# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 01:49:46 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: 2-[(4-chlorophenyl)methyl]-5-methoxy-3,10-diazatricyclo[6.4.1.0^{4,13}]trideca-1,4(13),5,7-tetraen-9-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2C(=O)NCCc3c(Cc4ccc(Cl)cc4)[nH]c1c23
#
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
 2OI  2OI  "2-[(4-chlorophenyl)methyl]-5-methoxy-3,10-diazatricyclo[6.4.1.0^{4,13}]trideca-1,4(13),5,7-tetraen-9-one"
  ligand  41  24  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2OI
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
 2OI  C1   C   C     0   0.461  34.7770  -30.7824  -36.6668
 2OI  C2   C   CR6   0  -0.174  36.1207  -30.5853  -37.2719
 2OI  C4   C   CR5   0  -0.087  35.6652  -31.0419  -39.8112
 2OI  C6   C   CH2   0  -0.318  33.9809  -32.3135  -38.5202
 2OI  C8   C   CR16  0  -0.292  37.1479  -30.1899  -36.4303
 2OI  C9   C   CR16  0  -0.416  38.4394  -29.9046  -36.8856
 2OI  C10  C   CR6   0   0.347  38.7441  -29.9861  -38.2357
 2OI  C11  C   CR56  0   0.262  37.7168  -30.3775  -39.0989
 2OI  C15  C   CR6   0   0.140  36.9853  -32.4684  -42.8046
 2OI  C16  C   CR16  0  -0.280  36.7717  -33.6963  -42.1820
 2OI  C17  C   CR16  0  -0.194  37.4047  -34.8455  -42.6267
 2OI  C20  C   CR16  0  -0.337  37.8618  -32.4153  -43.8815
 2OI  O21  O   O     0  -0.491  34.5124  -30.3031  -35.5667
 2OI  C23  C   CH3   0  -0.434  40.9918  -29.3074  -37.9531
 2OI  C3   C   CR56  0   0.128  36.4194  -30.6870  -38.6502
 2OI  C5   C   CH2   0  -0.521  34.2583  -31.5344  -39.7995
 2OI  N7   N   NH1   0  -0.637  33.8390  -31.4762  -37.3455
 2OI  N12  N   NR15  0  -0.724  37.7434  -30.5337  -40.4529
 2OI  C13  C   CR5   0   0.331  36.5125  -30.9374  -40.8853
 2OI  C18  C   CR6   0  -0.056  38.2685  -34.7640  -43.7094
 2OI  C19  C   CR16  0  -0.193  38.5067  -33.5561  -44.3418
 2OI  O22  O   O2    0  -0.464  39.9338  -29.7242  -38.7961
 2OI  CL   CL  CL    0  -0.132  39.0596  -36.1979  -44.2815
 2OI  H1   H   HCH2  0   0.268  33.0412  -32.8540  -38.6186
 2OI  H2   H   HCH2  0   0.244  34.7622  -33.0633  -38.3685
 2OI  H3   H   HCR6  0   0.253  36.9521  -30.0894  -35.3715
 2OI  H4   H   HCR6  0   0.277  39.1897  -29.6139  -36.1633
 2OI  H5   H   HCH2  0   0.283  36.5516  -30.3762  -42.9390
 2OI  H6   H   HCH2  0   0.283  35.1876  -31.3614  -42.4732
 2OI  H7   H   HCR6  0   0.264  36.0984  -33.7630  -41.3351
 2OI  H8   H   HCR6  0   0.277  37.2256  -35.7929  -42.1362
 2OI  H9   H   HCR6  0   0.261  38.0462  -31.4706  -44.3786
 2OI  H10  H   HCH3  0   0.260  41.8519  -29.1402  -38.5963
 2OI  H11  H   HCH3  0   0.232  40.7511  -28.3772  -37.4331
 2OI  H12  H   HCH3  0   0.232  41.2444  -30.0715  -37.2140
