# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:58:07 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: [(2~{S},3~{R})-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
 D6C  D6C  '[(2~{S},3~{R})-5-[2-(dimethylamino)ethyl]-2-(4-methoxyphenyl)-4-oxidanylidene-2,3-dihydro-1,5-benzothiazepin-3-yl] ethanoate'  ligand  55  29  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D6C
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
 D6C  C13  C  CR16  0  -0.251   3.0774   3.2695  -1.6719
 D6C  C15  C  CR16  0  -0.275   3.3848   1.1135  -0.6543
 D6C  C21  C  CH3   0  -0.518   4.6358  -4.0768   0.4143
 D6C  C22  C  CH3   0  -0.524   2.4121  -4.6396  -0.2311
 D6C  C28  C  CH3   0  -0.766   2.4997   2.5148   2.7146
 D6C  C01  C  CH3   0  -0.438  -6.5627  -2.2724  -0.5254
 D6C  C03  C  CR6   0   0.377  -5.0550  -0.5500   0.0949
 D6C  C04  C  CR16  0  -0.328  -4.8218   0.6109   0.8354
 D6C  C05  C  CR16  0  -0.286  -3.5833   1.2212   0.7949
 D6C  C06  C  CR6   0   0.120  -2.5400   0.7001   0.0288
 D6C  C07  C  CR16  0  -0.258  -2.7861  -0.4510  -0.7086
 D6C  C08  C  CR16  0  -0.371  -4.0264  -1.0757  -0.6832
 D6C  C09  C  CH1   0  -0.499  -1.1973   1.3838   0.0755
 D6C  S10  S  S2    0   0.058  -0.5252   1.4734  -1.6270
 D6C  C11  C  CR6   0  -0.156   1.1872   1.8035  -1.3530
 D6C  C12  C  CR16  0  -0.262   1.7190   3.0143  -1.7825
 D6C  C14  C  CR16  0  -0.253   3.9098   2.3140  -1.1076
 D6C  C16  C  CR6   0   0.352   2.0264   0.8428  -0.7773
 D6C  N17  N  NT    0  -0.543   1.5228  -0.4029  -0.3474
 D6C  C18  C  CH2   0  -0.345   2.1590  -1.6232  -0.8446
 D6C  C19  C  CH2   0  -0.273   2.9798  -2.3446   0.2208
 D6C  N20  N  NT    0  -0.413   3.4451  -3.6255  -0.2732
 D6C  C23  C  C     0   0.520   0.4149  -0.5427   0.4263
 D6C  O24  O  O     0  -0.452  -0.1018  -1.6243   0.6324
 D6C  C25  C  CH1   0  -0.058  -0.2220   0.7019   1.0462
 D6C  O26  O  O2    0  -0.452   0.7043   1.6961   1.4593
 D6C  C27  C  C     0   0.572   1.6336   1.3496   2.3555
 D6C  O29  O  O     0  -0.431   1.7241   0.2335   2.7970
 D6C  H1   H  HCR6  0   0.266   3.4792   4.2114  -2.0199
 D6C  H2   H  HCR6  0   0.275   4.0400   0.3851  -0.1944
 D6C  H3   H  HCH3  0   0.232   4.9938  -5.0033  -0.0373
 D6C  H4   H  HCH3  0   0.234   5.4291  -3.3338   0.3221
 D6C  H5   H  HCH3  0   0.193   4.4777  -4.2698   1.4867
 D6C  H6   H  HCH3  0   0.194   2.0902  -4.8831   0.7933
 D6C  H7   H  HCH3  0   0.234   1.5291  -4.3246  -0.7870
 D6C  H8   H  HCH3  0   0.234   2.7748  -5.5582  -0.6942
 D6C  H9   H  HCH3  0   0.282   1.9172   3.2501   3.2717
 D6C  H10  H  HCH3  0   0.267   3.3365   2.1920   3.3269
 D6C  H11  H  HCH3  0   0.271   2.8743   3.0080   1.8179
 D6C  H12  H  HCH3  0   0.261  -7.5962  -2.5295  -0.3075
 D6C  H13  H  HCH3  0   0.230  -6.4544  -2.1393  -1.6048
 D6C  H14  H  HCH3  0   0.230  -5.9195  -3.0961  -0.2053
 D6C  H15  H  HCR6  0   0.265  -5.6171   1.0314   1.4379
 D6C  H16  H  HCR6  0   0.260  -3.4230   2.1216   1.3762
 D6C  H17  H  HCR6  0   0.255  -2.0118  -0.8807  -1.3300
 D6C  H18  H  HCR6  0   0.281  -4.1668  -1.9686  -1.2769
