# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 18:12:35 2022
#   Inital geometry file: a 131 line input string
#   Ligand name: 5-[bis(fluoranyl)methoxy]-2-[(4-chlorophenyl)methyl]-10-(3-methoxypropyl)-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: COCCCN1CCc2c(Cc3ccc(Cl)cc3)[nH]c4c(OC(F)F)ccc(C1=O)c24
#
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
 2VI  2VI  "5-[bis(fluoranyl)methoxy]-2-[(4-chlorophenyl)methyl]-10-(3-methoxypropyl)-3,10-diazatricyclo[6.4.1.0^{4,13}]trideca-1,4(13),5,7-tetraen-9-one"
  ligand  54  31  .  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_2VI
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
 2VI  C1   C   CR16  0  -0.301  -35.6039  29.5705  -36.9615
 2VI  C2   C   CR16  0  -0.389  -36.9992  29.4806  -37.0038
 2VI  C4   C   CR56  0   0.270  -36.9105  29.8641  -39.3494
 2VI  C6   C   CR6   0  -0.143  -34.8312  29.8343  -38.0810
 2VI  C8   C   CR5   0   0.336  -36.2201  30.3457  -41.4104
 2VI  C9   C   CR5   0  -0.082  -35.0921  30.3288  -40.6310
 2VI  C11  C   C     0   0.526  -33.3480  29.7751  -37.9134
 2VI  C14  C   CH2   0  -0.513  -33.7016  30.7205  -40.9979
 2VI  C16  C   CR6   0   0.128  -37.3255  31.8034  -43.1030
 2VI  C17  C   CR16  0  -0.332  -38.5059  31.6193  -43.8120
 2VI  C20  C   CR16  0  -0.196  -37.9041  34.1344  -42.8085
 2VI  C24  C   CH2   0  -0.461  -30.4307  31.4418  -37.9736
 2VI  C25  C   CH2   0  -0.139  -30.8816  31.7014  -36.5498
 2VI  C27  C   CH2   0  -0.609  -36.3743  30.6570  -42.8604
 2VI  C19  C   CR6   0  -0.055  -39.0776  33.9212  -43.5183
 2VI  C18  C   CR16  0  -0.192  -39.3878  32.6712  -44.0246
 2VI  C21  C   CR16  0  -0.277  -37.0383  33.0726  -42.6049
 2VI  N7   N   NR15  0  -0.732  -37.3103  30.0529  -40.6372
 2VI  C3   C   CR6   0   0.333  -37.6641  29.6017  -38.2099
 2VI  O10  O   O2    0  -0.478  -39.0120  29.4993  -38.4022
 2VI  C29  C   CH1   0   0.642  -39.8236  29.1822  -37.3577
 2VI  C5   C   CR56  0   0.113  -35.5099  30.0116  -39.3034
 2VI  C13  C   CH2   0  -0.349  -33.0122  31.3590  -39.7965
 2VI  N12  N   NT    0  -0.456  -32.5520  30.3920  -38.8131
 2VI  O15  O   O     0  -0.501  -32.8863  29.1259  -36.9788
 2VI  O26  O   O2    0  -0.474  -32.1750  32.2557  -36.5461
 2VI  C28  C   CH3   0  -0.390  -32.6938  32.4013  -35.2527
 2VI  H1   H   HCR6  0   0.256  -35.1189  29.4230  -36.0068
 2VI  H2   H   HCR6  0   0.285  -37.5264  29.3101  -36.0754
 2VI  H3   H   HCH2  0   0.247  -33.1015  29.8722  -41.3410
 2VI  H4   H   HCH2  0   0.246  -33.7167  31.4398  -41.8203
 2VI  H5   H   HCR6  0   0.263  -38.7495  30.6406  -44.2070
 2VI  H6   H   HCR6  0   0.278  -37.6679  35.1152  -42.4182
 2VI  H7   H   HCH2  0   0.252  -30.8820  29.3431  -38.1537
 2VI  H8   H   HCH2  0   0.249  -30.6904  30.1715  -39.6830
 2VI  H9   H   HCH2  0   0.241  -29.3592  31.2258  -37.9514
 2VI  H10  H   HCH2  0   0.231  -30.5362  32.3592  -38.5611
 2VI  H11  H   HCH2  0   0.193  -30.8551  30.7677  -35.9716