 2OI  H13  H   HCH2  0   0.246  33.5335  -30.7191  -39.8817
 2OI  H14  H   HCH2  0   0.245  34.0807  -32.1946  -40.6518
 2OI  H15  H   HNH1  0   0.391  32.9486  -31.5234  -36.8743
 2OI  H16  H   HNR5  0   0.407  38.5428  -30.3781  -41.0453
 2OI  H17  H   HCR6  0   0.277  39.1842  -33.4981  -45.1830
 2OI  C14  C   CH2   0  -0.615  36.2616  -31.2326  -42.3251

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
 2OI  CL   C18  single    1.735  0.020  1.735
 2OI  C19  C18  aromatic  1.384  0.020  1.384
 2OI  C19  C20  aromatic  1.389  0.020  1.389
 2OI  C18  C17  aromatic  1.387  0.020  1.387
 2OI  C20  C15  aromatic  1.390  0.020  1.390
 2OI  C17  C16  aromatic  1.385  0.020  1.385
 2OI  C15  C16  aromatic  1.393  0.020  1.393
 2OI  C15  C14  single    1.510  0.020  1.510
 2OI  C14  C13  single    1.491  0.020  1.491
 2OI  C13  N12  aromatic  1.366  0.020  1.366
 2OI  C13  C4   aromatic  1.372  0.020  1.372
 2OI  N12  C11  aromatic  1.363  0.020  1.363
 2OI  C4   C5   single    1.491  0.020  1.491
 2OI  C4   C3   aromatic  1.429  0.020  1.429
 2OI  C5   C6   single    1.523  0.020  1.523
 2OI  C11  C3   aromatic  1.407  0.020  1.407
 2OI  C11  C10  aromatic  1.398  0.020  1.398
 2OI  O22  C10  single    1.341  0.020  1.341
 2OI  O22  C23  single    1.416  0.020  1.416
 2OI  C3   C2   aromatic  1.414  0.020  1.414
 2OI  C6   N7   single    1.450  0.020  1.450
 2OI  C10  C9   aromatic  1.387  0.020  1.387
 2OI  C2   C1   single    1.487  0.020  1.487
 2OI  C2   C8   aromatic  1.386  0.020  1.386
 2OI  N7   C1   single    1.350  0.020  1.350
 2OI  C9   C8   aromatic  1.399  0.020  1.399
 2OI  C1   O21  double    1.229  0.020  1.229
 2OI  C6   H1   single    0.970  0.020  1.090
 2OI  C6   H2   single    0.970  0.020  1.090
 2OI  C8   H3   single    0.930  0.020  1.080
 2OI  C9   H4   single    0.930  0.020  1.080
 2OI  C14  H5   single    0.970  0.020  1.090
 2OI  C14  H6   single    0.970  0.020  1.090
 2OI  C16  H7   single    0.930  0.020  1.080
 2OI  C17  H8   single    0.930  0.020  1.080
 2OI  C20  H9   single    0.930  0.020  1.080
 2OI  C23  H10  single    0.970  0.020  1.090
 2OI  C23  H11  single    0.970  0.020  1.090
 2OI  C23  H12  single    0.970  0.020  1.090
 2OI  C5   H13  single    0.970  0.020  1.090
 2OI  C5   H14  single    0.970  0.020  1.090
 2OI  N7   H15  single    0.860  0.020  1.020
 2OI  N12  H16  single    0.860  0.020  1.020
 2OI  C19  H17  single    0.930  0.020  1.080

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
 2OI  N7   C1   O21  120.07  3.000
 2OI  O21  C1   C2   120.49  3.000
 2OI  N7   C1   C2   119.44  3.000
 2OI  C3   C2   C8   117.13  3.000
 2OI  C8   C2   C1   117.42  3.000
 2OI  C3   C2   C1   125.32  3.000
