# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 05:07:39 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 6-azaspiro[3.4]octan-6-yl-[2,4-bis(chloranyl)-6-oxidanyl-phenyl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(Cl)cc(Cl)c1C(=O)N2CCC3(CCC3)C2
#
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
 H4T  H4T  6-azaspiro[3.4]octan-6-yl-[2,4-bis(chloranyl)-6-oxidanyl-phenyl]methanone  ligand  34  19  .  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_H4T
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
 H4T  C2   C   CR6   0   0.373   1.3116   1.1244  -0.7766
 H4T  C3   C   CR16  0  -0.337   2.5829   1.4951  -0.3511
 H4T  C4   C   CR6   0  -0.036   3.3757   0.5534   0.2815
 H4T  C6   C   CR16  0  -0.205   2.9454  -0.7427   0.5099
 H4T  C7   C   CR6   0  -0.059   1.6747  -1.0779   0.0697
 H4T  C15  C   C     0  -0.101  -3.7353   0.0634   0.3603
 H4T  C16  C   C     0  -0.434  -5.2198  -0.2977   0.5292
 H4T  C17  C   C     0  -0.453  -5.5310   1.1992   0.7208
 H4T  C18  C   C     0  -0.430  -4.1631   1.5268   0.0924
 H4T  C19  C   CH2   0  -0.239  -2.9073  -0.6432  -0.6997
 H4T  O1   O   OH1   0  -0.611   0.4776   1.9728  -1.3916
 H4T  CL5  CL  CL    0  -0.106   4.9556   1.0126   0.8103
 H4T  CL8  CL  CL    0  -0.098   1.0901  -2.6800   0.3561
 H4T  C9   C   CR6   0  -0.112   0.8428  -0.1731  -0.5666
 H4T  C10  C   C     0   0.517  -0.5006  -0.5713  -1.1096
 H4T  O11  O   O     0  -0.482  -0.5976  -1.0411  -2.2351
 H4T  N12  N   NT    0  -0.443  -1.5343  -0.3666  -0.2960
 H4T  C13  C   CH2   0  -0.264  -1.4576   0.1658   1.0639
 H4T  C14  C   CH2   0  -0.463  -2.8612  -0.0811   1.6018
 H4T  H1   H   HCR6  0   0.303   2.9464   2.5019  -0.5140
 H4T  H2   H   HCR6  0   0.302   3.5726  -1.4655   1.0110
 H4T  H3   H   H     0   0.234  -5.6475  -0.6829  -0.3989
 H4T  H4   H   H     0   0.232  -5.4742  -0.9844   1.3384
 H4T  H5   H   H     0   0.232  -6.4160   1.5927   0.2217
 H4T  H6   H   H     0   0.230  -5.5799   1.4780   1.7739
 H4T  H7   H   H     0   0.232  -3.5686   2.3174   0.5553
 H4T  H8   H   H     0   0.231  -4.2448   1.7344  -0.9761
 H4T  H9   H   HCH2  0   0.245  -3.1005  -1.7216  -0.6950
 H4T  H10  H   HCH2  0   0.250  -3.1064  -0.2720  -1.7060
 H4T  H11  H   HOH1  0   0.487   0.8733   2.8487  -1.4744
 H4T  H12  H   HCH2  0   0.257  -0.6932  -0.3406   1.6531
 H4T  H13  H   HCH2  0   0.248  -1.2205   1.2329   1.0479
 H4T  H14  H   HCH2  0   0.256  -3.1192   0.6112   2.4037
 H4T  H15  H   HCH2  0   0.247  -2.9391  -1.0977   1.9980

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
 H4T  CL5  C4   single    1.728  0.020  1.728
 H4T  C3   C4   aromatic  1.384  0.020  1.384
 H4T  C3   C2   aromatic  1.391  0.020  1.391
 H4T  C4   C6   aromatic  1.385  0.020  1.385
 H4T  O1   C2   single    1.339  0.020  1.339
 H4T  C2   C9   aromatic  1.395  0.020  1.395
 H4T  C6   C7   aromatic  1.386  0.020  1.386
