# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 20:26:57 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 5-[3-[[(1R,4S,5S)-5-bicyclo[2.2.1]heptanyl]oxy]-4-methoxy-phenyl]-1,3-diazinan-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1O[C@H]2C[C@@H]3CC[C@H]2C3)C4CNC(=O)NC4
#
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
 0CP  0CP  5-[3-[[(1R,4S,5S)-5-bicyclo[2.2.1]heptanyl]oxy]-4-methoxy-phenyl]-1,3-diazinan-2-one  ligand  47  23  .  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_0CP
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
 0CP  C1    C  CH3   0  -0.436   1.8081   4.5054  -0.0644
 0CP  N1    N  NH1   0  -0.658  -4.7150  -0.8908   1.0599
 0CP  O1    O  O2    0  -0.463   1.9288   3.1088   0.1066
 0CP  C2    C  CR6   0   0.279   0.8033   2.3685   0.0857
 0CP  N2    N  NH1   0  -0.658  -4.4884  -1.1239  -1.2175
 0CP  O2    O  O2    0  -0.481   2.2536   0.5779   0.4273
 0CP  C3    C  CR6   0   0.330   0.9820   0.9803   0.2562
 0CP  C4    C  CH1   0   0.035   2.5378  -0.8125   0.5321
 0CP  C5    C  CH2   0  -0.471   2.3476  -1.5665  -0.8098
 0CP  C6    C  CH1   0  -0.261   3.7711  -2.0184  -1.1695
 0CP  C7    C  CH2   0  -0.437   4.1608  -3.1567  -0.2192
 0CP  C8    C  CH2   0  -0.451   4.3028  -2.4284   1.1424
 0CP  C9    C  CH1   0  -0.290   4.0377  -0.9556   0.7915
 0CP  C10   C  CH2   0  -0.436   4.6142  -0.8601  -0.6258
 0CP  C11   C  CR16  0  -0.451  -0.1256   0.1475   0.2456
 0CP  C12   C  CR6   0   0.185  -1.4172   0.6515   0.0669
 0CP  C13   C  CR16  0  -0.340  -1.5789   2.0166  -0.0963
 0CP  C14   C  CR16  0  -0.369  -0.4764   2.8692  -0.0859
 0CP  C15   C  CH1   0  -0.418  -2.5858  -0.2972   0.0499
 0CP  C16   C  CH2   0  -0.224  -3.5807  -0.0017   1.1667
 0CP  C17   C  C     0   0.634  -5.2142  -1.3813  -0.1014
 0CP  C18   C  CH2   0  -0.223  -3.3334  -0.2570  -1.2786
 0CP  H1    H  HCH3  0   0.226   1.3709   4.7632  -1.0331
 0CP  H1A   H  HCH3  0   0.226   1.2052   4.9639   0.7241
 0CP  H1B   H  HCH3  0   0.258   2.8155   4.9114  -0.0154
 0CP  HN2   H  HNH1  0   0.395  -4.8868  -1.4464  -2.0832
 0CP  H4    H  HCH1  0   0.243   1.9463  -1.2419   1.3495
 0CP  H5    H  HCH2  0   0.240   1.6565  -2.4072  -0.7235
 0CP  H5A   H  HCH2  0   0.254   1.9411  -0.8966  -1.5710
 0CP  H6    H  HCH1  0   0.229   3.8991  -2.2569  -2.2256
 0CP  H7    H  HCH2  0   0.229   3.4118  -3.9503  -0.1978
 0CP  H7A   H  HCH2  0   0.234   5.1057  -3.6103  -0.5242
 0CP  H8    H  HCH2  0   0.233   3.6074  -2.8035   1.8968
 0CP  H8A   H  HCH2  0   0.243   5.3075  -2.5431   1.5509
 0CP  H9    H  HCH1  0   0.237   4.4163  -0.2532   1.5351
 0CP  H10   H  HCH2  0   0.236   5.6888  -1.0532  -0.6640
 0CP  H10A  H  HCH2  0   0.238   4.4156   0.0957  -1.1148
 0CP  H11   H  HCR6  0   0.274  -0.0056  -0.9207   0.3734
 0CP  H13   H  HCR6  0   0.249  -2.5626   2.4468  -0.2384