 2OI  C13  C4   C5   127.89  3.000
 2OI  C5   C4   C3   125.00  3.000
 2OI  C13  C4   C3   106.93  3.000
 2OI  H2   C6   H1   106.79  3.000
 2OI  H2   C6   N7   110.71  3.000
 2OI  H1   C6   N7   105.99  3.000
 2OI  H2   C6   C5   109.70  3.000
 2OI  H1   C6   C5   109.59  3.000
 2OI  N7   C6   C5   113.77  3.000
 2OI  H3   C8   C9   117.83  3.000
 2OI  H3   C8   C2   119.15  3.000
 2OI  C9   C8   C2   123.02  3.000
 2OI  H4   C9   C10  120.92  3.000
 2OI  H4   C9   C8   118.56  3.000
 2OI  C10  C9   C8   120.52  3.000
 2OI  O22  C10  C11  116.66  3.000
 2OI  O22  C10  C9   126.19  3.000
 2OI  C11  C10  C9   117.15  3.000
 2OI  N12  C11  C3   108.03  3.000
 2OI  C3   C11  C10  122.84  3.000
 2OI  N12  C11  C10  129.13  3.000
 2OI  C20  C15  C16  118.48  3.000
 2OI  C16  C15  C14  120.38  3.000
 2OI  C20  C15  C14  121.14  3.000
 2OI  H7   C16  C17  118.92  3.000
 2OI  H7   C16  C15  119.91  3.000
 2OI  C17  C16  C15  121.17  3.000
 2OI  H8   C17  C18  120.56  3.000
 2OI  H8   C17  C16  120.35  3.000
 2OI  C18  C17  C16  119.10  3.000
 2OI  H9   C20  C19  119.02  3.000
 2OI  H9   C20  C15  119.76  3.000
 2OI  C19  C20  C15  121.22  3.000
 2OI  H12  C23  H11  108.93  3.000
 2OI  H12  C23  H10  108.96  3.000
 2OI  H11  C23  H10  108.97  3.000
 2OI  H12  C23  O22  111.70  3.000
 2OI  H11  C23  O22  111.68  3.000
 2OI  H10  C23  O22  106.52  3.000
 2OI  C11  C3   C4   106.38  3.000
 2OI  C11  C3   C2   119.33  3.000
 2OI  C4   C3   C2   134.29  3.000
 2OI  H14  C5   H13  106.50  3.000
 2OI  H14  C5   C6   108.45  3.000
 2OI  H13  C5   C6   108.88  3.000
 2OI  H14  C5   C4   110.30  3.000
 2OI  H13  C5   C4   112.23  3.000
 2OI  C6   C5   C4   110.33  3.000
 2OI  H15  N7   C6   115.98  3.000
 2OI  H15  N7   C1   113.74  3.000
 2OI  C6   N7   C1   129.53  3.000
 2OI  H16  N12  C13  125.09  3.000
 2OI  H16  N12  C11  125.60  3.000
 2OI  C13  N12  C11  109.31  3.000
 2OI  N12  C13  C14  121.06  3.000
 2OI  N12  C13  C4   109.35  3.000
 2OI  C14  C13  C4   129.56  3.000
 2OI  CL   C18  C19  119.49  3.000
 2OI  C19  C18  C17  120.99  3.000
 2OI  CL   C18  C17  119.52  3.000
 2OI  H17  C19  C18  120.66  3.000
 2OI  H17  C19  C20  120.30  3.000
 2OI  C18  C19  C20  119.05  3.000
 2OI  C23  O22  C10  118.15  3.000
 2OI  H6   C14  H5   106.10  3.000
 2OI  H6   C14  C13  108.66  3.000
 2OI  H5   C14  C13  110.03  3.000
 2OI  H6   C14  C15  109.38  3.000
 2OI  H5   C14  C15  109.61  3.000
 2OI  C13  C14  C15  112.83  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
 2OI  CONST_01  C13  C4   C3   C2    180.00   0.0  0
 2OI  CONST_02  N12  C11  C3   C2    180.00   0.0  0
 2OI  CONST_03  C10  C11  C3   C2      0.00   0.0  0
 2OI  CONST_04  C10  C9   C8   C2      0.00   0.0  0
