# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 07:54:30 2022
#   Inital geometry file: a 125 line input string
#   Ligand name: ~{N}-[(1~{S},2~{R})-1-(3-fluoranyl-2-methyl-phenyl)-1-oxidanyl-pentan-2-yl]-2-oxidanylidene-1,3-dihydroindole-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC[C@@H](NC(=O)c1cccc2NC(=O)Cc12)[C@@H](O)c3cccc(F)c3C
#
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
 R7Z  R7Z  ~{N}-[(1~{S},2~{R})-1-(3-fluoranyl-2-methyl-phenyl)-1-oxidanyl-pentan-2-yl]-2-oxidanylidene-1,3-dihydroindole-4-carboxamide  ligand  50  27  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R7Z
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
 R7Z  C10  C  CR16  0  -0.311  40.4445   2.0399   5.2837
 R7Z  C13  C  CR56  0   0.426  38.7126   3.7385   3.9930
 R7Z  C15  C  CR5   0   0.517  36.7887   4.8548   4.5191
 R7Z  C17  C  CH2   0  -0.636  37.2535   4.1376   5.7768
 R7Z  C22  C  CR6   0   0.040  37.6239  -0.2686  10.9054
 R7Z  C24  C  CR16  0  -0.240  37.4386  -1.8748  12.7088
 R7Z  C26  C  CR6   0   0.530  37.2431   0.4439  13.1445
 R7Z  C28  C  CR6   0  -0.140  37.4231   0.7838  11.8097
 R7Z  C01  C  CH3   0  -0.660  42.8144  -1.0648   9.6925
 R7Z  C03  C  CH2   0  -0.428  40.3520  -0.5608   9.4281
 R7Z  C04  C  CH1   0  -0.098  39.2843   0.4974   9.1604
 R7Z  N06  N  NH1   0  -0.636  39.4083   0.9813   7.7994
 R7Z  O08  O  O     0  -0.478  38.6926   3.0887   8.1987
 R7Z  C09  C  CR6   0  -0.094  39.3503   2.5569   5.9868
 R7Z  C11  C  CR16  0  -0.255  40.6582   2.3846   3.9575
 R7Z  C12  C  CR16  0  -0.305  39.7891   3.2380   3.2853
 R7Z  N14  N  NR15  0  -0.742  37.7078   4.5837   3.5475
 R7Z  O16  O  O     0  -0.445  35.8012   5.5440   4.3867
 R7Z  C18  C  CR56  0   0.009  38.4922   3.4250   5.3344
 R7Z  C19  C  CH1   0  -0.005  37.8482   0.0079   9.4293
 R7Z  O21  O  OH1   0  -0.657  37.6322  -1.1192   8.6206
 R7Z  C23  C  CR16  0  -0.310  37.6245  -1.5840  11.3670
 R7Z  C25  C  CR16  0  -0.413  37.2443  -0.8493  13.6215
 R7Z  C29  C  CH3   0  -0.751  37.3938   2.2389  11.4328
 R7Z  H1   H  HCR6  0   0.265  41.1528   1.3870   5.7778
 R7Z  H2   H  HCH2  0   0.305  37.4392   4.8683   6.5665
 R7Z  H3   H  HCH2  0   0.300  36.4715   3.4695   6.1452
 R7Z  H4   H  HCR6  0   0.260  37.4445  -2.9023  13.0478
 R7Z  H5   H  HCH3  0   0.228  43.8255  -0.6629   9.6227
 R7Z  H6   H  HCH3  0   0.217  42.6728  -1.4299  10.7112
 R7Z  H7   H  HCH3  0   0.217  42.7555  -1.9258   9.0240
 R7Z  H8   H  HCH2  0   0.223  41.9662   0.3572   8.3235
 R7Z  H9   H  HCH2  0   0.216  41.8736   0.8464  10.0004
 R7Z  H10  H  HCH2  0   0.240  40.1929  -0.9639  10.4314
 R7Z  H11  H  HCH2  0   0.228  40.2349  -1.4018   8.7380
 R7Z  H12  H  HCH1  0   0.269  39.4723   1.3426   9.8264
 R7Z  H13  H  HNH1  0   0.404  39.6272   0.3037   7.0853
 R7Z  H14  H  HCR6  0   0.264  41.5176   1.9853   3.4356
 R7Z  H15  H  HCR6  0   0.272  39.9528   3.4988   2.2480
 R7Z  H16  H  HNR5  0   0.411  37.6401   4.9391   2.6052
 R7Z  H17  H  HCH1  0   0.242  37.1707   0.8166   9.1264
 R7Z  H18  H  HOH1  0   0.456  36.6916  -1.3240   8.6212