 D6C  H19  H  HCH1  0   0.324  -1.3484   2.4020   0.4422
 D6C  H20  H  HCR6  0   0.271   1.0612   3.7567  -2.2152
 D6C  H21  H  HCR6  0   0.269   4.9698   2.5044  -1.0058
 D6C  H22  H  HCH2  0   0.267   1.3832  -2.2723  -1.2510
 D6C  H23  H  HCH2  0   0.266   2.8031  -1.3478  -1.6781
 D6C  H24  H  HCH2  0   0.235   3.8516  -1.7323   0.4628
 D6C  H25  H  HCH2  0   0.216   2.4036  -2.4397   1.1530
 D6C  H27  H  HCH1  0   0.312  -0.7895   0.3548   1.9143
 D6C  O02  O  O2    0  -0.469  -6.2867  -1.0815   0.1861

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
 D6C  C21  N20  single    1.447  0.020  1.447
 D6C  N20  C22  single    1.448  0.020  1.448
 D6C  N20  C19  single    1.450  0.020  1.450
 D6C  S10  C11  single    1.765  0.020  1.765
 D6C  S10  C09  single    1.833  0.020  1.833
 D6C  C12  C11  aromatic  1.390  0.020  1.390
 D6C  C12  C13  aromatic  1.387  0.020  1.387
 D6C  C11  C16  aromatic  1.399  0.020  1.399
 D6C  O02  C03  single    1.345  0.020  1.345
 D6C  O02  C01  single    1.414  0.020  1.414
 D6C  C18  C19  single    1.526  0.020  1.526
 D6C  C18  N17  single    1.463  0.020  1.463
 D6C  C08  C03  aromatic  1.393  0.020  1.393
 D6C  C08  C07  aromatic  1.389  0.020  1.389
 D6C  C03  C04  aromatic  1.397  0.020  1.397
 D6C  C13  C14  aromatic  1.387  0.020  1.387
 D6C  C07  C06  aromatic  1.389  0.020  1.389
 D6C  C16  N17  single    1.411  0.020  1.411
 D6C  C16  C15  aromatic  1.391  0.020  1.391
 D6C  C04  C05  aromatic  1.381  0.020  1.381
 D6C  N17  C23  single    1.359  0.020  1.359
 D6C  C06  C05  aromatic  1.395  0.020  1.395
 D6C  C06  C09  single    1.507  0.020  1.507
 D6C  C14  C15  aromatic  1.386  0.020  1.386
 D6C  C09  C25  single    1.536  0.020  1.536
 D6C  C23  O24  double    1.216  0.020  1.216
 D6C  C23  C25  single    1.529  0.020  1.529
 D6C  C25  O26  single    1.420  0.020  1.420
 D6C  O26  C27  single    1.337  0.020  1.337
 D6C  O29  C27  double    1.204  0.020  1.204
 D6C  C27  C28  single    1.496  0.020  1.496
 D6C  C13  H1   single    0.930  0.020  1.080
 D6C  C15  H2   single    0.930  0.020  1.080
 D6C  C21  H3   single    0.970  0.020  1.090
 D6C  C21  H4   single    0.970  0.020  1.090
 D6C  C21  H5   single    0.970  0.020  1.090
 D6C  C22  H6   single    0.970  0.020  1.090
 D6C  C22  H7   single    0.970  0.020  1.090
 D6C  C22  H8   single    0.970  0.020  1.090
 D6C  C28  H9   single    0.970  0.020  1.090
 D6C  C28  H10  single    0.970  0.020  1.090
 D6C  C28  H11  single    0.970  0.020  1.090
 D6C  C01  H12  single    0.970  0.020  1.090
 D6C  C01  H13  single    0.970  0.020  1.090
 D6C  C01  H14  single    0.970  0.020  1.090
 D6C  C04  H15  single    0.930  0.020  1.080
 D6C  C05  H16  single    0.930  0.020  1.080
 D6C  C07  H17  single    0.930  0.020  1.080
 D6C  C08  H18  single    0.930  0.020  1.080
 D6C  C09  H19  single    0.970  0.020  1.090
 D6C  C12  H20  single    0.930  0.020  1.080
 D6C  C14  H21  single    0.930  0.020  1.080
 D6C  C18  H22  single    0.970  0.020  1.090
 D6C  C18  H23  single    0.970  0.020  1.090
 D6C  C19  H24  single    0.970  0.020  1.090