 2OI  CONST_05  C11  N12  C13  C4      0.00   0.0  0
 2OI  CONST_06  N12  C11  C3   C4      0.00   0.0  0
 2OI  CONST_07  C10  C11  C3   C4    180.00   0.0  0
 2OI  CONST_08  C8   C2   C3   C4    180.00   0.0  0
 2OI  CONST_09  C11  C3   C2   C8      0.00   0.0  0
 2OI  CONST_10  C11  C10  C9   C8      0.00   0.0  0
 2OI  CONST_11  N12  C11  C10  C9    180.00   0.0  0
 2OI  CONST_12  C3   C11  C10  C9      0.00   0.0  0
 2OI  CONST_13  C3   C2   C8   C9      0.00   0.0  0
 2OI  CONST_14  C13  N12  C11  C10   180.00   0.0  0
 2OI  CONST_15  C13  C4   C3   C11     0.00   0.0  0
 2OI  CONST_16  C18  C19  C20  C15     0.00   0.0  0
 2OI  CONST_17  C18  C17  C16  C15     0.00   0.0  0
 2OI  CONST_18  C19  C18  C17  C16     0.00   0.0  0
 2OI  CONST_19  C19  C20  C15  C16     0.00   0.0  0
 2OI  CONST_20  C20  C19  C18  C17     0.00   0.0  0
 2OI  CONST_21  C20  C15  C16  C17     0.00   0.0  0
 2OI  CONST_22  N12  C13  C4   C3      0.00   0.0  0
 2OI  CONST_23  C13  N12  C11  C3      0.00   0.0  0
 2OI  CONST_24  C6   N7   C1   C2      0.00   0.0  0
 2OI  CONST_25  O22  C10  C9   C8    180.00   0.0  0
 2OI  CONST_26  C14  C13  N12  C11   180.00   0.0  0
 2OI  CONST_27  C19  C20  C15  C14   180.00   0.0  0
 2OI  CONST_28  C17  C16  C15  C14   180.00   0.0  0
 2OI  CONST_29  C5   C4   C13  C14     0.00   0.0  0
 2OI  CONST_30  C3   C4   C13  C14   180.00   0.0  0
 2OI  CONST_31  CL   C18  C17  C16   180.00   0.0  0
 2OI  CONST_32  CL   C18  C19  C20   180.00   0.0  0
 2OI  CONST_33  O22  C10  C11  C3    180.00   0.0  0
 2OI  CONST_34  O22  C10  C11  N12     0.00   0.0  0
 2OI  CONST_35  O21  C1   N7   C6    180.00   0.0  0
 2OI  CONST_36  H3   C8   C2   C1      0.00   0.0  0
 2OI  CONST_37  H4   C9   C8   C2    180.00   0.0  0
 2OI  CONST_38  H16  N12  C13  C4    180.00   0.0  0
 2OI  CONST_39  H16  N12  C11  C10     0.00   0.0  0
 2OI  CONST_40  H3   C8   C9   C10   180.00   0.0  0
 2OI  CONST_41  H4   C9   C10  C11   180.00   0.0  0
 2OI  CONST_42  H17  C19  C20  C15   180.00   0.0  0
 2OI  CONST_43  H8   C17  C16  C15   180.00   0.0  0
 2OI  CONST_44  H9   C20  C15  C16   180.00   0.0  0
 2OI  CONST_45  H17  C19  C18  C17   180.00   0.0  0
 2OI  CONST_46  H7   C16  C15  C20   180.00   0.0  0
 2OI  CONST_47  H16  N12  C11  C3    180.00   0.0  0
 2OI  CONST_48  H3   C8   C2   C3    180.00   0.0  0
 2OI  CONST_49  H9   C20  C19  C18   180.00   0.0  0
 2OI  CONST_50  H7   C16  C17  C18   180.00   0.0  0
 2OI  CONST_51  H8   C17  C18  C19   180.00   0.0  0
 2OI  CONST_52  H15  N7   C1   C2    180.00   0.0  0
 2OI  CONST_53  H15  N7   C1   O21     0.00   0.0  0
 2OI  Var_01    C5   C6   N7   C1    -71.53  30.0  1
 2OI  Var_02    N7   C6   C5   C4     74.31  30.0  1
