# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 23:16:41 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (1~{S},10~{S})-12-cyclobutyl-5-methyl-1-oxidanyl-10-propan-2-yl-9,12-diazatricyclo[8.2.1.0^{2,7}]trideca-2(7),3,5-trien-11-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@]12C[C@@](O)(N(C3CCC3)C1=O)c4ccc(C)cc4CN2
#
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
 JRW  JRW  (1~{S},10~{S})-12-cyclobutyl-5-methyl-1-oxidanyl-10-propan-2-yl-9,12-diazatricyclo[8.2.1.0^{2,7}]trideca-2(7),3,5-trien-11-one  ligand  49  23  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JRW
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
 JRW  C10  C  CR5   0   0.547  -1.7911   0.0955  -0.2721
 JRW  N12  N  NH1   0  -0.594  -0.4012   2.0675  -0.6503
 JRW  C13  C  CH2   0  -0.437   0.5583   1.1962  -1.3197
 JRW  C15  C  CR6   0   0.071   1.3834  -0.2061   0.6821
 JRW  C17  C  CR16  0  -0.292   3.7487  -0.7010   0.8447
 JRW  C20  C  CR16  0  -0.358   2.9441   0.6786  -0.9163
 JRW  C21  C  CH1   0  -0.241  -2.5169   2.4430   0.5542
 JRW  C22  C  CH3   0  -0.675  -3.6166   1.8230   1.4172
 JRW  O01  O  OH1   0  -0.653   0.0192  -1.1465   2.3549
 JRW  C02  C  CR5   0   0.314  -0.0240  -0.3134   1.2417
 JRW  N03  N  NR5   0  -0.488  -0.9595  -0.8368   0.2428
 JRW  C04  C  C     0  -0.061  -0.8478  -2.1953  -0.2279
 JRW  C05  C  C     0  -0.444  -2.0544  -3.1500  -0.1813
 JRW  C06  C  C     0  -0.459  -1.5043  -3.7963  -1.4694
 JRW  C07  C  C     0  -0.459  -0.6810  -2.5173  -1.7258
 JRW  C08  C  CH2   0  -0.494  -0.6173   1.0657   1.5467
 JRW  C09  C  CR5   0  -0.002  -1.3585   1.4620   0.2762
 JRW  O11  O  O     0  -0.476  -2.6539  -0.1106  -1.1084
 JRW  C14  C  CR6   0   0.147   1.6335   0.5596  -0.4674
 JRW  C16  C  CR16  0  -0.281   2.4500  -0.8250   1.3208
 JRW  C18  C  CR6   0   0.113   4.0195   0.0603  -0.2820
 JRW  C19  C  CH3   0  -0.711   5.4170   0.2331  -0.7999
 JRW  C23  C  CH3   0  -0.676  -3.1582   3.0513  -0.6960
 JRW  H1   H  HNH1  0   0.369  -0.9091   2.5383  -1.3862
 JRW  H3   H  HCH2  0   0.237   0.0796   0.4017  -1.9114
 JRW  H4   H  HCH2  0   0.266   1.0583   1.8277  -2.0549
 JRW  H6   H  HCR6  0   0.241   3.1352   1.2735  -1.8036
 JRW  H7   H  HCH1  0   0.238  -2.0708   3.2666   1.1244
 JRW  H8   H  HCH3  0   0.230  -4.1166   1.0023   0.9013
 JRW  H9   H  HCH3  0   0.232  -3.2557   1.4497   2.3754
 JRW  H10  H  HCH3  0   0.236  -4.3742   2.5760   1.6378
 JRW  H11  H  HOH1  0   0.456  -0.8504  -1.1545   2.7719
 JRW  H12  H  H     0   0.262  -0.0214  -2.6510   0.3193
 JRW  H13  H  H     0   0.231  -2.1583  -3.7737   0.7068
 JRW  H14  H  H     0   0.239  -2.9935  -2.6315  -0.3668
 JRW  H15  H  H     0   0.229  -0.8673  -4.6550  -1.2548
 JRW  H16  H  H     0   0.233  -2.2292  -4.0811  -2.2306