 2VI  H12  H   HCH2  0   0.203  -30.1743  32.3916  -36.0660
 2VI  H13  H   HCH2  0   0.285  -36.7237  29.7708  -43.3973
 2VI  H14  H   HCH2  0   0.283  -35.3919  30.8930  -43.2738
 2VI  H15  H   HCR6  0   0.277  -40.3037  32.5119  -44.5774
 2VI  H16  H   HCR6  0   0.262  -36.1255  33.2375  -42.0440
 2VI  H17  H   HNR5  0   0.411  -38.2609  30.0165  -40.9690
 2VI  H18  H   HCH1  0   0.205  -39.4588  28.3612  -36.7366
 2VI  H19  H   HCH2  0   0.272  -32.1351  31.9074  -40.1360
 2VI  H20  H   HCH2  0   0.255  -33.6708  32.0971  -39.3329
 2VI  H21  H   HCH3  0   0.228  -33.6866  32.8437  -35.3332
 2VI  H22  H   HCH3  0   0.198  -32.7871  31.4379  -34.7362
 2VI  H23  H   HCH3  0   0.198  -32.0744  33.0570  -34.6273
 2VI  C23  C   CH2   0  -0.332  -31.1091  30.2689  -38.6778
 2VI  CL   CL  CL    0  -0.131  -40.1740  35.2412  -43.7706
 2VI  F31  F   F     0  -0.304  -41.0090  28.8601  -37.8921
 2VI  F30  F   F     0  -0.330  -40.0231  30.2731  -36.5830

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
 2VI  CL   C19  single    1.734  0.020  1.734
 2VI  C18  C17  aromatic  1.389  0.020  1.389
 2VI  C18  C19  aromatic  1.384  0.020  1.384
 2VI  C17  C16  aromatic  1.389  0.020  1.389
 2VI  C19  C20  aromatic  1.388  0.020  1.388
 2VI  C16  C27  single    1.509  0.020  1.509
 2VI  C16  C21  aromatic  1.393  0.020  1.393
 2VI  C20  C21  aromatic  1.385  0.020  1.385
 2VI  C27  C8   single    1.491  0.020  1.491
 2VI  C8   N7   aromatic  1.368  0.020  1.368
 2VI  C8   C9   aromatic  1.371  0.020  1.371
 2VI  C14  C9   single    1.490  0.020  1.490
 2VI  C14  C13  single    1.525  0.020  1.525
 2VI  N7   C4   aromatic  1.362  0.020  1.362
 2VI  C9   C5   aromatic  1.427  0.020  1.427
 2VI  C13  N12  single    1.454  0.020  1.454
 2VI  C4   C5   aromatic  1.409  0.020  1.409
 2VI  C4   C3   aromatic  1.391  0.020  1.391
 2VI  C5   C6   aromatic  1.409  0.020  1.409
 2VI  N12  C23  single    1.454  0.020  1.454
 2VI  N12  C11  single    1.350  0.020  1.350
 2VI  C23  C24  single    1.527  0.020  1.527
 2VI  O10  C3   single    1.365  0.020  1.365
 2VI  O10  C29  single    1.360  0.020  1.360
 2VI  C3   C2   aromatic  1.383  0.020  1.383
 2VI  C24  C25  single    1.516  0.020  1.516
 2VI  C6   C11  single    1.494  0.020  1.494
 2VI  C6   C1   aromatic  1.386  0.020  1.386
 2VI  F31  C29  single    1.340  0.020  1.340
 2VI  C11  O15  double    1.228  0.020  1.228
 2VI  C29  F30  single    1.353  0.020  1.353
 2VI  C2   C1   aromatic  1.399  0.020  1.399
 2VI  C25  O26  single    1.407  0.020  1.407
 2VI  O26  C28  single    1.401  0.020  1.401
 2VI  C1   H1   single    0.930  0.020  1.080
 2VI  C2   H2   single    0.930  0.020  1.080
 2VI  C14  H3   single    0.970  0.020  1.090
 2VI  C14  H4   single    0.970  0.020  1.090
 2VI  C17  H5   single    0.930  0.020  1.080
 2VI  C20  H6   single    0.930  0.020  1.080
 2VI  C23  H7   single    0.970  0.020  1.090
 2VI  C23  H8   single    0.970  0.020  1.090