 2OI  Var_03    C13  C4   C5   C6    143.58  30.0  1
 2OI  Var_04    C3   C4   C5   C6    -30.98  30.0  1
 2OI  Var_05    N7   C1   C2   C8   -163.44  30.0  1
 2OI  Var_06    N7   C1   C2   C3     20.75  30.0  1
 2OI  Var_07    C15  C14  C13  C4   -109.32  30.0  1
 2OI  Var_08    O21  C1   C2   C8     17.60  30.0  1
 2OI  Var_09    N12  C13  C14  C15    68.47  30.0  2
 2OI  Var_10    C13  C14  C15  C16    57.47  30.0  2
 2OI  Var_11    C13  C14  C15  C20  -123.38  30.0  2
 2OI  Var_12    C3   C2   C1   O21  -158.22  30.0  1
 2OI  Var_13    H1   C6   N7   C1    167.98  30.0  1
 2OI  Var_14    H2   C6   N7   C1     52.54  30.0  1
 2OI  Var_15    H1   C6   C5   C4   -167.25  30.0  1
 2OI  Var_16    H2   C6   C5   C4    -50.31  30.0  1
 2OI  Var_17    H13  C5   C4   C3     90.64  30.0  1
 2OI  Var_18    H14  C5   C4   C3   -150.78  30.0  1
 2OI  Var_19    H15  N7   C6   C5    119.14  30.0  1
 2OI  Var_20    H13  C5   C6   N7    -49.28  30.0  1
 2OI  Var_21    H14  C5   C6   N7   -164.79  30.0  1
 2OI  Var_22    H13  C5   C4   C13   -94.80  30.0  1
 2OI  Var_23    H14  C5   C4   C13    23.78  30.0  1
 2OI  Var_24    C23  O22  C10  C9     -0.82  30.0  3
 2OI  Var_25    C23  O22  C10  C11   179.15  30.0  3
 2OI  Var_26    H5   C14  C13  C4    127.92  30.0  1
 2OI  Var_27    H6   C14  C13  C4     12.16  30.0  1
 2OI  Var_28    H5   C14  C15  C16  -179.53  30.0  2
 2OI  Var_29    H6   C14  C15  C16   -63.59  30.0  2
 2OI  Var_30    H5   C14  C15  C20    -0.38  30.0  2
 2OI  Var_31    H6   C14  C15  C20   115.56  30.0  2
 2OI  Var_32    H5   C14  C13  N12   -54.29  30.0  1
 2OI  Var_33    H6   C14  C13  N12  -170.06  30.0  1
 2OI  Var_34    H10  C23  O22  C10  -179.45  30.0  3
 2OI  Var_35    H11  C23  O22  C10   -60.59  30.0  3
 2OI  Var_36    H12  C23  O22  C10    61.68  30.0  3

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
 2OI  plan-1  C15  0.020
 2OI  plan-1  C16  0.020
 2OI  plan-1  C17  0.020
 2OI  plan-1  C20  0.020
 2OI  plan-1  C18  0.020
 2OI  plan-1  C19  0.020
 2OI  plan-1  CL   0.020
 2OI  plan-1  H7   0.020
 2OI  plan-1  H8   0.020
 2OI  plan-1  H9   0.020
 2OI  plan-1  H17  0.020
 2OI  plan-1  C14  0.020
 2OI  plan-2  C1   0.020
 2OI  plan-2  C2   0.020
 2OI  plan-2  C4   0.020
 2OI  plan-2  C8   0.020
 2OI  plan-2  C9   0.020
 2OI  plan-2  C10  0.020
 2OI  plan-2  C11  0.020
 2OI  plan-2  C3   0.020
 2OI  plan-2  C5   0.020
 2OI  plan-2  N12  0.020
 2OI  plan-2  C13  0.020
 2OI  plan-2  O22  0.020
 2OI  plan-2  H3   0.020
 2OI  plan-2  H4   0.020
 2OI  plan-2  H16  0.020
 2OI  plan-2  C14  0.020
 2OI  plan-3  C1   0.020
 2OI  plan-3  C2   0.020
 2OI  plan-3  C6   0.020
 2OI  plan-3  O21  0.020
 2OI  plan-3  N7   0.020
 2OI  plan-3  H15  0.020