 D6C  C19  H25  single    0.970  0.020  1.090
 D6C  C25  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
 D6C  H1   C13  C14  120.52  3.000
 D6C  H1   C13  C12  119.91  3.000
 D6C  C14  C13  C12  119.57  3.000
 D6C  H2   C15  C16  119.86  3.000
 D6C  H2   C15  C14  119.50  3.000
 D6C  C16  C15  C14  120.64  3.000
 D6C  H5   C21  H4   107.83  3.000
 D6C  H5   C21  H3   107.54  3.000
 D6C  H4   C21  H3   107.74  3.000
 D6C  H5   C21  N20  113.53  3.000
 D6C  H4   C21  N20  110.24  3.000
 D6C  H3   C21  N20  109.76  3.000
 D6C  H8   C22  H7   107.24  3.000
 D6C  H8   C22  H6   107.82  3.000
 D6C  H7   C22  H6   107.55  3.000
 D6C  H8   C22  N20  109.89  3.000
 D6C  H7   C22  N20  111.14  3.000
 D6C  H6   C22  N20  112.98  3.000
 D6C  H11  C28  H10  109.49  3.000
 D6C  H11  C28  H9   107.38  3.000
 D6C  H10  C28  H9   108.89  3.000
 D6C  H11  C28  C27  110.74  3.000
 D6C  H10  C28  C27  110.49  3.000
 D6C  H9   C28  C27  109.78  3.000
 D6C  H14  C01  H13  108.82  3.000
 D6C  H14  C01  H12  108.82  3.000
 D6C  H13  C01  H12  108.73  3.000
 D6C  H14  C01  O02  111.86  3.000
 D6C  H13  C01  O02  112.02  3.000
 D6C  H12  C01  O02  106.49  3.000
 D6C  C08  C03  C04  119.12  3.000
 D6C  C04  C03  O02  116.47  3.000
 D6C  C08  C03  O02  124.41  3.000
 D6C  H15  C04  C05  120.23  3.000
 D6C  H15  C04  C03  119.68  3.000
 D6C  C05  C04  C03  120.09  3.000
 D6C  H16  C05  C06  119.62  3.000
 D6C  H16  C05  C04  118.94  3.000
 D6C  C06  C05  C04  121.44  3.000
 D6C  C09  C06  C07  123.38  3.000
 D6C  C09  C06  C05  118.66  3.000
 D6C  C07  C06  C05  117.94  3.000
 D6C  H17  C07  C08  118.10  3.000
 D6C  H17  C07  C06  120.48  3.000
 D6C  C08  C07  C06  121.41  3.000
 D6C  H18  C08  C07  118.51  3.000
 D6C  H18  C08  C03  121.50  3.000
 D6C  C07  C08  C03  119.99  3.000
 D6C  H19  C09  C25  106.82  3.000
 D6C  H19  C09  S10  108.48  3.000
 D6C  C25  C09  S10  112.09  3.000
 D6C  H19  C09  C06  108.05  3.000
 D6C  C25  C09  C06  112.57  3.000
 D6C  S10  C09  C06  108.66  3.000
 D6C  C11  S10  C09  102.75  3.000
 D6C  C16  C11  C12  119.70  3.000
 D6C  C16  C11  S10  121.14  3.000
 D6C  C12  C11  S10  119.07  3.000
 D6C  H20  C12  C11  119.24  3.000
 D6C  H20  C12  C13  120.07  3.000
 D6C  C11  C12  C13  120.69  3.000
 D6C  H21  C14  C15  119.51  3.000
 D6C  H21  C14  C13  120.34  3.000
 D6C  C15  C14  C13  120.15  3.000
 D6C  N17  C16  C11  121.16  3.000
 D6C  N17  C16  C15  119.58  3.000
 D6C  C11  C16  C15  119.24  3.000
 D6C  C23  N17  C18  117.53  3.000
 D6C  C23  N17  C16  123.75  3.000
 D6C  C18  N17  C16  118.53  3.000
 D6C  H23  C18  H22  106.63  3.000
 D6C  H23  C18  C19  109.62  3.000
 D6C  H22  C18  C19  111.20  3.000
 D6C  H23  C18  N17  107.85  3.000
 D6C  H22  C18  N17  108.29  3.000
 D6C  C19  C18  N17  113.00  3.000
 D6C  H25  C19  H24  106.19  3.000
 D6C  H25  C19  N20  112.36  3.000
 D6C  H24  C19  N20  108.34  3.000
 D6C  H25  C19  C18  110.53  3.000
 D6C  H24  C19  C18  108.60  3.000
 D6C  N20  C19  C18  110.63  3.000
 D6C  C19  N20  C22  112.33  3.000
 D6C  C19  N20  C21  112.19  3.000
 D6C  C22  N20  C21  110.78  3.000