 JRW  H17  H  H     0   0.238  -1.2217  -1.8210  -2.3645
 JRW  H18  H  H     0   0.244   0.3394  -2.6239  -2.0944
 JRW  H19  H  HCH2  0   0.266  -1.3134   0.9659   2.3816
 JRW  H20  H  HCH2  0   0.286   0.1358   1.8003   1.8213
 JRW  H21  H  HCR6  0   0.251   2.2798  -1.4185   2.2073
 JRW  H22  H  HCH3  0   0.243   5.7768   1.2496  -0.6291
 JRW  H23  H  HCH3  0   0.235   6.1112  -0.4490  -0.3106
 JRW  H24  H  HCH3  0   0.240   5.4712   0.0520  -1.8739
 JRW  H25  H  HCH3  0   0.242  -3.6133   2.2907  -1.3286
 JRW  H26  H  HCH3  0   0.229  -3.9450   3.7434  -0.3933
 JRW  H27  H  HCH3  0   0.216  -2.4638   3.6335  -1.3032
 JRW  H5   H  HCR6  0   0.221   4.5549  -1.2039   1.3653

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
 JRW  C22  C21  single    1.529  0.020  1.529
 JRW  C21  C23  single    1.531  0.020  1.531
 JRW  C21  C09  single    1.543  0.020  1.543
 JRW  N12  C09  single    1.463  0.020  1.463
 JRW  N12  C13  single    1.459  0.020  1.459
 JRW  C08  C09  single    1.523  0.020  1.523
 JRW  C08  C02  single    1.532  0.020  1.532
 JRW  C09  C10  single    1.535  0.020  1.535
 JRW  C19  C18  single    1.500  0.020  1.500
 JRW  C18  C20  aromatic  1.393  0.020  1.393
 JRW  C18  C17  aromatic  1.387  0.020  1.387
 JRW  C20  C14  aromatic  1.390  0.020  1.390
 JRW  C17  C16  aromatic  1.389  0.020  1.389
 JRW  C14  C13  single    1.512  0.020  1.512
 JRW  C14  C15  aromatic  1.404  0.020  1.404
 JRW  C16  C15  aromatic  1.389  0.020  1.389
 JRW  C15  C02  single    1.518  0.020  1.518
 JRW  C02  O01  single    1.391  0.020  1.391
 JRW  C02  N03  single    1.465  0.020  1.465
 JRW  C10  N03  single    1.351  0.020  1.351
 JRW  C10  O11  double    1.219  0.020  1.219
 JRW  N03  C04  single    1.442  0.020  1.442
 JRW  C04  C05  single    1.539  0.020  1.539
 JRW  C04  C07  single    1.541  0.020  1.541
 JRW  C05  C06  single    1.543  0.020  1.543
 JRW  C07  C06  single    1.543  0.020  1.543
 JRW  N12  H1   single    0.890  0.020  1.040
 JRW  C13  H3   single    0.970  0.020  1.090
 JRW  C13  H4   single    0.970  0.020  1.090
 JRW  C17  H5   single    0.930  0.020  1.080
 JRW  C20  H6   single    0.930  0.020  1.080
 JRW  C21  H7   single    0.970  0.020  1.090
 JRW  C22  H8   single    0.970  0.020  1.090
 JRW  C22  H9   single    0.970  0.020  1.090
 JRW  C22  H10  single    0.970  0.020  1.090
 JRW  O01  H11  single    0.850  0.020  0.980
 JRW  C04  H12  single    0.970  0.020  1.090
 JRW  C05  H13  single    0.970  0.020  1.090
 JRW  C05  H14  single    0.970  0.020  1.090
 JRW  C06  H15  single    0.970  0.020  1.090
 JRW  C06  H16  single    0.970  0.020  1.090
 JRW  C07  H17  single    0.970  0.020  1.090
 JRW  C07  H18  single    0.970  0.020  1.090
 JRW  C08  H19  single    0.970  0.020  1.090
