  HCR5  0   0.259  -1.0696   0.4223  -1.8382
 RGY  H3   H  HCH2  0   0.229  -3.4028  -0.0718  -2.1309
 RGY  H4   H  HCH2  0   0.194  -3.4360  -1.0809  -0.6790
 RGY  H5   H  HCH2  0   0.208  -2.8819   0.3038   1.6365
 RGY  H6   H  HCH2  0   0.228  -2.2608   1.9171   1.2806
 RGY  H7   H  HCH1  0   0.240   0.1955   1.5641   1.4239
 RGY  H8   H  HCH3  0   0.206   0.5792  -0.5596   2.5531
 RGY  H9   H  HCH3  0   0.243  -1.1231  -0.3791   2.9975
 RGY  H10  H  HCH3  0   0.242  -0.4293  -1.9832   2.8136
 RGY  H11  H  HCH3  0   0.258   2.8152   2.6394  -1.0975
 RGY  H12  H  HCH3  0   0.258   3.1931   2.5108   0.6145
 RGY  H13  H  HCH3  0   0.261   4.3417   1.9128  -0.5868
 RGY  H14  H  HCH1  0   0.276   0.1372  -2.7788   0.4303
 RGY  H15  H  HCH2  0   0.248  -1.6549  -2.4238  -1.1721
 RGY  H16  H  HCH2  0   0.251  -0.2857  -1.7979  -2.0873
 RGY  H17  H  HNR5  0   0.348  -4.2577   1.1058  -0.0927
 RGY  H19  H  HOH1  0   0.460   0.3339   3.0428  -0.1351

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
 RGY  C1   N1   single    1.444  0.020  1.444
 RGY  N1   C2   single    1.454  0.020  1.454
 RGY  N1   C7   single    1.464  0.020  1.464
 RGY  C2   C10  single    1.497  0.020  1.497
 RGY  C2   C3   single    1.534  0.020  1.534
 RGY  C10  O2   aromatic  1.328  0.020  1.328
 RGY  C10  C9   aromatic  1.350  0.020  1.350
 RGY  O2   N3   aromatic  1.375  0.020  1.375
 RGY  C6   C7   single    1.537  0.020  1.537
 RGY  C6   N2   single    1.457  0.020  1.457
 RGY  N3   C11  aromatic  1.305  0.020  1.305
 RGY  C7   C8   single    1.546  0.020  1.546
 RGY  C7   C4   single    1.553  0.020  1.553
 RGY  C9   C8   single    1.498  0.020  1.498
 RGY  C9   C11  aromatic  1.420  0.020  1.420
 RGY  C8   O1   single    1.409  0.020  1.409
 RGY  C11  C12  single    1.486  0.020  1.486
 RGY  N2   C5   single    1.451  0.020  1.451
 RGY  C3   C4   single    1.538  0.020  1.538
 RGY  C4   C5   single    1.526  0.020  1.526
 RGY  C4   H2   single    0.970  0.020  1.090
 RGY  C5   H3   single    0.970  0.020  1.090
 RGY  C5   H4   single    0.970  0.020  1.090
 RGY  C6   H5   single    0.970  0.020  1.090
 RGY  C6   H6   single    0.970  0.020  1.090
 RGY  C8   H7   single    0.970  0.020  1.090
 RGY  C1   H8   single    0.970  0.020  1.090
 RGY  C1   H9   single    0.970  0.020  1.090
 RGY  C1   H10  single    0.970  0.020  1.090
 RGY  C12  H11  single    0.970  0.020  1.090
 RGY  C12  H12  single    0.970  0.020  1.090
 RGY  C12  H13  single    0.970  0.020  1.090
 RGY  C2   H14  single    0.970  0.020  1.090
 RGY  C3   H15  single    0.970  0.020  1.090
 RGY  C3   H16  single    0.970  0.020  1.090
 RGY  N2   H17  single    0.890  0.020  1.040
 RGY  O1   H19  single    0.850  0.020  0.980

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
 RGY  C2   N1   C1   116.61  3.000
 RGY  C2   N1   C7   104.49  3.000
 RGY  C1   N1   C7   118.26  3.000
 RGY  O2   N3   C11  106.63  3.000
 RGY  H2   C4   C3   111.33  3.000
 RGY  H2   C4   C7   111.32  3.000
 RGY  C3   C4   C7   105.75  3.000
 RGY  H2   C4   C5   109.44  3.000
 RGY  C3   C4   C5   115.93  3.000
