# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 22:20:39 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [(2~{S},3~{S})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@@H]2Sc3ccccc3N(CCN(C)C)C(=O)[C@@H]2OC(C)=O
#
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
 C9F  C9F  '[(2~{S},3~{S})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate'  ligand  55  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C9F
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
 C9F  C10  C  CR16  0  -0.331   4.3746   0.6758   0.7712
 C9F  C13  C  CH3   0  -0.437   5.8063  -2.6283   0.2927
 C9F  C15  C  CR16  0  -0.268   2.0417  -0.8054   0.6513
 C9F  C20  C  CH3   0  -0.771   1.7630   3.0386  -3.2778
 C9F  C21  C  CR16  0  -0.261  -2.8111   1.7288   2.4795
 C9F  C22  C  CR16  0  -0.246  -4.0965   2.1445   2.1706
 C9F  C24  C  CR16  0  -0.273  -3.8831   1.1590  -0.0117
 C9F  C26  C  CH2   0  -0.265  -2.0883  -2.4488  -0.2387
 C9F  C28  C  CH3   0  -0.528  -2.0915  -4.2156  -1.8757
 C9F  O01  O  O     0  -0.457   0.0218  -0.3705  -1.8372
 C9F  C02  C  C     0   0.523  -0.6178   0.2965  -1.0487
 C9F  N03  N  NT    0  -0.547  -1.8760  -0.0312  -0.6583
 C9F  C04  C  CR6   0   0.344  -2.6020   0.7141   0.2989
 C9F  C05  C  CR6   0  -0.170  -2.0628   1.0030   1.5570
 C9F  S06  S  S2    0   0.072  -0.4760   0.3842   2.0229
 C9F  C07  C  CH1   0  -0.494   0.6485   1.3117   0.9123
 C9F  C08  C  CR6   0   0.145   1.9558   0.5704   0.8211
 C9F  C09  C  CR16  0  -0.277   3.1456   1.2956   0.8833
 C9F  C11  C  CR6   0   0.375   4.4476  -0.7071   0.5909
 C9F  O12  O  O2    0  -0.469   5.6812  -1.2332   0.4878
 C9F  C14  C  CR16  0  -0.374   3.2689  -1.4467   0.5379
 C9F  C16  C  CH1   0  -0.046  -0.0282   1.5696  -0.4456
 C9F  O17  O  O2    0  -0.445   0.9778   2.0807  -1.2926
 C9F  C18  C  C     0   0.568   0.5941   2.5433  -2.4862
 C9F  O19  O  O     0  -0.442  -0.5562   2.5543  -2.8412
 C9F  C23  C  CR16  0  -0.256  -4.6304   1.8595   0.9211
 C9F  N27  N  NT    0  -0.410  -2.7081  -3.6820  -0.6787
 C9F  C29  C  CH3   0  -0.520  -2.7180  -4.6747   0.3748
 C9F  H1   H  HCR6  0   0.263   5.2858   1.2585   0.8241
 C9F  H2   H  HCH3  0   0.229   5.4006  -3.1965   1.1339
 C9F  H3   H  HCH3  0   0.229   5.3129  -2.9571  -0.6254
 C9F  H4   H  HCH3  0   0.260   6.8705  -2.8349   0.2123
 C9F  H5   H  HCR6  0   0.259   1.1467  -1.4135   0.6221
 C9F  H6   H  HCH3  0   0.265   1.4427   3.3689  -4.2614
 C9F  H7   H  HCH3  0   0.277   2.2415   3.8710  -2.7605
 C9F  H8   H  HCH3  0   0.274   2.5107   2.2529  -3.3871
 C9F  H9   H  HCR6  0   0.274  -2.3808   1.9608   3.4448
 C9F  H10  H  HCR6  0   0.269  -4.6727   2.6997   2.8985
 C9F  H11  H  HCR6  0   0.280  -4.2942   0.9614  -0.9933
 C9F  H12  H  HCH2  0   0.209  -0.9910  -2.5356  -0.1720
 C9F  H13  H  HCH2  0   0.235  -2.4458  -2.2253   0.7699
 C9F  H14  H  HCH3  0   0.237  -2.6228  -5.1129  -2.1951
 C9F  H15  H  HCH3  0   0.236  -2.1417  -3.5010  -2.6971
 C9F  H16  H  HCH3  0   0.194  -1.0336  -4.4854  -1.7305
 C9F  H17  H  HCH1  0   0.321   0.8340   2.2913   1.3588
 C9F  H18  H  HCR6  0   0.255   3.1108   2.3693   1.0217
