# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:12:14 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: (4R,4aS,7aS,9S)-6-ethyl-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: CCN1C[C@@H]2C[C@@H]3N(C)[C@@]2(C1)[C@H](O)c4c(C)noc34
#
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
 RKJ  RKJ  (4R,4aS,7aS,9S)-6-ethyl-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  40  19  .  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_RKJ
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
 RKJ  N1   N  NT    0  -0.395  -0.2652  -0.9632   1.0823
 RKJ  N3   N  N     0  -0.191   3.8491  -0.3499  -0.6025
 RKJ  C4   C  CH1   0  -0.269  -0.8590  -0.2410  -1.0780
 RKJ  C5   C  CH2   0  -0.264  -2.3673  -0.0473  -1.2435
 RKJ  C6   C  CH2   0  -0.261  -1.8903   0.8718   0.8133
 RKJ  C7   C  CT    0   0.048  -0.5657   0.2770   0.3619
 RKJ  C8   C  CH1   0  -0.027   0.6385   1.2406   0.4002
 RKJ  C10  C  CR5   0   0.429   1.7917  -0.9252  -0.0868
 RKJ  C1   C  CH3   0  -0.542   0.2205  -0.8697   2.4396
 RKJ  C11  C  CR5   0   0.227   3.1816   0.7335  -0.3131
 RKJ  C12  C  CH3   0  -0.748   3.8275   2.0710  -0.3691
 RKJ  C14  C  CH3   0  -0.680  -5.2528  -0.3108  -0.4399
 RKJ  C2   C  CH1   0  -0.237   0.5491  -1.7280   0.1542
 RKJ  C3   C  CH2   0  -0.402  -0.3477  -1.6920  -1.0853
 RKJ  C9   C  CR5   0  -0.155   1.8396   0.4210   0.0281
 RKJ  N2   N  NT    0  -0.412  -2.8743   0.0708   0.1115
 RKJ  O1   O  OH1   0  -0.659   0.4253   2.3068  -0.4970
 RKJ  O2   O  O     0  -0.347   2.9745  -1.4006  -0.4594
 RKJ  H2   H  HCH1  0   0.263  -0.3289   0.3424  -1.8297
 RKJ  H3   H  HCH2  0   0.194  -2.5610   0.8688  -1.8278
 RKJ  H4   H  HCH2  0   0.233  -2.8384  -0.8744  -1.7792
 RKJ  H5   H  HCH2  0   0.234  -2.0361   0.8162   1.8955
 RKJ  H6   H  HCH2  0   0.202  -1.9437   1.9361   0.5306
 RKJ  H7   H  HCH1  0   0.241   0.7524   1.6328   1.4207
 RKJ  H8   H  HCH2  0   0.182  -4.2938   1.6038  -0.2185
 RKJ  H9   H  HCH2  0   0.225  -4.4574   0.6937   1.2772
 RKJ  H10  H  HCH3  0   0.206   1.2402  -0.4752   2.5454
 RKJ  H11  H  HCH3  0   0.242  -0.4431  -0.2352   3.0272
 RKJ  H12  H  HCH3  0   0.243   0.2068  -1.8610   2.8947
 RKJ  H13  H  HCH3  0   0.258   3.3503   2.6966  -1.1237
 RKJ  H14  H  HCH3  0   0.258   3.7332   2.5849   0.5881
 RKJ  H15  H  HCH3  0   0.260   4.8850   1.9893  -0.6113
 RKJ  H16  H  HCH3  0   0.221  -5.1765  -1.3311  -0.0617
 RKJ  H17  H  HCH3  0   0.232  -6.2580   0.0529  -0.2262
 RKJ  H18  H  HCH3  0   0.227  -5.1419  -0.3428  -1.5244
 RKJ  H19  H  HCH1  0   0.275   0.7600  -2.7352   0.5205
 RKJ  H20  H  HCH2  0   0.250  -1.1612  -2.4065  -0.9481
 RKJ  H21  H  HCH2  0   0.247   0.1754  -1.9519  -2.0058
 RKJ  H23  H  HOH1  0   0.461   0.8677   3.0892  -0.1570
 RKJ  C13  C  CH2   0  -0.271  -4.2191   0.5904   0.2148

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
 RKJ  C1   N1   single    1.445  0.020  1.445