 RGY  C7   C4   C5   102.69  3.000
 RGY  H4   C5   H3   107.44  3.000
 RGY  H4   C5   N2   113.38  3.000
 RGY  H3   C5   N2   111.18  3.000
 RGY  H4   C5   C4   109.65  3.000
 RGY  H3   C5   C4   112.76  3.000
 RGY  N2   C5   C4   102.49  3.000
 RGY  H6   C6   H5   107.34  3.000
 RGY  H6   C6   N2   110.73  3.000
 RGY  H5   C6   N2   112.88  3.000
 RGY  H6   C6   C7   112.89  3.000
 RGY  H5   C6   C7   108.63  3.000
 RGY  N2   C6   C7   104.44  3.000
 RGY  C8   C7   C6   112.92  3.000
 RGY  C8   C7   C4   113.02  3.000
 RGY  C6   C7   C4   105.02  3.000
 RGY  C4   C7   N1   101.04  3.000
 RGY  C8   C7   N1   111.28  3.000
 RGY  C6   C7   N1   112.83  3.000
 RGY  H7   C8   O1   109.52  3.000
 RGY  H7   C8   C9   109.55  3.000
 RGY  O1   C8   C9   112.66  3.000
 RGY  H7   C8   C7   108.52  3.000
 RGY  O1   C8   C7   109.27  3.000
 RGY  C9   C8   C7   107.21  3.000
 RGY  O2   C10  C9   110.53  3.000
 RGY  C9   C10  C2   123.11  3.000
 RGY  O2   C10  C2   126.29  3.000
 RGY  H10  C1   H9   107.35  3.000
 RGY  H10  C1   H8   107.37  3.000
 RGY  H9   C1   H8   107.81  3.000
 RGY  H10  C1   N1   109.26  3.000
 RGY  H9   C1   N1   109.60  3.000
 RGY  H8   C1   N1   115.16  3.000
 RGY  C9   C11  C12  128.17  3.000
 RGY  C12  C11  N3   121.12  3.000
 RGY  C9   C11  N3   110.71  3.000
 RGY  H13  C12  H12  108.36  3.000
 RGY  H13  C12  H11  108.35  3.000
 RGY  H12  C12  H11  107.44  3.000
 RGY  H13  C12  C11  111.29  3.000
 RGY  H12  C12  C11  110.65  3.000
 RGY  H11  C12  C11  110.62  3.000
 RGY  H14  C2   C3   114.03  3.000
 RGY  H14  C2   C10  112.94  3.000
 RGY  C3   C2   C10  108.60  3.000
 RGY  H14  C2   N1   112.07  3.000
 RGY  C3   C2   N1   101.06  3.000
 RGY  C10  C2   N1   107.32  3.000
 RGY  H16  C3   H15  107.77  3.000
 RGY  H16  C3   C2   112.62  3.000
 RGY  H15  C3   C2   109.30  3.000
 RGY  H16  C3   C4   113.02  3.000
 RGY  H15  C3   C4   111.55  3.000
 RGY  C2   C3   C4   102.55  3.000
 RGY  C11  C9   C10  103.41  3.000
 RGY  C11  C9   C8   134.51  3.000
 RGY  C10  C9   C8   122.08  3.000
 RGY  H17  N2   C6   111.54  3.000
 RGY  H17  N2   C5   111.98  3.000
 RGY  C6   N2   C5   105.94  3.000
 RGY  H19  O1   C8   108.72  3.000
 RGY  C10  O2   N3   108.72  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
 RGY  CONST_01  C11  N3   O2   C10    0.00   0.0  0
 RGY  CONST_02  O2   N3   C11  C9     0.00   0.0  0
 RGY  CONST_03  O2   N3   C11  C12  180.00   0.0  0
 RGY  Var_01    C6   N2   C5   C4   -45.54  30.0  1
 RGY  Var_02    C7   C6   N2   C5    35.22  30.0  1
 RGY  Var_03    H11  C12  C11  N3   117.85  30.0  2
 RGY  Var_04    H8   C1   N1   C7   -68.55  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
 RGY  chir_01  C4  C7  C3   C5  negativ
 RGY  chir_02  C7  C6  C8   C4  positiv
 RGY  chir_03  C8  O1  C7   C9  negativ
 RGY  chir_04  C2  N1  C10  C3  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
 RGY  plan-1  N3   0.020
 RGY  plan-1  C8   0.020
 RGY  plan-1  C10  0.020
 RGY  plan-1  C11  0.020
 RGY  plan-1  C12  0.020
 RGY  plan-1  C2   0.020
 RGY  plan-1  C9   0.020
 RGY  plan-1  O2   0.020