 R7Z  H19  H  HCR6  0   0.252  37.7746  -2.3949  10.6677
 R7Z  H20  H  HCR6  0   0.272  37.0963  -1.0464  14.6752
 R7Z  H21  H  HCH3  0   0.255  36.5063   2.7314  11.8307
 R7Z  H22  H  HCH3  0   0.253  38.2613   2.7662  11.8339
 R7Z  H23  H  HCH3  0   0.255  37.3981   2.3960  10.3592
 R7Z  C07  C  C     0   0.510  39.1173   2.2375   7.4276
 R7Z  F27  F  F     0  -0.316  37.0540   1.4462  14.0239
 R7Z  C02  C  CH2   0  -0.419  41.7726  -0.0147   9.3331

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
 R7Z  C12  C11  aromatic  1.391  0.020  1.391
 R7Z  C12  C13  aromatic  1.382  0.020  1.382
 R7Z  N14  C13  single    1.387  0.020  1.387
 R7Z  N14  C15  single    1.365  0.020  1.365
 R7Z  C11  C10  aromatic  1.387  0.020  1.387
 R7Z  C13  C18  aromatic  1.395  0.020  1.395
 R7Z  O16  C15  double    1.211  0.020  1.211
 R7Z  C15  C17  single    1.521  0.020  1.521
 R7Z  C10  C09  aromatic  1.400  0.020  1.400
 R7Z  C18  C09  aromatic  1.384  0.020  1.384
 R7Z  C18  C17  single    1.496  0.020  1.496
 R7Z  C09  C07  single    1.494  0.020  1.494
 R7Z  C07  N06  single    1.342  0.020  1.342
 R7Z  C07  O08  double    1.224  0.020  1.224
 R7Z  N06  C04  single    1.450  0.020  1.450
 R7Z  O21  C19  single    1.404  0.020  1.404
 R7Z  C04  C19  single    1.541  0.020  1.541
 R7Z  C04  C03  single    1.527  0.020  1.527
 R7Z  C02  C03  single    1.525  0.020  1.525
 R7Z  C02  C01  single    1.522  0.020  1.522
 R7Z  C19  C22  single    1.518  0.020  1.518
 R7Z  C22  C23  aromatic  1.394  0.020  1.394
 R7Z  C22  C28  aromatic  1.402  0.020  1.402
 R7Z  C23  C24  aromatic  1.386  0.020  1.386
 R7Z  C29  C28  single    1.503  0.020  1.503
 R7Z  C28  C26  aromatic  1.389  0.020  1.389
 R7Z  C24  C25  aromatic  1.386  0.020  1.386
 R7Z  C26  C25  aromatic  1.378  0.020  1.378
 R7Z  C26  F27  single    1.347  0.020  1.347
 R7Z  C10  H1   single    0.930  0.020  1.080
 R7Z  C17  H2   single    0.970  0.020  1.090
 R7Z  C17  H3   single    0.970  0.020  1.090
 R7Z  C24  H4   single    0.930  0.020  1.080
 R7Z  C01  H5   single    0.970  0.020  1.090
 R7Z  C01  H6   single    0.970  0.020  1.090
 R7Z  C01  H7   single    0.970  0.020  1.090
 R7Z  C02  H8   single    0.970  0.020  1.090
 R7Z  C02  H9   single    0.970  0.020  1.090
 R7Z  C03  H10  single    0.970  0.020  1.090
 R7Z  C03  H11  single    0.970  0.020  1.090
 R7Z  C04  H12  single    0.970  0.020  1.090
 R7Z  N06  H13  single    0.860  0.020  1.020
 R7Z  C11  H14  single    0.930  0.020  1.080
 R7Z  C12  H15  single    0.930  0.020  1.080
 R7Z  N14  H16  single    0.860  0.020  1.020
 R7Z  C19  H17  single    0.970  0.020  1.090
 R7Z  O21  H18  single    0.850  0.020  0.980
 R7Z  C23  H19  single    0.930  0.020  1.080
 R7Z  C25  H20  single    0.930  0.020  1.080
 R7Z  C29  H21  single    0.970  0.020  1.090
 R7Z  C29  H22  single    0.970  0.020  1.090
 R7Z  C29  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
 R7Z  H1   C10  C11  119.05  3.000
 R7Z  H1   C10  C09  120.33  3.000
 R7Z  C11  C10  C09  120.60  3.000
 R7Z  C18  C13  N14  109.36  3.000