 H4T  C16  C17  single    1.541  0.020  1.541
 H4T  C16  C15  single    1.537  0.020  1.537
 H4T  C19  C15  single    1.519  0.020  1.519
 H4T  C19  N12  single    1.458  0.020  1.458
 H4T  C9   C7   aromatic  1.384  0.020  1.384
 H4T  C9   C10  single    1.503  0.020  1.503
 H4T  C17  C18  single    1.541  0.020  1.541
 H4T  C7   CL8  single    1.729  0.020  1.729
 H4T  C15  C14  single    1.525  0.020  1.525
 H4T  C15  C18  single    1.548  0.020  1.548
 H4T  N12  C10  single    1.331  0.020  1.331
 H4T  N12  C13  single    1.462  0.020  1.462
 H4T  C10  O11  double    1.223  0.020  1.223
 H4T  C14  C13  single    1.523  0.020  1.523
 H4T  C3   H1   single    0.930  0.020  1.080
 H4T  C6   H2   single    0.930  0.020  1.080
 H4T  C16  H3   single    0.970  0.020  1.090
 H4T  C16  H4   single    0.970  0.020  1.090
 H4T  C17  H5   single    0.970  0.020  1.090
 H4T  C17  H6   single    0.970  0.020  1.090
 H4T  C18  H7   single    0.970  0.020  1.090
 H4T  C18  H8   single    0.970  0.020  1.090
 H4T  C19  H9   single    0.970  0.020  1.090
 H4T  C19  H10  single    0.970  0.020  1.090
 H4T  O1   H11  single    0.850  0.020  0.980
 H4T  C13  H12  single    0.970  0.020  1.090
 H4T  C13  H13  single    0.970  0.020  1.090
 H4T  C14  H14  single    0.970  0.020  1.090
 H4T  C14  H15  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
 H4T  C9   C2   O1   116.67  3.000
 H4T  C9   C2   C3   120.58  3.000
 H4T  O1   C2   C3   122.74  3.000
 H4T  H1   C3   C4   120.61  3.000
 H4T  H1   C3   C2   120.57  3.000
 H4T  C4   C3   C2   118.82  3.000
 H4T  CL5  C4   C6   118.84  3.000
 H4T  C6   C4   C3   122.30  3.000
 H4T  CL5  C4   C3   118.86  3.000
 H4T  H2   C6   C7   121.19  3.000
 H4T  H2   C6   C4   121.49  3.000
 H4T  C7   C6   C4   117.32  3.000
 H4T  C9   C7   CL8  118.59  3.000
 H4T  CL8  C7   C6   118.78  3.000
 H4T  C9   C7   C6   122.62  3.000
 H4T  C14  C15  C19  102.22  3.000
 H4T  C14  C15  C18  112.88  3.000
 H4T  C19  C15  C18  118.00  3.000
 H4T  C18  C15  C16   88.52  3.000
 H4T  C14  C15  C16  116.22  3.000
 H4T  C19  C15  C16  119.58  3.000
 H4T  H4   C16  H3   108.47  3.000
 H4T  H4   C16  C17  118.16  3.000
 H4T  H3   C16  C17  111.67  3.000
 H4T  H4   C16  C15  117.02  3.000
 H4T  H3   C16  C15  111.58  3.000
 H4T  C17  C16  C15   88.89  3.000
 H4T  H6   C17  H5   108.28  3.000
 H4T  H6   C17  C18  112.29  3.000
 H4T  H5   C17  C18  117.23  3.000
 H4T  H6   C17  C16  112.18  3.000
 H4T  H5   C17  C16  117.25  3.000
 H4T  C18  C17  C16   88.65  3.000
 H4T  H8   C18  H7   108.54  3.000
 H4T  H8   C18  C17  111.92  3.000
 H4T  H7   C18  C17  117.67  3.000
 H4T  H8   C18  C15  111.71  3.000
 H4T  H7   C18  C15  117.42  3.000
 H4T  C17  C18  C15   88.50  3.000
 H4T  H10  C19  H9   107.87  3.000
 H4T  H10  C19  N12  111.27  3.000
 H4T  H9   C19  N12  110.59  3.000
 H4T  H10  C19  C15  112.70  3.000