 2VI  C24  H9   single    0.970  0.020  1.090
 2VI  C24  H10  single    0.970  0.020  1.090
 2VI  C25  H11  single    0.970  0.020  1.090
 2VI  C25  H12  single    0.970  0.020  1.090
 2VI  C27  H13  single    0.970  0.020  1.090
 2VI  C27  H14  single    0.970  0.020  1.090
 2VI  C18  H15  single    0.930  0.020  1.080
 2VI  C21  H16  single    0.930  0.020  1.080
 2VI  N7   H17  single    0.860  0.020  1.020
 2VI  C29  H18  single    0.970  0.020  1.090
 2VI  C13  H19  single    0.970  0.020  1.090
 2VI  C13  H20  single    0.970  0.020  1.090
 2VI  C28  H21  single    0.970  0.020  1.090
 2VI  C28  H22  single    0.970  0.020  1.090
 2VI  C28  H23  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
 2VI  H1   C1   C6   119.30  3.000
 2VI  H1   C1   C2   117.73  3.000
 2VI  C6   C1   C2   122.96  3.000
 2VI  H2   C2   C3   121.90  3.000
 2VI  H2   C2   C1   118.07  3.000
 2VI  C3   C2   C1   120.03  3.000
 2VI  C5   C4   C3   122.11  3.000
 2VI  C3   C4   N7   129.93  3.000
 2VI  C5   C4   N7   107.95  3.000
 2VI  C5   C6   C11  125.48  3.000
 2VI  C11  C6   C1   117.10  3.000
 2VI  C5   C6   C1   117.14  3.000
 2VI  N7   C8   C27  120.78  3.000
 2VI  N7   C8   C9   109.37  3.000
 2VI  C27  C8   C9   129.82  3.000
 2VI  C5   C9   C14  124.08  3.000
 2VI  C5   C9   C8   106.89  3.000
 2VI  C14  C9   C8   128.63  3.000
 2VI  O15  C11  N12  121.80  3.000
 2VI  O15  C11  C6   118.66  3.000
 2VI  N12  C11  C6   119.50  3.000
 2VI  H4   C14  H3   106.38  3.000
 2VI  H4   C14  C13  108.88  3.000
 2VI  H3   C14  C13  108.88  3.000
 2VI  H4   C14  C9   110.20  3.000
 2VI  H3   C14  C9   112.65  3.000
 2VI  C13  C14  C9   109.74  3.000
 2VI  C21  C16  C27  120.30  3.000
 2VI  C21  C16  C17  118.57  3.000
 2VI  C27  C16  C17  121.13  3.000
 2VI  H5   C17  C18  119.06  3.000
 2VI  H5   C17  C16  119.79  3.000
 2VI  C18  C17  C16  121.15  3.000
 2VI  H6   C20  C21  120.37  3.000
 2VI  H6   C20  C19  120.56  3.000
 2VI  C21  C20  C19  119.07  3.000
 2VI  H10  C24  H9   105.73  3.000
 2VI  H10  C24  C25  109.39  3.000
 2VI  H9   C24  C25  107.83  3.000
 2VI  H10  C24  C23  110.70  3.000
 2VI  H9   C24  C23  107.04  3.000
 2VI  C25  C24  C23  115.62  3.000
 2VI  H12  C25  H11  106.63  3.000
 2VI  H12  C25  O26  110.03  3.000
 2VI  H11  C25  O26  110.83  3.000
 2VI  H12  C25  C24  109.22  3.000
 2VI  H11  C25  C24  109.98  3.000
 2VI  O26  C25  C24  110.08  3.000
 2VI  H14  C27  H13  106.07  3.000
 2VI  H14  C27  C16  110.00  3.000
 2VI  H13  C27  C16  109.59  3.000
 2VI  H14  C27  C8   108.68  3.000
 2VI  H13  C27  C8   109.96  3.000
 2VI  C16  C27  C8   112.34  3.000
 2VI  C18  C19  CL   119.51  3.000
 2VI  C18  C19  C20  121.02  3.000
 2VI  CL   C19  C20  119.47  3.000
 2VI  H15  C18  C19  120.65  3.000
 2VI  H15  C18  C17  120.29  3.000
 2VI  C19  C18  C17  119.06  3.000
 2VI  H16  C21  C20  119.07  3.000
 2VI  H16  C21  C16  119.81  3.000
 2VI  C20  C21  C16  121.13  3.000
 2VI  H17  N7   C8   124.99  3.000