 C9F  H19  H  HCR6  0   0.279   3.2810  -2.5206   0.4112
 C9F  H20  H  HCH1  0   0.302  -0.8071   2.3239  -0.3049
 C9F  H21  H  HCR6  0   0.270  -5.6257   2.1959   0.6641
 C9F  H22  H  HCH2  0   0.260  -2.1289  -1.4371  -2.1690
 C9F  H23  H  HCH2  0   0.263  -3.5420  -1.1717  -1.1676
 C9F  H25  H  HCH3  0   0.193  -1.7103  -4.9820   0.6948
 C9F  H26  H  HCH3  0   0.234  -3.2436  -4.2916   1.2504
 C9F  H27  H  HCH3  0   0.233  -3.2433  -5.5692   0.0370
 C9F  C25  C  CH2   0  -0.340  -2.4585  -1.2785  -1.1445

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
 C9F  C20  C18  single    1.496  0.020  1.496
 C9F  C18  O19  double    1.204  0.020  1.204
 C9F  C18  O17  single    1.336  0.020  1.336
 C9F  O17  C16  single    1.411  0.020  1.411
 C9F  O01  C02  double    1.215  0.020  1.215
 C9F  C16  C02  single    1.527  0.020  1.527
 C9F  C16  C07  single    1.539  0.020  1.539
 C9F  C10  C09  aromatic  1.381  0.020  1.381
 C9F  C10  C11  aromatic  1.396  0.020  1.396
 C9F  O12  C11  single    1.345  0.020  1.345
 C9F  O12  C13  single    1.414  0.020  1.414
 C9F  C09  C08  aromatic  1.395  0.020  1.395
 C9F  C11  C14  aromatic  1.393  0.020  1.393
 C9F  C28  N27  single    1.448  0.020  1.448
 C9F  C02  N03  single    1.358  0.020  1.358
 C9F  N27  C29  single    1.448  0.020  1.448
 C9F  N27  C26  single    1.449  0.020  1.449
 C9F  C08  C07  single    1.506  0.020  1.506
 C9F  C08  C15  aromatic  1.389  0.020  1.389
 C9F  C14  C15  aromatic  1.389  0.020  1.389
 C9F  C07  S06  single    1.832  0.020  1.832
 C9F  N03  C25  single    1.460  0.020  1.460
 C9F  N03  C04  single    1.414  0.020  1.414
 C9F  C26  C25  single    1.526  0.020  1.526
 C9F  S06  C05  single    1.766  0.020  1.766
 C9F  C04  C05  aromatic  1.399  0.020  1.399
 C9F  C04  C24  aromatic  1.391  0.020  1.391
 C9F  C05  C21  aromatic  1.392  0.020  1.392
 C9F  C24  C23  aromatic  1.385  0.020  1.385
 C9F  C21  C22  aromatic  1.386  0.020  1.386
 C9F  C23  C22  aromatic  1.388  0.020  1.388
 C9F  C10  H1   single    0.930  0.020  1.080
 C9F  C13  H2   single    0.970  0.020  1.090
 C9F  C13  H3   single    0.970  0.020  1.090
 C9F  C13  H4   single    0.970  0.020  1.090
 C9F  C15  H5   single    0.930  0.020  1.080
 C9F  C20  H6   single    0.970  0.020  1.090
 C9F  C20  H7   single    0.970  0.020  1.090
 C9F  C20  H8   single    0.970  0.020  1.090
 C9F  C21  H9   single    0.930  0.020  1.080
 C9F  C22  H10  single    0.930  0.020  1.080
 C9F  C24  H11  single    0.930  0.020  1.080
 C9F  C26  H12  single    0.970  0.020  1.090
 C9F  C26  H13  single    0.970  0.020  1.090
 C9F  C28  H14  single    0.970  0.020  1.090
 C9F  C28  H15  single    0.970  0.020  1.090
 C9F  C28  H16  single    0.970  0.020  1.090
 C9F  C07  H17  single    0.970  0.020  1.090
 C9F  C09  H18  single    0.930  0.020  1.080
 C9F  C14  H19  single    0.930  0.020  1.080
 C9F  C16  H20  single    0.970  0.020  1.090
 C9F  C23  H21  single    0.930  0.020  1.080
 C9F  C25  H22  single    0.970  0.020  1.090
 C9F  C25  H23  single    0.970  0.020  1.090
 C9F  C29  H25  single    0.970  0.020  1.090