 H4T  H9   C19  C15  111.02  3.000
 H4T  N12  C19  C15  103.40  3.000
 H4T  H11  O1   C2   111.05  3.000
 H4T  C10  C9   C7   122.02  3.000
 H4T  C10  C9   C2   119.49  3.000
 H4T  C7   C9   C2   118.36  3.000
 H4T  N12  C10  O11  124.03  3.000
 H4T  O11  C10  C9   120.34  3.000
 H4T  N12  C10  C9   115.63  3.000
 H4T  C13  N12  C10  125.70  3.000
 H4T  C13  N12  C19  112.09  3.000
 H4T  C10  N12  C19  122.20  3.000
 H4T  H13  C13  H12  108.02  3.000
 H4T  H13  C13  C14  111.30  3.000
 H4T  H12  C13  C14  112.34  3.000
 H4T  H13  C13  N12  110.68  3.000
 H4T  H12  C13  N12  111.73  3.000
 H4T  C14  C13  N12  102.77  3.000
 H4T  H15  C14  H14  107.87  3.000
 H4T  H15  C14  C13  110.13  3.000
 H4T  H14  C14  C13  112.01  3.000
 H4T  H15  C14  C15  110.00  3.000
 H4T  H14  C14  C15  113.76  3.000
 H4T  C13  C14  C15  103.02  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
 H4T  CONST_01  C6   C4   C3   C2      0.00   0.0  0
 H4T  CONST_02  C6   C7   C9   C2      0.00   0.0  0
 H4T  CONST_03  C7   C6   C4   C3      0.00   0.0  0
 H4T  CONST_04  C7   C9   C2   C3      0.00   0.0  0
 H4T  CONST_05  C9   C2   C3   C4      0.00   0.0  0
 H4T  CONST_06  C9   C7   C6   C4      0.00   0.0  0
 H4T  CONST_07  CL5  C4   C3   C2    180.00   0.0  0
 H4T  CONST_08  CL8  C7   C9   C2    180.00   0.0  0
 H4T  CONST_09  C10  C9   C2   C3    180.00   0.0  0
 H4T  CONST_10  O1   C2   C3   C4    180.00   0.0  0
 H4T  CONST_11  CL8  C7   C6   C4    180.00   0.0  0
 H4T  CONST_12  C10  C9   C7   C6    180.00   0.0  0
 H4T  CONST_13  CL5  C4   C6   C7    180.00   0.0  0
 H4T  CONST_14  O1   C2   C9   C7    180.00   0.0  0
 H4T  CONST_15  C9   C10  N12  C19   180.00   0.0  0
 H4T  CONST_16  C13  N12  C10  C9      0.00   0.0  0
 H4T  CONST_17  H2   C6   C4   C3    180.00   0.0  0
 H4T  CONST_18  H1   C3   C4   C6    180.00   0.0  0
 H4T  CONST_19  O11  C10  N12  C19     0.00   0.0  0
 H4T  CONST_20  C13  N12  C10  O11   180.00   0.0  0
 H4T  Var_01    C18  C17  C16  C15    17.60  30.0  1
 H4T  Var_02    C13  N12  C19  C15    13.44  30.0  1
 H4T  Var_03    N12  C13  C14  C15   -32.40  30.0  1
 H4T  Var_04    N12  C19  C15  C16  -163.11  30.0  1
 H4T  Var_05    C13  C14  C15  C16   172.85  30.0  1
 H4T  Var_06    C19  C15  C16  C17  -139.20  30.0  3
 H4T  Var_07    C14  C13  N12  C19    11.98  30.0  1
 H4T  Var_08    N12  C10  C9   C2    -89.78  30.0  2

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
 H4T  plan-1  C19  0.020
 H4T  plan-1  C9   0.020
 H4T  plan-1  C10  0.020
 H4T  plan-1  O11  0.020
 H4T  plan-1  N12  0.020
 H4T  plan-1  C13  0.020
 H4T  plan-2  C2   0.020
 H4T  plan-2  C3   0.020
 H4T  plan-2  C4   0.020
 H4T  plan-2  C6   0.020
 H4T  plan-2  C7   0.020
 H4T  plan-2  O1   0.020
 H4T  plan-2  CL5  0.020
 H4T  plan-2  CL8  0.020
 H4T  plan-2  C9   0.020
 H4T  plan-2  C10  0.020
 H4T  plan-2  H1   0.020
 H4T  plan-2  H2   0.020