 JRW  C08  H20  single    0.970  0.020  1.090
 JRW  C16  H21  single    0.930  0.020  1.080
 JRW  C19  H22  single    0.970  0.020  1.090
 JRW  C19  H23  single    0.970  0.020  1.090
 JRW  C19  H24  single    0.970  0.020  1.090
 JRW  C23  H25  single    0.970  0.020  1.090
 JRW  C23  H26  single    0.970  0.020  1.090
 JRW  C23  H27  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
 JRW  O11  C10  C09  126.53  3.000
 JRW  O11  C10  N03  125.47  3.000
 JRW  C09  C10  N03  107.74  3.000
 JRW  H1   N12  C09  108.96  3.000
 JRW  H1   N12  C13  105.94  3.000
 JRW  C09  N12  C13  118.28  3.000
 JRW  H4   C13  H3   104.78  3.000
 JRW  H4   C13  C14  107.32  3.000
 JRW  H3   C13  C14  107.96  3.000
 JRW  H4   C13  N12  105.37  3.000
 JRW  H3   C13  N12  113.08  3.000
 JRW  C14  C13  N12  117.41  3.000
 JRW  C16  C15  C14  118.88  3.000
 JRW  C16  C15  C02  120.73  3.000
 JRW  C14  C15  C02  120.36  3.000
 JRW  H5   C17  C18  120.00  3.000
 JRW  H5   C17  C16  119.32  3.000
 JRW  C18  C17  C16  120.68  3.000
 JRW  H6   C20  C18  118.65  3.000
 JRW  H6   C20  C14  118.48  3.000
 JRW  C18  C20  C14  122.86  3.000
 JRW  H7   C21  C23  107.25  3.000
 JRW  H7   C21  C09  105.41  3.000
 JRW  C23  C21  C09  114.83  3.000
 JRW  H7   C21  C22  107.68  3.000
 JRW  C09  C21  C22  112.57  3.000
 JRW  C23  C21  C22  108.70  3.000
 JRW  H10  C22  H9   106.78  3.000
 JRW  H10  C22  H8   107.26  3.000
 JRW  H9   C22  H8   108.05  3.000
 JRW  H10  C22  C21  109.50  3.000
 JRW  H9   C22  C21  113.38  3.000
 JRW  H8   C22  C21  111.58  3.000
 JRW  H11  O01  C02  108.84  3.000
 JRW  C08  C02  N03  102.12  3.000
 JRW  N03  C02  O01  110.58  3.000
 JRW  C08  C02  O01  113.07  3.000
 JRW  N03  C02  C15  111.46  3.000
 JRW  O01  C02  C15  107.97  3.000
 JRW  C08  C02  C15  111.64  3.000
 JRW  C04  N03  C02  120.63  3.000
 JRW  C04  N03  C10  124.98  3.000
 JRW  C02  N03  C10  113.97  3.000
 JRW  H12  C04  C07  108.56  3.000
 JRW  H12  C04  C05  108.64  3.000
 JRW  C07  C04  C05   89.12  3.000
 JRW  H12  C04  N03  106.77  3.000
 JRW  C07  C04  N03  121.49  3.000
 JRW  C05  C04  N03  120.91  3.000
 JRW  H14  C05  H13  109.21  3.000
 JRW  H14  C05  C06  111.40  3.000
 JRW  H13  C05  C06  118.33  3.000
 JRW  H14  C05  C04  112.07  3.000
 JRW  H13  C05  C04  117.01  3.000
 JRW  C06  C05  C04   87.42  3.000
 JRW  H16  C06  H15  108.68  3.000
 JRW  H16  C06  C07  117.12  3.000
 JRW  H15  C06  C07  111.95  3.000
 JRW  H16  C06  C05  117.13  3.000
 JRW  H15  C06  C05  111.96  3.000
 JRW  C07  C06  C05   88.96  3.000
 JRW  H18  C07  H17  109.21  3.000
 JRW  H18  C07  C06  118.34  3.000
 JRW  H17  C07  C06  111.27  3.000
 JRW  H18  C07  C04  116.77  3.000
 JRW  H17  C07  C04  112.51  3.000
 JRW  C06  C07  C04   87.35  3.000
 JRW  H20  C08  H19  108.08  3.000
