# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 12:58:54 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: (2~{S},3~{S})-2-(fluoranylmethyl)-~{N}7-methyl-~{N}5-[(1~{R},5~{S})-3-oxabicyclo[3.1.0]hexan-6-yl]-3-phenyl-2,3-dihydro-1-benzofuran-5,7-dicarboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(cc2[C@@H]([C@@H](CF)Oc12)c3ccccc3)C(=O)NC4[C@@H]5COC[C@H]45
#
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
 QC8  QC8  (2~{S},3~{S})-2-(fluoranylmethyl)-~{N}7-methyl-~{N}5-[(1~{R},5~{S})-3-oxabicyclo[3.1.0]hexan-6-yl]-3-phenyl-2,3-dihydro-1-benzofuran-5,7-dicarboxamide  ligand  53  30  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_QC8
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
 QC8  C10  C  CR15  0  -0.479  40.3345  18.9887  10.3828
 QC8  C17  C  CR56  0   0.408  41.0618  17.5936   8.6303
 QC8  C20  C  CR16  0  -0.239  39.6972  16.6487  13.3098
 QC8  C21  C  CR16  0  -0.267  39.5507  17.5475  14.3605
 QC8  C22  C  CR16  0  -0.240  39.6601  18.9087  14.1181
 QC8  C24  C  C     0   0.542  45.1711  17.5608   9.7213
 QC8  C01  C  CH3   0  -0.516  39.8275  15.4603   5.0047
 QC8  C03  C  C     0   0.567  41.5441  16.0634   6.6145
 QC8  O04  O  O     0  -0.494  42.3756  15.3648   6.0457
 QC8  C05  C  CR6   0  -0.139  41.9235  16.8474   7.8320
 QC8  C06  C  CR16  0  -0.347  43.2664  16.8456   8.2139
 QC8  C07  C  CR6   0  -0.025  43.7345  17.5514   9.3146
 QC8  C08  C  CR16  0  -0.345  42.8381  18.3127  10.0732
 QC8  C09  C  CR56  0   0.096  41.5101  18.3191   9.7254
 QC8  C12  C  CR15  0  -0.040  39.2086  18.6784   9.3643
 QC8  C14  C  CH2   0   0.000  38.8283  19.9140   8.5885
 QC8  F15  F  F     0  -0.368  37.8623  19.6022   7.6438
 QC8  O16  O  O     0  -0.501  39.7348  17.6901   8.4560
 QC8  C18  C  CR6   0   0.201  40.0628  18.4766  11.7758
 QC8  C19  C  CR16  0  -0.302  39.9536  17.1100  12.0278
 QC8  C23  C  CR16  0  -0.326  39.9143  19.3687  12.8313
 QC8  O25  O  O     0  -0.484  45.6341  18.4816  10.3790
 QC8  N26  N  NH1   0  -0.685  45.9104  16.5014   9.3429
 QC8  C27  C  CH1   0  -0.027  47.3009  16.4048   9.6347
 QC8  C29  C  CH1   0  -0.303  47.7078  16.1039  11.0452
 QC8  C31  C  CH2   0  -0.152  49.1278  16.4582  11.4090
 QC8  O32  O  O2    0  -0.499  49.9289  15.9586  10.3503
 QC8  C33  C  CH2   0  -0.148  49.2923  14.8245   9.7864
 QC8  C34  C  CH1   0  -0.352  47.8145  15.0458   9.9923
 QC8  H1   H  HCR5  0   0.303  40.4958  20.0699  10.4407
 QC8  H3   H  HCR6  0   0.258  39.3531  17.1863  15.3613
 QC8  H4   H  HCR6  0   0.258  39.5492  19.6170  14.9288
 QC8  H5   H  HCH3  0   0.250  38.7614  15.6355   4.8948
 QC8  H6   H  HCH3  0   0.239  40.3292  15.8098   4.1011