 C9F  C29  H26  single    0.970  0.020  1.090
 C9F  C29  H27  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
 C9F  H1   C10  C11  119.69  3.000
 C9F  H1   C10  C09  120.22  3.000
 C9F  C11  C10  C09  120.09  3.000
 C9F  H4   C13  H3   108.82  3.000
 C9F  H4   C13  H2   108.75  3.000
 C9F  H3   C13  H2   108.81  3.000
 C9F  H4   C13  O12  106.52  3.000
 C9F  H3   C13  O12  111.88  3.000
 C9F  H2   C13  O12  111.95  3.000
 C9F  H5   C15  C14  117.95  3.000
 C9F  H5   C15  C08  120.58  3.000
 C9F  C14  C15  C08  121.46  3.000
 C9F  H8   C20  H7   107.26  3.000
 C9F  H8   C20  H6   109.31  3.000
 C9F  H7   C20  H6   109.08  3.000
 C9F  H8   C20  C18  110.51  3.000
 C9F  H7   C20  C18  110.16  3.000
 C9F  H6   C20  C18  110.46  3.000
 C9F  H9   C21  C05  119.29  3.000
 C9F  H9   C21  C22  120.23  3.000
 C9F  C05  C21  C22  120.48  3.000
 C9F  H10  C22  C23  120.41  3.000
 C9F  H10  C22  C21  119.87  3.000
 C9F  C23  C22  C21  119.72  3.000
 C9F  H11  C24  C23  119.87  3.000
 C9F  H11  C24  C04  119.59  3.000
 C9F  C23  C24  C04  120.53  3.000
 C9F  H13  C26  H12  106.60  3.000
 C9F  H13  C26  N27  108.32  3.000
 C9F  H12  C26  N27  112.15  3.000
 C9F  H13  C26  C25  108.16  3.000
 C9F  H12  C26  C25  109.74  3.000
 C9F  N27  C26  C25  111.65  3.000
 C9F  H16  C28  H15  107.71  3.000
 C9F  H16  C28  H14  107.76  3.000
 C9F  H15  C28  H14  107.24  3.000
 C9F  H16  C28  N27  112.97  3.000
 C9F  H15  C28  N27  111.20  3.000
 C9F  H14  C28  N27  109.74  3.000
 C9F  C16  C02  N03  116.46  3.000
 C9F  N03  C02  O01  122.82  3.000
 C9F  C16  C02  O01  120.72  3.000
 C9F  C25  N03  C04  118.10  3.000
 C9F  C04  N03  C02  122.91  3.000
 C9F  C25  N03  C02  118.70  3.000
 C9F  C05  C04  N03  121.32  3.000
 C9F  C05  C04  C24  119.32  3.000
 C9F  N03  C04  C24  119.36  3.000
 C9F  S06  C05  C04  120.75  3.000
 C9F  C04  C05  C21  119.77  3.000
 C9F  S06  C05  C21  119.40  3.000
 C9F  C07  S06  C05  102.37  3.000
 C9F  H17  C07  C16  106.56  3.000
 C9F  H17  C07  C08  108.59  3.000
 C9F  C16  C07  C08  114.26  3.000
 C9F  H17  C07  S06  108.08  3.000
 C9F  C08  C07  S06  108.69  3.000
 C9F  C16  C07  S06  110.47  3.000
 C9F  C09  C08  C07  118.82  3.000
 C9F  C07  C08  C15  123.28  3.000
 C9F  C09  C08  C15  117.89  3.000
 C9F  H18  C09  C08  119.58  3.000
 C9F  H18  C09  C10  118.94  3.000
 C9F  C08  C09  C10  121.48  3.000
 C9F  C14  C11  O12  124.44  3.000
 C9F  C14  C11  C10  119.12  3.000
 C9F  O12  C11  C10  116.43  3.000
 C9F  C11  O12  C13  118.52  3.000
 C9F  H19  C14  C11  121.50  3.000
 C9F  H19  C14  C15  118.55  3.000
 C9F  C11  C14  C15  119.95  3.000
 C9F  H20  C16  O17  109.59  3.000
 C9F  H20  C16  C07  108.38  3.000
 C9F  O17  C16  C07  106.07  3.000
 C9F  H20  C16  C02  110.54  3.000
 C9F  C07  C16  C02  112.24  3.000
 C9F  O17  C16  C02  109.89  3.000
 C9F  C18  O17  C16  117.18  3.000
 C9F  O19  C18  O17  122.74  3.000
 C9F  O17  C18  C20  111.27  3.000
 C9F  O19  C18  C20  125.98  3.000
 C9F  H21  C23  C24  119.57  3.000
 C9F  H21  C23  C22  120.26  3.000
 C9F  C24  C23  C22  120.16  3.000
 C9F  C29  N27  C28  110.59  3.000