 D6C  C25  C23  O24  118.56  3.000
 D6C  C25  C23  N17  119.13  3.000
 D6C  O24  C23  N17  122.31  3.000
 D6C  H27  C25  O26  109.25  3.000
 D6C  H27  C25  C23  106.24  3.000
 D6C  O26  C25  C23  114.58  3.000
 D6C  H27  C25  C09  108.25  3.000
 D6C  O26  C25  C09  106.69  3.000
 D6C  C23  C25  C09  111.69  3.000
 D6C  C27  O26  C25  117.84  3.000
 D6C  O29  C27  O26  122.58  3.000
 D6C  O29  C27  C28  126.21  3.000
 D6C  O26  C27  C28  111.20  3.000
 D6C  C03  O02  C01  118.52  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
 D6C  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 D6C  CONST_02  C12  C13  C14  C15    0.00   0.0  0
 D6C  CONST_03  C06  C07  C08  C03    0.00   0.0  0
 D6C  CONST_04  C06  C05  C04  C03    0.00   0.0  0
 D6C  CONST_05  C07  C08  C03  C04    0.00   0.0  0
 D6C  CONST_06  C07  C06  C05  C04    0.00   0.0  0
 D6C  CONST_07  C08  C03  C04  C05    0.00   0.0  0
 D6C  CONST_08  C08  C07  C06  C05    0.00   0.0  0
 D6C  CONST_09  C14  C13  C12  C11    0.00   0.0  0
 D6C  CONST_10  C09  C06  C05  C04  180.00   0.0  0
 D6C  CONST_11  C09  C06  C07  C08  180.00   0.0  0
 D6C  CONST_12  C07  C08  C03  O02  180.00   0.0  0
 D6C  CONST_13  C05  C04  C03  O02  180.00   0.0  0
 D6C  CONST_14  H2   C15  C14  C13  180.00   0.0  0
 D6C  CONST_15  H1   C13  C14  C15  180.00   0.0  0
 D6C  CONST_16  H17  C07  C08  C03  180.00   0.0  0
 D6C  CONST_17  H16  C05  C04  C03  180.00   0.0  0
 D6C  CONST_18  H18  C08  C03  C04  180.00   0.0  0
 D6C  CONST_19  H15  C04  C05  C06  180.00   0.0  0
 D6C  CONST_20  H21  C14  C13  C12  180.00   0.0  0
 D6C  CONST_21  H20  C12  C13  C14  180.00   0.0  0
 D6C  Var_01    C08  C03  O02  C01    1.57  30.0  2
 D6C  Var_02    N20  C19  C18  N17  172.77  30.0  3
 D6C  Var_03    O29  C27  O26  C25    1.42  30.0  3
 D6C  Var_04    H12  C01  O02  C03  179.46  30.0  3
 D6C  Var_05    C18  C19  N20  C21  155.50  30.0  3
 D6C  Var_06    H6   C22  N20  C21   61.64  30.0  3
 D6C  Var_07    H3   C21  N20  C22   57.83  30.0  3
 D6C  Var_08    H9   C28  C27  O26   68.19  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
 D6C  chir_01  C09  S10  C06  C25  negativ
 D6C  chir_02  C25  O26  C09  C23  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
 D6C  plan-1  C03  0.020
 D6C  plan-1  C04  0.020
 D6C  plan-1  C05  0.020
 D6C  plan-1  C06  0.020
 D6C  plan-1  C07  0.020
 D6C  plan-1  C08  0.020
 D6C  plan-1  C09  0.020
 D6C  plan-1  H15  0.020
 D6C  plan-1  H16  0.020
 D6C  plan-1  H17  0.020
 D6C  plan-1  H18  0.020
 D6C  plan-1  O02  0.020
 D6C  plan-2  C13  0.020
 D6C  plan-2  C15  0.020
 D6C  plan-2  S10  0.020
 D6C  plan-2  C11  0.020
 D6C  plan-2  C12  0.020
 D6C  plan-2  C14  0.020
 D6C  plan-2  C16  0.020
 D6C  plan-2  N17  0.020
 D6C  plan-2  H1   0.020
 D6C  plan-2  H2   0.020
 D6C  plan-2  H20  0.020
 D6C  plan-2  H21  0.020
 D6C  plan-3  C16  0.020
 D6C  plan-3  N17  0.020
 D6C  plan-3  C18  0.020
 D6C  plan-3  C23  0.020
 D6C  plan-3  O24  0.020
 D6C  plan-3  C25  0.020
 D6C  plan-4  C28  0.020
 D6C  plan-4  O26  0.020
 D6C  plan-4  C27  0.020
 D6C  plan-4  O29  0.020