 QC8  H7   H  HCH3  0   0.241  39.9925  14.3867   5.0923
 QC8  H8   H  HNH1  0   0.413  39.6358  16.7786   6.6447
 QC8  H9   H  HCR6  0   0.261  43.9481  16.2819   7.5906
 QC8  H10  H  HCR6  0   0.266  43.1858  18.8723  10.9320
 QC8  H11  H  HCR5  0   0.287  38.3271  18.2425   9.8368
 QC8  H12  H  HCH2  0   0.221  39.6936  20.3399   8.0751
 QC8  H13  H  HCH2  0   0.228  38.4210  20.6596   9.2737
 QC8  H14  H  HCR6  0   0.255  40.0706  16.3946  11.2216
 QC8  H15  H  HCR6  0   0.256  39.9981  20.4335  12.6483
 QC8  H16  H  HNH1  0   0.410  45.4798  15.7440   8.8387
 QC8  H17  H  HCH1  0   0.269  47.9413  17.0584   9.0450
 QC8  H18  H  HCH1  0   0.276  46.9528  16.0682  11.8194
 QC8  H19  H  HCH2  0   0.216  49.3879  15.9950  12.3694
 QC8  H20  H  HCH2  0   0.232  49.3086  17.5324  11.4900
 QC8  H21  H  HCH2  0   0.217  49.5952  13.8961  10.2872
 QC8  H22  H  HCH2  0   0.232  49.5895  14.7571   8.7375
 QC8  H23  H  HCH1  0   0.280  47.1430  14.1960   9.9635
 QC8  H2   H  HCR6  0   0.259  39.6144  15.5848  13.4906
 QC8  N02  N  NH1   0  -0.663  40.2827  16.1636   6.1805

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
 QC8  C01  N02  single    1.444  0.020  1.444
 QC8  O04  C03  double    1.226  0.020  1.226
 QC8  N02  C03  single    1.338  0.020  1.338
 QC8  C03  C05  single    1.497  0.020  1.497
 QC8  F15  C14  single    1.387  0.020  1.387
 QC8  C05  C06  aromatic  1.396  0.020  1.396
 QC8  C05  C17  aromatic  1.392  0.020  1.392
 QC8  C14  C12  single    1.508  0.020  1.508
 QC8  C06  C07  aromatic  1.389  0.020  1.389
 QC8  O16  C17  single    1.342  0.020  1.342
 QC8  O16  C12  single    1.442  0.020  1.442
 QC8  C17  C09  aromatic  1.388  0.020  1.388
 QC8  C12  C10  single    1.550  0.020  1.550
 QC8  C07  C24  single    1.493  0.020  1.493
 QC8  C07  C08  aromatic  1.400  0.020  1.400
 QC8  C33  C34  single    1.508  0.020  1.508
 QC8  C33  O32  single    1.418  0.020  1.418
 QC8  N26  C24  single    1.346  0.020  1.346
 QC8  N26  C27  single    1.424  0.020  1.424
 QC8  C34  C27  single    1.496  0.020  1.496
 QC8  C34  C29  single    1.497  0.020  1.497
 QC8  C09  C08  aromatic  1.373  0.020  1.373
 QC8  C09  C10  single    1.504  0.020  1.504
 QC8  C24  O25  double    1.223  0.020  1.223
 QC8  C27  C29  single    1.499  0.020  1.499
 QC8  C10  C18  single    1.509  0.020  1.509
 QC8  O32  C31  single    1.419  0.020  1.419
 QC8  C29  C31  single    1.508  0.020  1.508
 QC8  C18  C19  aromatic  1.394  0.020  1.394
 QC8  C18  C23  aromatic  1.390  0.020  1.390
 QC8  C19  C20  aromatic  1.386  0.020  1.386
 QC8  C23  C22  aromatic  1.390  0.020  1.390
 QC8  C20  C21  aromatic  1.390  0.020  1.390
 QC8  C22  C21  aromatic  1.387  0.020  1.387