 C9F  C29  N27  C26  111.45  3.000
 C9F  C28  N27  C26  112.49  3.000
 C9F  H27  C29  H26  107.73  3.000
 C9F  H27  C29  H25  107.57  3.000
 C9F  H26  C29  H25  107.80  3.000
 C9F  H27  C29  N27  109.89  3.000
 C9F  H26  C29  N27  110.28  3.000
 C9F  H25  C29  N27  113.37  3.000
 C9F  H23  C25  H22  107.21  3.000
 C9F  H23  C25  N03  108.68  3.000
 C9F  H22  C25  N03  108.50  3.000
 C9F  H23  C25  C26  109.22  3.000
 C9F  H22  C25  C26  111.95  3.000
 C9F  N03  C25  C26  111.15  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
 C9F  CONST_01  C15  C08  C09  C10     0.00   0.0  0
 C9F  CONST_02  C15  C14  C11  C10     0.00   0.0  0
 C9F  CONST_03  C24  C23  C22  C21     0.00   0.0  0
 C9F  CONST_04  C04  C24  C23  C22     0.00   0.0  0
 C9F  CONST_05  C23  C22  C21  C05     0.00   0.0  0
 C9F  CONST_06  C11  C10  C09  C08     0.00   0.0  0
 C9F  CONST_07  C11  C14  C15  C08     0.00   0.0  0
 C9F  CONST_08  C14  C11  C10  C09     0.00   0.0  0
 C9F  CONST_09  C14  C15  C08  C09     0.00   0.0  0
 C9F  CONST_10  C07  C08  C09  C10   180.00   0.0  0
 C9F  CONST_11  C14  C15  C08  C07   180.00   0.0  0
 C9F  CONST_12  O12  C11  C14  C15   180.00   0.0  0
 C9F  CONST_13  O12  C11  C10  C09   180.00   0.0  0
 C9F  CONST_14  H19  C14  C11  C10   180.00   0.0  0
 C9F  CONST_15  H18  C09  C08  C15   180.00   0.0  0
 C9F  CONST_16  H21  C23  C22  C21   180.00   0.0  0
 C9F  CONST_17  H11  C24  C23  C22   180.00   0.0  0
 C9F  CONST_18  H10  C22  C23  C24   180.00   0.0  0
 C9F  CONST_19  H5   C15  C08  C07     0.00   0.0  0
 C9F  CONST_20  H1   C10  C09  C08   180.00   0.0  0
 C9F  CONST_21  H9   C21  C22  C23   180.00   0.0  0
 C9F  Var_01    C14  C11  O12  C13     0.95  30.0  2
 C9F  Var_02    N27  C26  C25  N03   177.52  30.0  1
 C9F  Var_03    O19  C18  O17  C16     1.11  30.0  2
 C9F  Var_04    H2   C13  O12  C11   -62.63  30.0  3
 C9F  Var_05    C25  C26  N27  C28    73.36  30.0  3
 C9F  Var_06    H14  C28  N27  C26  -177.15  30.0  3
 C9F  Var_07    H25  C29  N27  C26   -63.04  30.0  3
 C9F  Var_08    H6   C20  C18  O17   177.41  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
 C9F  chir_01  C07  C16  C08  S06  positiv
 C9F  chir_02  C16  O17  C07  C02  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
 C9F  plan-1  C10  0.020
 C9F  plan-1  C15  0.020
 C9F  plan-1  C07  0.020
 C9F  plan-1  C08  0.020
 C9F  plan-1  C09  0.020
 C9F  plan-1  C11  0.020
 C9F  plan-1  O12  0.020
 C9F  plan-1  C14  0.020
 C9F  plan-1  H1   0.020
 C9F  plan-1  H5   0.020
 C9F  plan-1  H18  0.020
 C9F  plan-1  H19  0.020
 C9F  plan-2  C21  0.020
 C9F  plan-2  C22  0.020
 C9F  plan-2  C24  0.020
 C9F  plan-2  N03  0.020
 C9F  plan-2  C04  0.020
 C9F  plan-2  C05  0.020
 C9F  plan-2  S06  0.020
 C9F  plan-2  C23  0.020
 C9F  plan-2  H9   0.020
 C9F  plan-2  H10  0.020
 C9F  plan-2  H11  0.020
 C9F  plan-2  H21  0.020
 C9F  plan-3  O01  0.020
 C9F  plan-3  C02  0.020
 C9F  plan-3  N03  0.020
 C9F  plan-3  C04  0.020
 C9F  plan-3  C16  0.020
 C9F  plan-3  C25  0.020
 C9F  plan-4  C20  0.020
 C9F  plan-4  O17  0.020
 C9F  plan-4  C18  0.020
 C9F  plan-4  O19  0.020