 R7Z  C18  C13  C12  122.28  3.000
 R7Z  N14  C13  C12  128.36  3.000
 R7Z  O16  C15  N14  125.75  3.000
 R7Z  O16  C15  C17  127.43  3.000
 R7Z  N14  C15  C17  106.82  3.000
 R7Z  H3   C17  H2   106.68  3.000
 R7Z  H3   C17  C18  113.65  3.000
 R7Z  H2   C17  C18  113.08  3.000
 R7Z  H3   C17  C15  110.40  3.000
 R7Z  H2   C17  C15  109.55  3.000
 R7Z  C18  C17  C15  103.48  3.000
 R7Z  C23  C22  C19  119.58  3.000
 R7Z  C23  C22  C28  119.65  3.000
 R7Z  C19  C22  C28  120.76  3.000
 R7Z  H4   C24  C25  119.80  3.000
 R7Z  H4   C24  C23  120.13  3.000
 R7Z  C25  C24  C23  120.07  3.000
 R7Z  F27  C26  C25  118.19  3.000
 R7Z  F27  C26  C28  117.61  3.000
 R7Z  C25  C26  C28  124.20  3.000
 R7Z  C29  C28  C26  118.37  3.000
 R7Z  C26  C28  C22  117.04  3.000
 R7Z  C29  C28  C22  124.58  3.000
 R7Z  H7   C01  H6   107.50  3.000
 R7Z  H7   C01  H5   107.55  3.000
 R7Z  H6   C01  H5   107.66  3.000
 R7Z  H7   C01  C02  111.26  3.000
 R7Z  H6   C01  C02  111.25  3.000
 R7Z  H5   C01  C02  111.42  3.000
 R7Z  H11  C03  H10  106.26  3.000
 R7Z  H11  C03  C04  110.32  3.000
 R7Z  H10  C03  C04  108.35  3.000
 R7Z  H11  C03  C02  109.61  3.000
 R7Z  H10  C03  C02  108.96  3.000
 R7Z  C04  C03  C02  113.10  3.000
 R7Z  H12  C04  C19  107.45  3.000
 R7Z  H12  C04  N06  107.42  3.000
 R7Z  C19  C04  N06  110.46  3.000
 R7Z  H12  C04  C03  107.99  3.000
 R7Z  C19  C04  C03  113.64  3.000
 R7Z  N06  C04  C03  109.64  3.000
 R7Z  H13  N06  C07  118.67  3.000
 R7Z  H13  N06  C04  117.33  3.000
 R7Z  C07  N06  C04  123.64  3.000
 R7Z  C18  C09  C07  119.47  3.000
 R7Z  C07  C09  C10  121.83  3.000
 R7Z  C18  C09  C10  118.66  3.000
 R7Z  H14  C11  C12  119.31  3.000
 R7Z  H14  C11  C10  119.47  3.000
 R7Z  C12  C11  C10  121.22  3.000
 R7Z  H15  C12  C11  121.10  3.000
 R7Z  H15  C12  C13  121.43  3.000
 R7Z  C11  C12  C13  117.47  3.000
 R7Z  H16  N14  C15  123.34  3.000
 R7Z  H16  N14  C13  124.28  3.000
 R7Z  C15  N14  C13  112.36  3.000
 R7Z  C09  C18  C17  132.28  3.000
 R7Z  C17  C18  C13  107.95  3.000
 R7Z  C09  C18  C13  119.75  3.000
 R7Z  H17  C19  O21  109.73  3.000
 R7Z  H17  C19  C04  107.04  3.000
 R7Z  O21  C19  C04  107.34  3.000
 R7Z  H17  C19  C22  108.13  3.000
 R7Z  C04  C19  C22  111.42  3.000
 R7Z  O21  C19  C22  113.02  3.000
 R7Z  H18  O21  C19  108.71  3.000
 R7Z  H19  C23  C24  119.18  3.000
 R7Z  H19  C23  C22  119.57  3.000
 R7Z  C24  C23  C22  121.24  3.000
 R7Z  H20  C25  C26  120.51  3.000
 R7Z  H20  C25  C24  121.70  3.000
 R7Z  C26  C25  C24  117.79  3.000
 R7Z  H23  C29  H22  106.89  3.000
 R7Z  H23  C29  H21  107.39  3.000
 R7Z  H22  C29  H21  107.13  3.000
 R7Z  H23  C29  C28  112.84  3.000
 R7Z  H22  C29  C28  111.09  3.000
 R7Z  H21  C29  C28  111.20  3.000
 R7Z  C09  C07  O08  120.85  3.000
 R7Z  O08  C07  N06  123.47  3.000
 R7Z  C09  C07  N06  115.69  3.000
 R7Z  H9   C02  H8   106.21  3.000
 R7Z  H9   C02  C03  109.26  3.000
 R7Z  H8   C02  C03  110.14  3.000
 R7Z  H9   C02  C01  109.62  3.000
 R7Z  H8   C02  C01  109.37  3.000
 R7Z  C03  C02  C01  112.07  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
