# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 21:10:26 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (2R)-2-hydroxy-7-methoxy-2-(pentafluoroethyl)-2,3-dihydro-4H-1-benzopyran-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2C(=O)C[C@@](O)(Oc2c1)C(F)(F)C(F)(F)F
#
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
 R7M  R7M  (2R)-2-hydroxy-7-methoxy-2-(pentafluoroethyl)-2,3-dihydro-4H-1-benzopyran-4-one  ligand  30  21  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R7M
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
 R7M  C10  C  CT    0   0.325  161.4909  144.8177  170.6862
 R7M  C13  C  C     0   0.397  160.3806  143.7329  172.6420
 R7M  C15  C  CR6   0   0.426  159.1422  144.8060  170.7831
 R7M  C17  C  CR16  0  -0.452  157.9791  145.0782  170.0927
 R7M  C20  C  CR16  0  -0.382  156.7576  143.6467  171.6215
 R7M  C21  C  CH3   0  -0.441  154.4414  144.2854  170.1627
 R7M  C11  C  CH2   0  -0.658  161.5666  144.5564  172.1867
 R7M  C12  C  CT    0   0.598  162.5552  145.8515  170.2391
 R7M  C14  C  CR6   0  -0.134  159.1441  143.9620  171.8996
 R7M  C16  C  CT    0   0.970  162.7442  146.0538  168.7137
 R7M  C18  C  CR16  0  -0.259  157.9337  143.3889  172.2914
 R7M  C19  C  CR6   0   0.415  156.7777  144.5083  170.5162
 R7M  F01  F  F     0  -0.322  162.2693  147.0533  170.7752
 R7M  F02  F  F     0  -0.333  163.7580  145.4639  170.7175
 R7M  F03  F  F     0  -0.287  161.5915  146.2412  168.0856
 R7M  F04  F  F     0  -0.302  163.5007  147.1310  168.5072
 R7M  F05  F  F     0  -0.293  163.3584  145.0143  168.1630
 R7M  O06  O  O2    0  -0.491  160.2713  145.4061  170.3378
 R7M  O07  O  OH1   0  -0.635  161.6070  143.6556  169.9456
 R7M  O08  O  O     0  -0.387  160.4613  142.9858  173.5937
 R7M  O09  O  O2    0  -0.455  155.7001  144.8275  169.7992
 R7M  H1   H  HCR6  0   0.284  157.9958  145.7303  169.2285
 R7M  H2   H  HCR6  0   0.289  155.8420  143.1856  171.9632
 R7M  H3   H  HCH3  0   0.265  153.7207  144.6900  169.4572
 R7M  H4   H  HCH3  0   0.237  154.4340  143.1957  170.0907
 R7M  H5   H  HCH3  0   0.237  154.1506  144.5792  171.1736
 R7M  H6   H  HCH2  0   0.310  162.4930  144.0496  172.4602
 R7M  H7   H  HCH2  0   0.320  161.5371  145.4974  172.7466
 R7M  H8   H  HCR6  0   0.275  157.9192  142.7304  173.1502
 R7M  H9   H  HOH1  0   0.481  162.2094  143.0292  170.3656

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
 R7M  F03  C16  single    1.326  0.020  1.326
 R7M  F04  C16  single    1.332  0.020  1.332
 R7M  C16  F05  single    1.327  0.020  1.327
 R7M  C16  C12  single    1.550  0.020  1.550
 R7M  O06  C10  single    1.398  0.020  1.398
 R7M  O06  C15  single    1.354  0.020  1.354
 R7M  O07  C10  single    1.383  0.020  1.383
 R7M  O09  C21  single    1.418  0.020  1.418
 R7M  O09  C19  single    1.333  0.020  1.333
 R7M  C17  C15  aromatic  1.380  0.020  1.380
 R7M  C17  C19  aromatic  1.395  0.020  1.395
 R7M  C12  C10  single    1.550  0.020  1.550
 R7M  C12  F01  single    1.347  0.020  1.347
 R7M  C12  F02  single    1.351  0.020  1.351
 R7M  C10  C11  single    1.525  0.020  1.525
 R7M  C15  C14  aromatic  1.400  0.020  1.400
 R7M  C19  C20  aromatic  1.402  0.020  1.402
 R7M  C20  C18  aromatic  1.378  0.020  1.378
 R7M  C14  C18  aromatic  1.395  0.020  1.395
 R7M  C14  C13  single    1.460  0.020  1.460
 R7M  C11  C13  single    1.514  0.020  1.514
 R7M  C13  O08  double    1.213  0.020  1.213
 R7M  C17  H1   single    0.930  0.020  1.080
 R7M  C20  H2   single    0.930  0.020  1.080
 R7M  C21  H3   single    0.970  0.020  1.090
 R7M  C21  H4   single    0.970  0.020  1.090