 QC8  C10  H1   single    0.970  0.020  1.090
 QC8  C20  H2   single    0.930  0.020  1.080
 QC8  C21  H3   single    0.930  0.020  1.080
 QC8  C22  H4   single    0.930  0.020  1.080
 QC8  C01  H5   single    0.970  0.020  1.090
 QC8  C01  H6   single    0.970  0.020  1.090
 QC8  C01  H7   single    0.970  0.020  1.090
 QC8  N02  H8   single    0.860  0.020  1.020
 QC8  C06  H9   single    0.930  0.020  1.080
 QC8  C08  H10  single    0.930  0.020  1.080
 QC8  C12  H11  single    0.970  0.020  1.090
 QC8  C14  H12  single    0.970  0.020  1.090
 QC8  C14  H13  single    0.970  0.020  1.090
 QC8  C19  H14  single    0.930  0.020  1.080
 QC8  C23  H15  single    0.930  0.020  1.080
 QC8  N26  H16  single    0.860  0.020  1.020
 QC8  C27  H17  single    0.970  0.020  1.090
 QC8  C29  H18  single    0.970  0.020  1.090
 QC8  C31  H19  single    0.970  0.020  1.090
 QC8  C31  H20  single    0.970  0.020  1.090
 QC8  C33  H21  single    0.970  0.020  1.090
 QC8  C33  H22  single    0.970  0.020  1.090
 QC8  C34  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
 QC8  H1   C10  C18  108.24  3.000
 QC8  H1   C10  C12  109.85  3.000
 QC8  C18  C10  C12  114.08  3.000
 QC8  H1   C10  C09  110.34  3.000
 QC8  C18  C10  C09  113.15  3.000
 QC8  C12  C10  C09  101.03  3.000
 QC8  O16  C17  C09  112.60  3.000
 QC8  C09  C17  C05  122.20  3.000
 QC8  O16  C17  C05  125.20  3.000
 QC8  H2   C20  C19  119.71  3.000
 QC8  H2   C20  C21  120.08  3.000
 QC8  C19  C20  C21  120.20  3.000
 QC8  H3   C21  C22  120.24  3.000
 QC8  H3   C21  C20  120.15  3.000
 QC8  C22  C21  C20  119.61  3.000
 QC8  H4   C22  C23  119.72  3.000
 QC8  H4   C22  C21  120.22  3.000
 QC8  C23  C22  C21  120.07  3.000
 QC8  N26  C24  O25  122.41  3.000
 QC8  O25  C24  C07  121.04  3.000
 QC8  N26  C24  C07  116.54  3.000
 QC8  H7   C01  H6   108.21  3.000
 QC8  H7   C01  H5   108.40  3.000
 QC8  H6   C01  H5   108.42  3.000
 QC8  H7   C01  N02  111.52  3.000
 QC8  H6   C01  N02  111.93  3.000
 QC8  H5   C01  N02  108.26  3.000
 QC8  C05  C03  O04  120.26  3.000
 QC8  C05  C03  N02  117.62  3.000
 QC8  O04  C03  N02  122.12  3.000
 QC8  C06  C05  C03  117.75  3.000
 QC8  C06  C05  C17  116.06  3.000
 QC8  C03  C05  C17  126.19  3.000
 QC8  H9   C06  C07  120.59  3.000
 QC8  H9   C06  C05  116.68  3.000
 QC8  C07  C06  C05  122.71  3.000
 QC8  C08  C07  C06  119.35  3.000
 QC8  C08  C07  C24  117.72  3.000
 QC8  C06  C07  C24  122.92  3.000
 QC8  H10  C08  C09  120.62  3.000
 QC8  H10  C08  C07  120.37  3.000
 QC8  C09  C08  C07  119.00  3.000
 QC8  C08  C09  C17  120.66  3.000
 QC8  C08  C09  C10  130.35  3.000
 QC8  C17  C09  C10  108.97  3.000
 QC8  H11  C12  O16  107.09  3.000