 2VI  H17  N7   C4   125.70  3.000
 2VI  C8   N7   C4   109.28  3.000
 2VI  O10  C3   C4   115.69  3.000
 2VI  O10  C3   C2   126.23  3.000
 2VI  C4   C3   C2   118.07  3.000
 2VI  C29  O10  C3   119.89  3.000
 2VI  H18  C29  F30  109.25  3.000
 2VI  H18  C29  F31  109.98  3.000
 2VI  F30  C29  F31  106.97  3.000
 2VI  H18  C29  O10  114.37  3.000
 2VI  F30  C29  O10  109.86  3.000
 2VI  F31  C29  O10  106.12  3.000
 2VI  C9   C5   C6   133.92  3.000
 2VI  C6   C5   C4   119.59  3.000
 2VI  C9   C5   C4   106.49  3.000
 2VI  H20  C13  H19  106.12  3.000
 2VI  H20  C13  N12  110.68  3.000
 2VI  H19  C13  N12  106.91  3.000
 2VI  H20  C13  C14  110.16  3.000
 2VI  H19  C13  C14  109.23  3.000
 2VI  N12  C13  C14  113.41  3.000
 2VI  C13  N12  C23  115.67  3.000
 2VI  C23  N12  C11  118.96  3.000
 2VI  C13  N12  C11  124.60  3.000
 2VI  C28  O26  C25  112.57  3.000
 2VI  H23  C28  H22  107.72  3.000
 2VI  H23  C28  H21  108.29  3.000
 2VI  H22  C28  H21  108.29  3.000
 2VI  H23  C28  O26  112.27  3.000
 2VI  H22  C28  O26  112.01  3.000
 2VI  H21  C28  O26  108.14  3.000
 2VI  H8   C23  H7   106.69  3.000
 2VI  H8   C23  N12  107.58  3.000
 2VI  H7   C23  N12  108.90  3.000
 2VI  H8   C23  C24  108.80  3.000
 2VI  H7   C23  C24  109.80  3.000
 2VI  N12  C23  C24  114.75  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
 2VI  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 2VI  CONST_02  N7   C4   C3   C2    180.00   0.0  0
 2VI  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 2VI  CONST_04  C9   C8   N7   C4      0.00   0.0  0
 2VI  CONST_05  C3   C2   C1   C6      0.00   0.0  0
 2VI  CONST_06  C5   C4   N7   C8      0.00   0.0  0
 2VI  CONST_07  C3   C4   N7   C8    180.00   0.0  0
 2VI  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 2VI  CONST_09  C19  C20  C21  C16     0.00   0.0  0
 2VI  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 2VI  CONST_11  C20  C21  C16  C17     0.00   0.0  0
 2VI  CONST_12  C21  C16  C17  C18     0.00   0.0  0
 2VI  CONST_13  C21  C20  C19  C18     0.00   0.0  0
 2VI  CONST_14  O10  C3   C2   C1    180.00   0.0  0
 2VI  CONST_15  C27  C8   N7   C4    180.00   0.0  0
 2VI  CONST_16  CL   C19  C18  C17   180.00   0.0  0
 2VI  CONST_17  C27  C16  C21  C20   180.00   0.0  0
 2VI  CONST_18  C18  C17  C16  C27   180.00   0.0  0
 2VI  CONST_19  C21  C20  C19  CL    180.00   0.0  0
 2VI  CONST_20  O10  C3   C4   N7      0.00   0.0  0
 2VI  CONST_21  C5   C4   C3   O10   180.00   0.0  0
 2VI  CONST_22  H2   C2   C3   C4    180.00   0.0  0
 2VI  CONST_23  H2   C2   C1   C6    180.00   0.0  0
 2VI  CONST_24  H17  N7   C8   C9    180.00   0.0  0
 2VI  CONST_25  H15  C18  C17  C16   180.00   0.0  0
 2VI  CONST_26  H6   C20  C21  C16   180.00   0.0  0
 2VI  CONST_27  H16  C21  C16  C17   180.00   0.0  0
 2VI  CONST_28  H15  C18  C19  C20   180.00   0.0  0
 2VI  CONST_29  H5   C17  C18  C19   180.00   0.0  0