 RKJ  N1   C2   single    1.452  0.020  1.452
 RKJ  N1   C7   single    1.465  0.020  1.465
 RKJ  C2   C10  single    1.499  0.020  1.499
 RKJ  C2   C3   single    1.530  0.020  1.530
 RKJ  C10  O2   aromatic  1.328  0.020  1.328
 RKJ  C10  C9   aromatic  1.352  0.020  1.352
 RKJ  C6   C7   single    1.521  0.020  1.521
 RKJ  C6   N2   single    1.450  0.020  1.450
 RKJ  O2   N3   aromatic  1.374  0.020  1.374
 RKJ  C8   C7   single    1.543  0.020  1.543
 RKJ  C8   C9   single    1.501  0.020  1.501
 RKJ  C8   O1   single    1.410  0.020  1.410
 RKJ  C7   C4   single    1.558  0.020  1.558
 RKJ  C9   C11  aromatic  1.419  0.020  1.419
 RKJ  N3   C11  aromatic  1.305  0.020  1.305
 RKJ  C11  C12  single    1.486  0.020  1.486
 RKJ  N2   C13  single    1.445  0.020  1.445
 RKJ  N2   C5   single    1.452  0.020  1.452
 RKJ  C13  C14  single    1.520  0.020  1.520
 RKJ  C3   C4   single    1.538  0.020  1.538
 RKJ  C4   C5   single    1.530  0.020  1.530
 RKJ  C4   H2   single    0.970  0.020  1.090
 RKJ  C5   H3   single    0.970  0.020  1.090
 RKJ  C5   H4   single    0.970  0.020  1.090
 RKJ  C6   H5   single    0.970  0.020  1.090
 RKJ  C6   H6   single    0.970  0.020  1.090
 RKJ  C8   H7   single    0.970  0.020  1.090
 RKJ  C13  H8   single    0.970  0.020  1.090
 RKJ  C13  H9   single    0.970  0.020  1.090
 RKJ  C1   H10  single    0.970  0.020  1.090
 RKJ  C1   H11  single    0.970  0.020  1.090
 RKJ  C1   H12  single    0.970  0.020  1.090
 RKJ  C12  H13  single    0.970  0.020  1.090
 RKJ  C12  H14  single    0.970  0.020  1.090
 RKJ  C12  H15  single    0.970  0.020  1.090
 RKJ  C14  H16  single    0.970  0.020  1.090
 RKJ  C14  H17  single    0.970  0.020  1.090
 RKJ  C14  H18  single    0.970  0.020  1.090
 RKJ  C2   H19  single    0.970  0.020  1.090
 RKJ  C3   H20  single    0.970  0.020  1.090
 RKJ  C3   H21  single    0.970  0.020  1.090
 RKJ  O1   H23  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
 RKJ  C2   N1   C1   116.48  3.000
 RKJ  C2   N1   C7   104.27  3.000
 RKJ  C1   N1   C7   118.43  3.000
 RKJ  O2   N3   C11  106.62  3.000
 RKJ  H2   C4   C3   109.89  3.000
 RKJ  H2   C4   C7   111.60  3.000
 RKJ  C3   C4   C7   104.80  3.000
 RKJ  H2   C4   C5   109.72  3.000
 RKJ  C3   C4   C5   116.53  3.000
 RKJ  C7   C4   C5   104.09  3.000
 RKJ  H4   C5   H3   107.05  3.000
 RKJ  H4   C5   N2   111.64  3.000
 RKJ  H3   C5   N2   111.43  3.000
 RKJ  H4   C5   C4   112.49  3.000
 RKJ  H3   C5   C4   109.60  3.000
 RKJ  N2   C5   C4   104.70  3.000
 RKJ  H6   C6   H5   107.24  3.000
 RKJ  H6   C6   N2   112.11  3.000
 RKJ  H5   C6   N2   111.13  3.000
 RKJ  H6   C6   C7   110.10  3.000
 RKJ  H5   C6   C7   112.96  3.000
 RKJ  N2   C6   C7   103.38  3.000
 RKJ  C8   C7   C6   115.36  3.000
 RKJ  C8   C7   C4   112.18  3.000
 RKJ  C6   C7   C4   103.91  3.000
 RKJ  C4   C7   N1   102.21  3.000
 RKJ  C8   C7   N1   110.88  3.000
 RKJ  C6   C7   N1   111.33  3.000