 R7Z  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 R7Z  CONST_02  C13  C18  C09  C10     0.00   0.0  0
 R7Z  CONST_03  C25  C24  C23  C22     0.00   0.0  0
 R7Z  CONST_04  C25  C26  C28  C22     0.00   0.0  0
 R7Z  CONST_05  C28  C22  C23  C24     0.00   0.0  0
 R7Z  CONST_06  C28  C26  C25  C24     0.00   0.0  0
 R7Z  CONST_07  C23  C22  C28  C26     0.00   0.0  0
 R7Z  CONST_08  C23  C24  C25  C26     0.00   0.0  0
 R7Z  CONST_09  C12  C11  C10  C09     0.00   0.0  0
 R7Z  CONST_10  C12  C13  C18  C09     0.00   0.0  0
 R7Z  CONST_11  C18  C13  C12  C11     0.00   0.0  0
 R7Z  CONST_12  C18  C09  C10  C11     0.00   0.0  0
 R7Z  CONST_13  C17  C15  N14  C13     0.00   0.0  0
 R7Z  CONST_14  C07  C09  C18  C13   180.00   0.0  0
 R7Z  CONST_15  C07  C09  C18  C17     0.00   0.0  0
 R7Z  CONST_16  F27  C26  C28  C22   180.00   0.0  0
 R7Z  CONST_17  C19  C22  C23  C24   180.00   0.0  0
 R7Z  CONST_18  F27  C26  C25  C24   180.00   0.0  0
 R7Z  CONST_19  C19  C22  C28  C26   180.00   0.0  0
 R7Z  CONST_20  C11  C10  C09  C07   180.00   0.0  0
 R7Z  CONST_21  C29  C28  C22  C23   180.00   0.0  0
 R7Z  CONST_22  C29  C28  C26  C25   180.00   0.0  0
 R7Z  CONST_23  O16  C15  N14  C13   180.00   0.0  0
 R7Z  CONST_24  H15  C12  C11  C10   180.00   0.0  0
 R7Z  CONST_25  H14  C11  C12  C13   180.00   0.0  0
 R7Z  CONST_26  H4   C24  C23  C22   180.00   0.0  0
 R7Z  CONST_27  H19  C23  C22  C28   180.00   0.0  0
 R7Z  CONST_28  H20  C25  C26  C28   180.00   0.0  0
 R7Z  CONST_29  H1   C10  C11  C12   180.00   0.0  0
 R7Z  CONST_30  H16  N14  C15  C17   180.00   0.0  0
 R7Z  CONST_31  C09  C07  N06  C04   180.00   0.0  0
 R7Z  CONST_32  H13  N06  C07  C09     0.00   0.0  0
 R7Z  CONST_33  O08  C07  N06  C04     0.00   0.0  0
 R7Z  Var_01    H2   C17  C18  C13  -117.01  30.0  1
 R7Z  Var_02    N06  C07  C09  C10   -37.83  30.0  2
 R7Z  Var_03    H21  C29  C28  C22   129.27  30.0  2
 R7Z  Var_04    C04  C03  C02  C01   176.27  30.0  3
 R7Z  Var_05    H5   C01  C02  C03  -179.90  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
 R7Z  chir_01  C04  N06  C19  C03  negativ
 R7Z  chir_02  C19  O21  C04  C22  positiv

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
 R7Z  plan-1  C22  0.020
 R7Z  plan-1  C24  0.020
 R7Z  plan-1  C26  0.020
 R7Z  plan-1  C28  0.020
 R7Z  plan-1  C19  0.020
 R7Z  plan-1  C23  0.020
 R7Z  plan-1  C25  0.020
 R7Z  plan-1  C29  0.020
 R7Z  plan-1  H4   0.020
 R7Z  plan-1  H19  0.020
 R7Z  plan-1  H20  0.020
 R7Z  plan-1  F27  0.020
 R7Z  plan-2  C04  0.020
 R7Z  plan-2  N06  0.020
 R7Z  plan-2  O08  0.020
 R7Z  plan-2  C09  0.020
 R7Z  plan-2  H13  0.020
 R7Z  plan-2  C07  0.020
 R7Z  plan-3  C10  0.020
 R7Z  plan-3  C13  0.020
 R7Z  plan-3  C15  0.020
 R7Z  plan-3  C17  0.020
 R7Z  plan-3  C09  0.020
 R7Z  plan-3  C11  0.020
 R7Z  plan-3  C12  0.020
 R7Z  plan-3  N14  0.020
 R7Z  plan-3  O16  0.020
 R7Z  plan-3  C18  0.020
 R7Z  plan-3  H1   0.020
 R7Z  plan-3  H14  0.020
 R7Z  plan-3  H15  0.020
 R7Z  plan-3  H16  0.020
 R7Z  plan-3  C07  0.020