 QC8  H11  C12  C14  110.27  3.000
 QC8  O16  C12  C14  109.25  3.000
 QC8  H11  C12  C10  112.48  3.000
 QC8  O16  C12  C10  106.63  3.000
 QC8  C14  C12  C10  110.94  3.000
 QC8  H13  C14  H12  108.92  3.000
 QC8  H13  C14  F15  108.74  3.000
 QC8  H12  C14  F15  108.61  3.000
 QC8  H13  C14  C12  109.33  3.000
 QC8  H12  C14  C12  111.19  3.000
 QC8  F15  C14  C12  110.00  3.000
 QC8  C12  O16  C17  109.17  3.000
 QC8  C23  C18  C19  118.92  3.000
 QC8  C23  C18  C10  120.16  3.000
 QC8  C19  C18  C10  120.92  3.000
 QC8  H14  C19  C18  120.27  3.000
 QC8  H14  C19  C20  119.21  3.000
 QC8  C18  C19  C20  120.53  3.000
 QC8  H15  C23  C18  119.61  3.000
 QC8  H15  C23  C22  119.71  3.000
 QC8  C18  C23  C22  120.68  3.000
 QC8  H16  N26  C27  117.99  3.000
 QC8  H16  N26  C24  119.87  3.000
 QC8  C27  N26  C24  122.14  3.000
 QC8  H17  C27  C34  118.22  3.000
 QC8  H17  C27  C29  118.08  3.000
 QC8  C34  C27  C29   59.96  3.000
 QC8  H17  C27  N26  115.01  3.000
 QC8  C29  C27  N26  118.13  3.000
 QC8  C34  C27  N26  116.47  3.000
 QC8  H18  C29  C34  121.99  3.000
 QC8  H18  C29  C31  119.48  3.000
 QC8  C34  C29  C31  105.59  3.000
 QC8  H18  C29  C27  119.39  3.000
 QC8  C31  C29  C27  115.82  3.000
 QC8  C34  C29  C27   59.94  3.000
 QC8  H20  C31  H19  108.12  3.000
 QC8  H20  C31  O32  107.95  3.000
 QC8  H19  C31  O32  111.76  3.000
 QC8  H20  C31  C29  113.87  3.000
 QC8  H19  C31  C29  109.58  3.000
 QC8  O32  C31  C29  105.60  3.000
 QC8  C33  O32  C31  108.97  3.000
 QC8  H22  C33  H21  108.11  3.000
 QC8  H22  C33  C34  114.00  3.000
 QC8  H21  C33  C34  109.40  3.000
 QC8  H22  C33  O32  108.01  3.000
 QC8  H21  C33  O32  111.80  3.000
 QC8  C34  C33  O32  105.56  3.000
 QC8  H23  C34  C33  119.24  3.000
 QC8  H23  C34  C29  121.94  3.000
 QC8  C33  C34  C29  105.64  3.000
 QC8  H23  C34  C27  119.56  3.000
 QC8  C29  C34  C27   60.10  3.000
 QC8  C33  C34  C27  115.90  3.000
 QC8  H8   N02  C03  120.16  3.000
 QC8  H8   N02  C01  118.09  3.000
 QC8  C03  N02  C01  121.67  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
 QC8  CONST_01  C07  C06  C05  C17     0.00   0.0  0
 QC8  CONST_02  C07  C08  C09  C17     0.00   0.0  0
 QC8  CONST_03  C23  C18  C19  C20     0.00   0.0  0
 QC8  CONST_04  C23  C22  C21  C20     0.00   0.0  0
 QC8  CONST_05  C18  C19  C20  C21     0.00   0.0  0
 QC8  CONST_06  C18  C23  C22  C21     0.00   0.0  0
 QC8  CONST_07  C19  C18  C23  C22     0.00   0.0  0
 QC8  CONST_08  C19  C20  C21  C22     0.00   0.0  0
 QC8  CONST_09  C08  C07  C06  C05     0.00   0.0  0
 QC8  CONST_10  C08  C09  C17  C05     0.00   0.0  0
 QC8  CONST_11  C09  C17  C05  C06     0.00   0.0  0