 RKJ  H7   C8   O1   109.68  3.000
 RKJ  H7   C8   C9   110.00  3.000
 RKJ  O1   C8   C9   112.10  3.000
 RKJ  H7   C8   C7   109.07  3.000
 RKJ  O1   C8   C7   109.79  3.000
 RKJ  C9   C8   C7   106.11  3.000
 RKJ  O2   C10  C9   110.41  3.000
 RKJ  C9   C10  C2   123.30  3.000
 RKJ  O2   C10  C2   126.28  3.000
 RKJ  H12  C1   H11  107.24  3.000
 RKJ  H12  C1   H10  107.32  3.000
 RKJ  H11  C1   H10  107.71  3.000
 RKJ  H12  C1   N1   109.20  3.000
 RKJ  H11  C1   N1   109.85  3.000
 RKJ  H10  C1   N1   115.21  3.000
 RKJ  C9   C11  C12  128.17  3.000
 RKJ  C12  C11  N3   121.09  3.000
 RKJ  C9   C11  N3   110.74  3.000
 RKJ  H15  C12  H14  108.36  3.000
 RKJ  H15  C12  H13  108.33  3.000
 RKJ  H14  C12  H13  107.42  3.000
 RKJ  H15  C12  C11  111.29  3.000
 RKJ  H14  C12  C11  110.70  3.000
 RKJ  H13  C12  C11  110.62  3.000
 RKJ  H18  C14  H17  107.37  3.000
 RKJ  H18  C14  H16  108.07  3.000
 RKJ  H17  C14  H16  107.97  3.000
 RKJ  H18  C14  C13  112.12  3.000
 RKJ  H17  C14  C13  110.18  3.000
 RKJ  H16  C14  C13  110.96  3.000
 RKJ  H19  C2   C3   113.98  3.000
 RKJ  H19  C2   C10  112.81  3.000
 RKJ  C3   C2   C10  110.06  3.000
 RKJ  H19  C2   N1   112.31  3.000
 RKJ  C3   C2   N1   100.17  3.000
 RKJ  C10  C2   N1   106.59  3.000
 RKJ  H21  C3   H20  107.93  3.000
 RKJ  H21  C3   C2   113.40  3.000
 RKJ  H20  C3   C2   108.63  3.000
 RKJ  H21  C3   C4   112.85  3.000
 RKJ  H20  C3   C4   111.67  3.000
 RKJ  C2   C3   C4   102.30  3.000
 RKJ  C11  C9   C10  103.43  3.000
 RKJ  C11  C9   C8   134.10  3.000
 RKJ  C10  C9   C8   122.44  3.000
 RKJ  C13  N2   C6   113.47  3.000
 RKJ  C13  N2   C5   114.90  3.000
 RKJ  C6   N2   C5   105.05  3.000
 RKJ  H23  O1   C8   108.72  3.000
 RKJ  C10  O2   N3   108.80  3.000
 RKJ  H9   C13  H8   106.24  3.000
 RKJ  H9   C13  N2   107.82  3.000
 RKJ  H8   C13  N2   111.39  3.000
 RKJ  H9   C13  C14  109.05  3.000
 RKJ  H8   C13  C14  109.21  3.000
 RKJ  N2   C13  C14  112.89  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
 RKJ  CONST_01  C11  N3   O2   C10    0.00   0.0  0
 RKJ  CONST_02  O2   N3   C11  C9     0.00   0.0  0
 RKJ  CONST_03  O2   N3   C11  C12  180.00   0.0  0
 RKJ  Var_01    C6   N2   C5   C4    39.82  30.0  1
 RKJ  Var_02    C7   C6   N2   C5   -44.22  30.0  1
 RKJ  Var_03    C14  C13  N2   C5    63.22  30.0  3
 RKJ  Var_04    H13  C12  C11  N3   117.08  30.0  2
 RKJ  Var_05    H10  C1   N1   C7   -70.25  30.0  3
 RKJ  Var_06    H16  C14  C13  N2    53.17  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
 RKJ  chir_01  C4  C7  C3   C5  negativ
 RKJ  chir_02  C7  C6  C8   C4  positiv
 RKJ  chir_03  C8  O1  C7   C9  negativ
 RKJ  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
 RKJ  plan-1  N3   0.020
 RKJ  plan-1  C8   0.020
 RKJ  plan-1  C10  0.020
 RKJ  plan-1  C11  0.020
 RKJ  plan-1  C12  0.020
 RKJ  plan-1  C2   0.020
 RKJ  plan-1  C9   0.020
 RKJ  plan-1  O2   0.020