 JRW  H20  C08  C09  111.83  3.000
 JRW  H19  C08  C09  110.57  3.000
 JRW  H20  C08  C02  112.97  3.000
 JRW  H19  C08  C02  108.48  3.000
 JRW  C09  C08  C02  104.87  3.000
 JRW  C08  C09  C21  112.36  3.000
 JRW  C08  C09  N12  108.50  3.000
 JRW  C21  C09  N12  110.01  3.000
 JRW  C08  C09  C10  101.74  3.000
 JRW  N12  C09  C10  109.06  3.000
 JRW  C21  C09  C10  114.76  3.000
 JRW  C20  C14  C15  118.62  3.000
 JRW  C15  C14  C13  124.37  3.000
 JRW  C20  C14  C13  116.88  3.000
 JRW  H21  C16  C17  118.53  3.000
 JRW  H21  C16  C15  120.08  3.000
 JRW  C17  C16  C15  121.39  3.000
 JRW  C19  C18  C20  120.71  3.000
 JRW  C20  C18  C17  117.57  3.000
 JRW  C19  C18  C17  121.71  3.000
 JRW  H24  C19  H23  107.86  3.000
 JRW  H24  C19  H22  107.00  3.000
 JRW  H23  C19  H22  107.62  3.000
 JRW  H24  C19  C18  111.54  3.000
 JRW  H23  C19  C18  111.49  3.000
 JRW  H22  C19  C18  111.11  3.000
 JRW  H27  C23  H26  105.97  3.000
 JRW  H27  C23  H25  108.38  3.000
 JRW  H26  C23  H25  107.63  3.000
 JRW  H27  C23  C21  113.58  3.000
 JRW  H26  C23  C21  109.12  3.000
 JRW  H25  C23  C21  111.83  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
 JRW  CONST_01  C18  C20  C14  C15     0.00   0.0  0
 JRW  CONST_02  C18  C17  C16  C15     0.00   0.0  0
 JRW  CONST_03  C14  C20  C18  C17     0.00   0.0  0
 JRW  CONST_04  C14  C15  C16  C17     0.00   0.0  0
 JRW  CONST_05  C16  C17  C18  C20     0.00   0.0  0
 JRW  CONST_06  C16  C15  C14  C20     0.00   0.0  0
 JRW  CONST_07  C19  C18  C20  C14   180.00   0.0  0
 JRW  CONST_08  C19  C18  C17  C16   180.00   0.0  0
 JRW  CONST_09  H6   C20  C14  C13     0.00   0.0  0
 JRW  CONST_10  H5   C17  C16  C15   180.00   0.0  0
 JRW  CONST_11  H21  C16  C15  C02     0.00   0.0  0
 JRW  Var_01    C20  C14  C13  N12  -129.99  30.0  2
 JRW  Var_02    C09  C10  N03  C02     6.07  30.0  2
 JRW  Var_03    C07  C06  C05  C04   -20.02  30.0  1
 JRW  Var_04    C14  C13  N12  C09   -68.70  30.0  3
 JRW  Var_05    H22  C19  C18  C17  -109.05  30.0  2
 JRW  Var_06    H8   C22  C21  C09   -65.17  30.0  3
 JRW  Var_07    H25  C23  C21  C09    62.34  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
 JRW  chir_01  C02  C15  O01  N03  positiv
 JRW  chir_02  C04  N03  C07  C05  positiv
 JRW  chir_03  C09  C21  C08  C10  negativ

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
 JRW  plan-1  C13  0.020
 JRW  plan-1  C15  0.020
 JRW  plan-1  C17  0.020
 JRW  plan-1  C20  0.020
 JRW  plan-1  C02  0.020
 JRW  plan-1  C14  0.020
 JRW  plan-1  C16  0.020
 JRW  plan-1  C18  0.020
 JRW  plan-1  C19  0.020
 JRW  plan-1  H6   0.020
 JRW  plan-1  H21  0.020
 JRW  plan-1  H5   0.020
 JRW  plan-2  C10  0.020
 JRW  plan-2  N03  0.020
 JRW  plan-2  C09  0.020
 JRW  plan-2  O11  0.020