 2VI  CONST_30  H16  C21  C20  C19   180.00   0.0  0
 2VI  CONST_31  H6   C20  C19  C18   180.00   0.0  0
 2VI  CONST_32  H5   C17  C16  C21   180.00   0.0  0
 2VI  CONST_33  H17  N7   C4   C3      0.00   0.0  0
 2VI  CONST_34  H1   C1   C2   C3    180.00   0.0  0
 2VI  CONST_35  H17  N7   C4   C5    180.00   0.0  0
 2VI  Var_01    C17  C16  C27  C8   -117.05  30.0  3
 2VI  Var_02    C21  C16  C27  C8     62.35  30.0  3
 2VI  Var_03    C16  C27  C8   C9   -121.94  30.0  1
 2VI  Var_04    N7   C8   C27  C16    56.09  30.0  2
 2VI  Var_05    C29  O10  C3   C2     -3.64  30.0  2
 2VI  Var_06    C29  O10  C3   C4    176.92  30.0  2
 2VI  Var_07    H13  C27  C8   C9    115.73  30.0  1
 2VI  Var_08    H14  C27  C8   C9      0.03  30.0  1
 2VI  Var_09    H13  C27  C16  C17     5.50  30.0  2
 2VI  Var_10    H14  C27  C16  C17   121.74  30.0  2
 2VI  Var_11    H13  C27  C16  C21  -175.10  30.0  2
 2VI  Var_12    H14  C27  C16  C21   -58.86  30.0  2
 2VI  Var_13    H13  C27  C8   N7    -66.24  30.0  1
 2VI  Var_14    H14  C27  C8   N7    178.05  30.0  1
 2VI  Var_15    N12  C23  C24  C25    60.50  30.0  1
 2VI  Var_16    F31  C29  O10  C3   -166.36  30.0  3
 2VI  Var_17    F30  C29  O10  C3     78.33  30.0  3
 2VI  Var_18    H18  C29  O10  C3    -44.94  30.0  3
 2VI  Var_19    H9   C24  C23  N12  -179.35  30.0  3
 2VI  Var_20    H10  C24  C23  N12   -64.59  30.0  3
 2VI  Var_21    O26  C25  C24  C23   -72.62  30.0  3
 2VI  Var_22    C28  O26  C25  C24   174.42  30.0  3
 2VI  Var_23    H11  C25  C24  C23    49.78  30.0  3
 2VI  Var_24    H12  C25  C24  C23   166.47  30.0  3
 2VI  Var_25    H7   C23  C24  C25   -62.54  30.0  1
 2VI  Var_26    H8   C23  C24  C25  -178.96  30.0  1
 2VI  Var_27    H21  C28  O26  C25   179.39  30.0  3
 2VI  Var_28    H22  C28  O26  C25   -61.36  30.0  3
 2VI  Var_29    H23  C28  O26  C25    59.99  30.0  3
 2VI  Var_30    H9   C24  C25  O26   167.67  30.0  1
 2VI  Var_31    H10  C24  C25  O26    53.15  30.0  1
 2VI  Var_32    H11  C25  O26  C28    52.53  30.0  2
 2VI  Var_33    H12  C25  O26  C28   -65.16  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
 2VI  plan-1  C16  0.020
 2VI  plan-1  C17  0.020
 2VI  plan-1  C20  0.020
 2VI  plan-1  C27  0.020
 2VI  plan-1  C19  0.020
 2VI  plan-1  C18  0.020
 2VI  plan-1  C21  0.020
 2VI  plan-1  H5   0.020
 2VI  plan-1  H6   0.020
 2VI  plan-1  H15  0.020
 2VI  plan-1  H16  0.020
 2VI  plan-1  CL   0.020
 2VI  plan-2  C1   0.020
 2VI  plan-2  C2   0.020
 2VI  plan-2  C4   0.020
 2VI  plan-2  C6   0.020
 2VI  plan-2  C8   0.020
 2VI  plan-2  C9   0.020
 2VI  plan-2  C11  0.020
 2VI  plan-2  C14  0.020
 2VI  plan-2  C27  0.020
 2VI  plan-2  N7   0.020
 2VI  plan-2  C3   0.020
 2VI  plan-2  O10  0.020
 2VI  plan-2  C5   0.020
 2VI  plan-2  H1   0.020
 2VI  plan-2  H2   0.020
 2VI  plan-2  H17  0.020
 2VI  plan-3  C6   0.020
 2VI  plan-3  C11  0.020
 2VI  plan-3  C13  0.020
 2VI  plan-3  N12  0.020
 2VI  plan-3  O15  0.020
 2VI  plan-3  C23  0.020