 R7M  C21  H5   single    0.970  0.020  1.090
 R7M  C11  H6   single    0.970  0.020  1.090
 R7M  C11  H7   single    0.970  0.020  1.090
 R7M  C18  H8   single    0.930  0.020  1.080
 R7M  O07  H9   single    0.850  0.020  0.980

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
 R7M  O07  C10  O06  107.06  3.000
 R7M  O07  C10  C12  110.39  3.000
 R7M  O06  C10  C12  104.27  3.000
 R7M  C12  C10  C11  111.35  3.000
 R7M  O07  C10  C11  112.26  3.000
 R7M  O06  C10  C11  111.14  3.000
 R7M  O08  C13  C14  123.50  3.000
 R7M  O08  C13  C11  121.27  3.000
 R7M  C14  C13  C11  115.16  3.000
 R7M  O06  C15  C14  121.91  3.000
 R7M  C14  C15  C17  121.28  3.000
 R7M  O06  C15  C17  116.81  3.000
 R7M  H1   C17  C19  120.10  3.000
 R7M  H1   C17  C15  120.34  3.000
 R7M  C19  C17  C15  119.56  3.000
 R7M  H2   C20  C19  121.59  3.000
 R7M  H2   C20  C18  119.32  3.000
 R7M  C19  C20  C18  119.09  3.000
 R7M  H5   C21  H4   109.12  3.000
 R7M  H5   C21  H3   108.92  3.000
 R7M  H4   C21  H3   108.92  3.000
 R7M  H5   C21  O09  111.77  3.000
 R7M  H4   C21  O09  111.75  3.000
 R7M  H3   C21  O09  106.26  3.000
 R7M  H7   C11  H6   107.08  3.000
 R7M  H7   C11  C13  107.01  3.000
 R7M  H6   C11  C13  109.70  3.000
 R7M  H7   C11  C10  110.76  3.000
 R7M  H6   C11  C10  111.63  3.000
 R7M  C13  C11  C10  110.50  3.000
 R7M  F02  C12  F01  107.70  3.000
 R7M  F02  C12  C16  106.10  3.000
 R7M  F01  C12  C16  107.52  3.000
 R7M  F02  C12  C10  108.54  3.000
 R7M  F01  C12  C10  109.56  3.000
 R7M  C16  C12  C10  117.04  3.000
 R7M  C18  C14  C15  118.07  3.000
 R7M  C18  C14  C13  121.82  3.000
 R7M  C15  C14  C13  120.08  3.000
 R7M  F05  C16  F04  107.83  3.000
 R7M  F05  C16  F03  108.45  3.000
 R7M  F04  C16  F03  107.81  3.000
 R7M  F05  C16  C12  111.25  3.000
 R7M  F04  C16  C12  109.10  3.000
 R7M  F03  C16  C12  112.24  3.000
 R7M  H8   C18  C14  118.97  3.000
 R7M  H8   C18  C20  119.23  3.000
 R7M  C14  C18  C20  121.80  3.000
 R7M  O09  C19  C20  124.04  3.000
 R7M  C20  C19  C17  120.18  3.000
 R7M  O09  C19  C17  115.78  3.000
 R7M  C15  O06  C10  117.32  3.000
 R7M  H9   O07  C10  111.39  3.000
 R7M  C19  O09  C21  119.22  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
 R7M  CONST_01  C20  C19  C17  C15     0.00   0.0  0
 R7M  CONST_02  C20  C18  C14  C15     0.00   0.0  0
 R7M  CONST_03  C18  C14  C15  C17     0.00   0.0  0
 R7M  CONST_04  C18  C20  C19  C17     0.00   0.0  0
 R7M  CONST_05  C19  C17  C15  C14     0.00   0.0  0
 R7M  CONST_06  C19  C20  C18  C14     0.00   0.0  0
 R7M  CONST_07  O09  C19  C17  C15   180.00   0.0  0
 R7M  CONST_08  O09  C19  C20  C18   180.00   0.0  0
 R7M  CONST_09  H8   C18  C14  C13     0.00   0.0  0
 R7M  CONST_10  H2   C20  C19  C17   180.00   0.0  0
 R7M  CONST_11  H1   C17  C19  C20   180.00   0.0  0
 R7M  Var_01    C17  C15  O06  C10  -158.16  30.0  1
 R7M  Var_02    C14  C13  C11  C10   -32.13  30.0  1
 R7M  Var_03    C11  C13  C14  C15     5.23  30.0  1
 R7M  Var_04    F03  C16  C12  C10    49.24  30.0  3
 R7M  Var_05    H3   C21  O09  C19   179.18  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
 R7M  chir_01  C10  O06  C12  C11  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
 R7M  plan-1  C13  0.020
 R7M  plan-1  C11  0.020
 R7M  plan-1  C14  0.020
 R7M  plan-1  O08  0.020
 R7M  plan-2  C13  0.020
 R7M  plan-2  C15  0.020
 R7M  plan-2  C17  0.020
 R7M  plan-2  C20  0.020
 R7M  plan-2  C14  0.020
 R7M  plan-2  C18  0.020
 R7M  plan-2  C19  0.020
 R7M  plan-2  O06  0.020
 R7M  plan-2  O09  0.020
 R7M  plan-2  H1   0.020
 R7M  plan-2  H2   0.020
 R7M  plan-2  H8   0.020