 0CP  H14   H  HCR6  0   0.280  -0.6396   3.9304  -0.2165
 0CP  H15   H  HCH1  0   0.269  -2.2088  -1.3143   0.1946
 0CP  H16   H  HCH2  0   0.229  -3.8927   1.0478   1.1193
 0CP  H16A  H  HCH2  0   0.258  -3.1108  -0.1536   2.1390
 0CP  H18   H  HCH2  0   0.258  -2.6846  -0.6000  -2.0851
 0CP  H18A  H  HCH2  0   0.229  -3.6239   0.7737  -1.5123
 0CP  HN1   H  HNH1  0   0.396  -5.2811  -1.0388   1.8788
 0CP  O3    O  O     0  -0.559  -6.2461  -2.0519  -0.1361

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
 0CP  C1   O1    single    1.412  0.020  1.412
 0CP  N1   C16   single    1.445  0.020  1.445
 0CP  N1   C17   single    1.356  0.020  1.356
 0CP  O1   C2    single    1.347  0.020  1.347
 0CP  C2   C3    aromatic  1.410  0.020  1.410
 0CP  C2   C14   aromatic  1.385  0.020  1.385
 0CP  N2   C17   single    1.356  0.020  1.356
 0CP  N2   C18   single    1.445  0.020  1.445
 0CP  O2   C3    single    1.345  0.020  1.345
 0CP  O2   C4    single    1.423  0.020  1.423
 0CP  C3   C11   aromatic  1.386  0.020  1.386
 0CP  O3   C17   double    1.231  0.020  1.231
 0CP  C4   C5    single    1.551  0.020  1.551
 0CP  C4   C9    single    1.529  0.020  1.529
 0CP  C5   C6    single    1.536  0.020  1.536
 0CP  C6   C7    single    1.533  0.020  1.533
 0CP  C6   C10   single    1.532  0.020  1.532
 0CP  C7   C8    single    1.551  0.020  1.551
 0CP  C8   C9    single    1.537  0.020  1.537
 0CP  C9   C10   single    1.533  0.020  1.533
 0CP  C11  C12   aromatic  1.398  0.020  1.398
 0CP  C12  C13   aromatic  1.384  0.020  1.384
 0CP  C12  C15   single    1.505  0.020  1.505
 0CP  C13  C14   aromatic  1.394  0.020  1.394
 0CP  C15  C16   single    1.525  0.020  1.525
 0CP  C15  C18   single    1.525  0.020  1.525
 0CP  C1   H1    single    0.970  0.020  1.090
 0CP  C1   H1A   single    0.970  0.020  1.090
 0CP  C1   H1B   single    0.970  0.020  1.090
 0CP  N1   HN1   single    0.860  0.020  1.020
 0CP  N2   HN2   single    0.860  0.020  1.020
 0CP  C4   H4    single    0.970  0.020  1.090
 0CP  C5   H5    single    0.970  0.020  1.090
 0CP  C5   H5A   single    0.970  0.020  1.090
 0CP  C6   H6    single    0.970  0.020  1.090
 0CP  C7   H7    single    0.970  0.020  1.090
 0CP  C7   H7A   single    0.970  0.020  1.090
 0CP  C8   H8    single    0.970  0.020  1.090
 0CP  C8   H8A   single    0.970  0.020  1.090
 0CP  C9   H9    single    0.970  0.020  1.090
 0CP  C10  H10   single    0.970  0.020  1.090
 0CP  C10  H10A  single    0.970  0.020  1.090
 0CP  C11  H11   single    0.930  0.020  1.080
 0CP  C13  H13   single    0.930  0.020  1.080
 0CP  C14  H14   single    0.930  0.020  1.080
 0CP  C15  H15   single    0.970  0.020  1.090
 0CP  C16  H16   single    0.970  0.020  1.090
 0CP  C16  H16A  single    0.970  0.020  1.090
 0CP  C18  H18   single    0.970  0.020  1.090