 QC8  CONST_12  C09  C08  C07  C06     0.00   0.0  0
 QC8  CONST_13  C20  C19  C18  C10   180.00   0.0  0
 QC8  CONST_14  C22  C23  C18  C10   180.00   0.0  0
 QC8  CONST_15  C05  C06  C07  C24   180.00   0.0  0
 QC8  CONST_16  C09  C08  C07  C24   180.00   0.0  0
 QC8  CONST_17  C07  C06  C05  C03   180.00   0.0  0
 QC8  CONST_18  O16  C17  C05  C03     0.00   0.0  0
 QC8  CONST_19  C09  C17  C05  C03   180.00   0.0  0
 QC8  CONST_20  H10  C08  C09  C10     0.00   0.0  0
 QC8  CONST_21  H14  C19  C18  C10     0.00   0.0  0
 QC8  CONST_22  H15  C23  C18  C10     0.00   0.0  0
 QC8  CONST_23  H9   C06  C05  C17   180.00   0.0  0
 QC8  CONST_24  H4   C22  C21  C20   180.00   0.0  0
 QC8  CONST_25  H2   C20  C21  C22   180.00   0.0  0
 QC8  CONST_26  H3   C21  C20  C19   180.00   0.0  0
 QC8  CONST_27  C27  N26  C24  C07   180.00   0.0  0
 QC8  CONST_28  C05  C03  N02  C01   180.00   0.0  0
 QC8  CONST_29  C27  N26  C24  O25     0.00   0.0  0
 QC8  CONST_30  H8   N02  C03  C05     0.00   0.0  0
 QC8  CONST_31  H16  N26  C24  C07     0.00   0.0  0
 QC8  CONST_32  O04  C03  N02  C01     0.00   0.0  0
 QC8  Var_01    O32  C33  C34  C27    46.66  30.0  1
 QC8  Var_02    C31  C29  C34  C27  -111.16  30.0  1
 QC8  Var_03    O32  C31  C29  C27   -46.61  30.0  1
 QC8  Var_04    C34  C33  O32  C31    29.36  30.0  1
 QC8  Var_05    O04  C03  C05  C17  -174.71  30.0  3
 QC8  Var_06    N26  C24  C07  C06   -25.04  30.0  2
 QC8  Var_07    H5   C01  N02  C03   175.83  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
 QC8  chir_01  C10  C12  C09  C18  positiv
 QC8  chir_02  C12  O16  C14  C10  positiv
 QC8  chir_03  C27  N26  C34  C29  both
 QC8  chir_04  C29  C34  C27  C31  both
 QC8  chir_05  C34  C29  C27  C33  both

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
 QC8  plan-1  C10  0.020
 QC8  plan-1  C20  0.020
 QC8  plan-1  C21  0.020
 QC8  plan-1  C22  0.020
 QC8  plan-1  C18  0.020
 QC8  plan-1  C19  0.020
 QC8  plan-1  C23  0.020
 QC8  plan-1  H3   0.020
 QC8  plan-1  H4   0.020
 QC8  plan-1  H14  0.020
 QC8  plan-1  H15  0.020
 QC8  plan-1  H2   0.020
 QC8  plan-2  C10  0.020
 QC8  plan-2  C17  0.020
 QC8  plan-2  C24  0.020
 QC8  plan-2  C03  0.020
 QC8  plan-2  C05  0.020
 QC8  plan-2  C06  0.020
 QC8  plan-2  C07  0.020
 QC8  plan-2  C08  0.020
 QC8  plan-2  C09  0.020
 QC8  plan-2  O16  0.020
 QC8  plan-2  H9   0.020
 QC8  plan-2  H10  0.020
 QC8  plan-3  C24  0.020
 QC8  plan-3  C07  0.020
 QC8  plan-3  O25  0.020
 QC8  plan-3  N26  0.020
 QC8  plan-3  C27  0.020
 QC8  plan-3  H16  0.020
 QC8  plan-4  C01  0.020
 QC8  plan-4  C03  0.020
 QC8  plan-4  O04  0.020
 QC8  plan-4  C05  0.020
 QC8  plan-4  H8   0.020
 QC8  plan-4  N02  0.020