 0CP  C18  H18A  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
 0CP  H1B   C1   H1A  108.78  3.000
 0CP  H1B   C1   H1   108.80  3.000
 0CP  H1A   C1   H1   108.64  3.000
 0CP  H1B   C1   O1   106.54  3.000
 0CP  H1A   C1   O1   111.99  3.000
 0CP  H1    C1   O1   112.00  3.000
 0CP  HN1   N1   C17  115.89  3.000
 0CP  HN1   N1   C16  118.15  3.000
 0CP  C17   N1   C16  125.09  3.000
 0CP  C2    O1   C1   118.04  3.000
 0CP  C14   C2   C3   119.21  3.000
 0CP  C14   C2   O1   125.12  3.000
 0CP  C3    C2   O1   115.67  3.000
 0CP  HN2   N2   C18  118.19  3.000
 0CP  HN2   N2   C17  115.81  3.000
 0CP  C18   N2   C17  125.19  3.000
 0CP  C4    O2   C3   119.38  3.000
 0CP  C11   C3   O2   125.23  3.000
 0CP  C11   C3   C2   119.31  3.000
 0CP  O2    C3   C2   115.46  3.000
 0CP  H4    C4   C9   111.47  3.000
 0CP  H4    C4   C5   112.86  3.000
 0CP  C9    C4   C5   102.81  3.000
 0CP  H4    C4   O2   109.25  3.000
 0CP  C9    C4   O2   107.45  3.000
 0CP  C5    C4   O2   112.75  3.000
 0CP  H5A   C5   H5   106.96  3.000
 0CP  H5A   C5   C6   111.22  3.000
 0CP  H5    C5   C6   112.25  3.000
 0CP  H5A   C5   C4   110.51  3.000
 0CP  H5    C5   C4   112.56  3.000
 0CP  C6    C5   C4   103.41  3.000
 0CP  H6    C6   C10  116.39  3.000
 0CP  H6    C6   C7   114.09  3.000
 0CP  C10   C6   C7   101.62  3.000
 0CP  H6    C6   C5   113.58  3.000
 0CP  C10   C6   C5   101.79  3.000
 0CP  C7    C6   C5   107.98  3.000
 0CP  H7A   C7   H7   107.29  3.000
 0CP  H7A   C7   C8   111.17  3.000
 0CP  H7    C7   C8   112.78  3.000
 0CP  H7A   C7   C6   110.82  3.000
 0CP  H7    C7   C6   112.19  3.000
 0CP  C8    C7   C6   102.64  3.000
 0CP  H8A   C8   H8   106.96  3.000
 0CP  H8A   C8   C9   110.19  3.000
 0CP  H8    C8   C9   112.14  3.000
 0CP  H8A   C8   C7   111.34  3.000
 0CP  H8    C8   C7   112.76  3.000
 0CP  C9    C8   C7   103.52  3.000
 0CP  H9    C9   C10  117.36  3.000
 0CP  H9    C9   C8   113.67  3.000
 0CP  C10   C9   C8   101.88  3.000
 0CP  H9    C9   C4   113.32  3.000
 0CP  C10   C9   C4   101.90  3.000
 0CP  C8    C9   C4   107.31  3.000
 0CP  H10A  C10  H10  108.54  3.000
 0CP  H10A  C10  C9   113.60  3.000
 0CP  H10   C10  C9   113.03  3.000
 0CP  H10A  C10  C6   113.75  3.000
 0CP  H10   C10  C6   113.27  3.000
 0CP  C9    C10  C6    94.25  3.000
 0CP  H11   C11  C12  118.25  3.000
 0CP  H11   C11  C3   120.23  3.000
 0CP  C12   C11  C3   121.52  3.000
 0CP  C15   C12  C13  121.97  3.000
 0CP  C15   C12  C11  119.44  3.000
 0CP  C13   C12  C11  118.59  3.000
 0CP  H13   C13  C14  118.46  3.000
 0CP  H13   C13  C12  120.88  3.000
 0CP  C14   C13  C12  120.66  3.000
 0CP  H14   C14  C13  118.68  3.000
 0CP  H14   C14  C2   120.61  3.000
 0CP  C13   C14  C2   120.71  3.000
 0CP  H15   C15  C18  107.97  3.000
 0CP  H15   C15  C16  107.95  3.000
 0CP  C18   C15  C16  108.25  3.000
 0CP  H15   C15  C12  108.47  3.000
 0CP  C18   C15  C12  111.95  3.000
 0CP  C16   C15  C12  112.09  3.000
 0CP  H16A  C16  H16  107.14  3.000
 0CP  H16A  C16  C15  110.18  3.000
 0CP  H16   C16  C15  109.86  3.000
 0CP  H16A  C16  N1   108.56  3.000
 0CP  H16   C16  N1   111.25  3.000
 0CP  C15   C16  N1   109.80  3.000
 0CP  O3    C17  N2   121.92  3.000
 0CP  O3    C17  N1   121.99  3.000
 0CP  N2    C17  N1   116.05  3.000
 0CP  H18A  C18  H18  107.20  3.000
 0CP  H18A  C18  C15  109.91  3.000
 0CP  H18   C18  C15  110.14  3.000
 0CP  H18A  C18  N2   111.18  3.000
 0CP  H18   C18  N2   108.54  3.000
 0CP  C15   C18  N2   109.82  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
 0CP  CONST_01  C12  C11  C3   C2     0.00   0.0  0
 0CP  CONST_02  C12  C13  C14  C2     0.00   0.0  0
 0CP  CONST_03  C13  C14  C2   C3     0.00   0.0  0
 0CP  CONST_04  C13  C12  C11  C3     0.00   0.0  0
 0CP  CONST_05  C14  C2   C3   C11    0.00   0.0  0
 0CP  CONST_06  C14  C13  C12  C11    0.00   0.0  0
 0CP  CONST_07  C15  C12  C11  C3   180.00   0.0  0
 0CP  CONST_08  C15  C12  C13  C14  180.00   0.0  0
 0CP  CONST_09  C18  N2   C17  N1     0.00   0.0  0
 0CP  CONST_10  C16  N1   C17  N2     0.00   0.0  0
 0CP  CONST_11  C11  C3   C2   O1   180.00   0.0  0
 0CP  CONST_12  C13  C14  C2   O1   180.00   0.0  0
 0CP  CONST_13  C14  C2   C3   O2   180.00   0.0  0
 0CP  CONST_14  C12  C11  C3   O2   180.00   0.0  0
 0CP  CONST_15  C16  N1   C17  O3   180.00   0.0  0
 0CP  CONST_16  C18  N2   C17  O3   180.00   0.0  0
 0CP  CONST_17  H11  C11  C3   C2   180.00   0.0  0
 0CP  CONST_18  H13  C13  C14  C2   180.00   0.0  0
 0CP  CONST_19  H14  C14  C2   C3   180.00   0.0  0
 0CP  CONST_20  HN2  N2   C17  N1   180.00   0.0  0
 0CP  CONST_21  HN1  N1   C17  N2   180.00   0.0  0
 0CP  Var_01    C9   C8   C7   C6    -2.39  30.0  1
 0CP  Var_02    C17  N1   C16  C15  -32.12  30.0  1
 0CP  Var_03    C17  N2   C18  C15   31.56  30.0  1
 0CP  Var_04    C11  C3   O2   C4     3.92  30.0  2
 0CP  Var_05    C3   C2   O1   C1   179.78  30.0  2
 0CP  Var_06    H1   C1   O1   C2   -61.20  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
 0CP  chir_01  C4   O2   C5   C9   negativ
 0CP  chir_02  C6   C10  C7   C5   negativ
 0CP  chir_03  C9   C4   C8   C10  negativ
 0CP  chir_04  C15  C12  C16  C18  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
 0CP  plan-1  O1   0.020
 0CP  plan-1  C2   0.020
 0CP  plan-1  O2   0.020
 0CP  plan-1  C3   0.020
 0CP  plan-1  C11  0.020
 0CP  plan-1  C12  0.020
 0CP  plan-1  C13  0.020
 0CP  plan-1  C14  0.020
 0CP  plan-1  C15  0.020
 0CP  plan-1  H11  0.020
 0CP  plan-1  H13  0.020
 0CP  plan-1  H14  0.020
 0CP  plan-2  N1   0.020
 0CP  plan-2  N2   0.020
 0CP  plan-2  C16  0.020
 0CP  plan-2  C17  0.020
 0CP  plan-2  C18  0.020
 0CP  plan-2  HN2  0.020
 0CP  plan-2  HN1  0.020
 0CP  plan-2  O3   0.020

