# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 09:06:38 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccc2Sc3ccccc3C[C@H](N4CCN(C)CC4)c2c1
#
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
 89F  89F  1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine  ligand  48  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_89F
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
 89F  C7   C  CR6   0  -0.194  -3.2169   0.4603   0.4306
 89F  C6   C  CH1   0  -0.121  -0.3600  -0.8986  -0.4088
 89F  C10  C  CR6   0   0.227  -2.8877  -0.7325  -0.2131
 89F  C9   C  CR16  0  -0.269   1.1952   0.9947  -0.6007
 89F  C4   C  CR16  0  -0.272   1.0371   3.1080   0.5140
 89F  C2   C  CR6   0   0.181   0.0189   0.5315  -0.0131
 89F  N1   N  NT    0  -0.416   0.7980  -1.7446  -0.1848
 89F  N2   N  NT    0  -0.415   2.5687  -3.8392   0.5220
 89F  C1   C  CR6   0  -0.234  -0.6655   1.4062   0.8400
 89F  C3   C  CR16  0  -0.209  -0.1443   2.6765   1.0871
 89F  C5   C  CH3   0  -0.516   3.8521  -4.4902   0.6396
 89F  C8   C  CH3   0  -0.797   3.5786   4.3360  -0.5761
 89F  C11  C  CH2   0  -0.275   2.2212  -3.5837  -0.8608
 89F  C12  C  CR6   0  -0.098   1.7172   2.2593  -0.3538
 89F  C13  C  CR16  0  -0.231  -4.3694   1.1636   0.1026
 89F  C14  C  CH2   0  -0.289   1.1300  -1.9910   1.2017
 89F  C15  C  CR16  0  -0.269  -5.2089   0.6822  -0.8926
 89F  C16  C  CR16  0  -0.329  -3.7305  -1.1877  -1.2228
 89F  C17  C  CH2   0  -0.291   0.8395  -2.9635  -0.9612
 89F  C18  C  CH2   0  -0.274   2.5104  -2.6144   1.2944
 89F  C19  C  CR16  0  -0.238  -4.8831  -0.4907  -1.5601
 89F  C20  C  CH2   0  -0.578  -1.6554  -1.4813   0.1819
 89F  S1   S  S2    0   0.042   3.2166   2.6766  -1.1750
 89F  S2   S  S2    0   0.021  -2.1643   1.0459   1.7254
 89F  H1   H  HCH1  0   0.263  -0.5042  -0.8738  -1.4958
 89F  H2   H  HCR6  0   0.260   1.7308   0.3139  -1.2516
 89F  H3   H  HCR6  0   0.268   1.3958   4.1024   0.7387
 89F  H6   H  HCR6  0   0.268  -0.6836   3.3497   1.7412
 89F  H7   H  HCH3  0   0.231   4.0688  -4.7045   1.6874
 89F  H8   H  HCH3  0   0.231   3.8407  -5.4384   0.0992
 89F  H9   H  HCH3  0   0.190   4.6852  -3.8895   0.2415
 89F  H10  H  HCH3  0   0.275   2.8073   5.0477  -0.8648
 89F  H11  H  HCH3  0   0.275   3.7165   4.3536   0.5036
 89F  H12  H  HCH3  0   0.296   4.5131   4.6275  -1.0513
 89F  H13  H  HCH2  0   0.188   2.9488  -2.9111  -1.3475
 89F  H14  H  HCH2  0   0.232   2.2322  -4.5266  -1.4136
 89F  H15  H  HCR6  0   0.266  -4.6039   2.0874   0.6157
 89F  H16  H  HCH2  0   0.240   1.1276  -1.0476   1.7529
 89F  H17  H  HCH2  0   0.200   0.4071  -2.6593   1.6967
 89F  H18  H  HCR6  0   0.261  -6.1073   1.2270  -1.1516
 89F  H19  H  HCR6  0   0.253  -3.4892  -2.1096  -1.7386
 89F  H20  H  HCH2  0   0.195   0.0915  -3.7073  -0.6403
 89F  H21  H  HCH2  0   0.237   0.6285  -2.7286  -2.0073
 89F  H22  H  HCH2  0   0.232   2.7319  -2.8422   2.3403
 89F  H23  H  HCH2  0   0.188   3.2606  -1.8790   0.9551
 89F  H24  H  HCR6  0   0.260  -5.5294  -0.8682  -2.3418
 89F  H25  H  HCH2  0   0.270  -1.7393  -2.5105  -0.1736
 89F  H26  H  HCH2  0   0.264  -1.5870  -1.5293   1.2712

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
 89F  C19  C15  aromatic  1.388  0.020  1.388
 89F  C19  C16  aromatic  1.389  0.020  1.389
 89F  C15  C13  aromatic  1.388  0.020  1.388
 89F  C16  C10  aromatic  1.392  0.020  1.392
 89F  C5   N2   single    1.444  0.020  1.444
 89F  N2   C18  single    1.449  0.020  1.449
 89F  N2   C11  single    1.449  0.020  1.449
 89F  C18  C14  single    1.517  0.020  1.517
 89F  C14  N1   single    1.447  0.020  1.447
 89F  C13  C7   aromatic  1.389  0.020  1.389
 89F  C10  C7   aromatic  1.395  0.020  1.395
 89F  C10  C20  single    1.495  0.020  1.495
 89F  C7   S2   single    1.768  0.020  1.768
 89F  C20  C6   single    1.538  0.020  1.538
 89F  C11  C17  single    1.518  0.020  1.518
 89F  C17  N1   single    1.446  0.020  1.446
 89F  N1   C6   single    1.452  0.020  1.452
 89F  C6   C2   single    1.532  0.020  1.532
 89F  S2   C1   single    1.778  0.020  1.778
 89F  C2   C1   aromatic  1.400  0.020  1.400
 89F  C2   C9   aromatic  1.394  0.020  1.394
 89F  C1   C3   aromatic  1.395  0.020  1.395
 89F  C9   C12  aromatic  1.390  0.020  1.390
 89F  C3   C4   aromatic  1.382  0.020  1.382
 89F  C12  C4   aromatic  1.391  0.020  1.391
 89F  C12  S1   single    1.760  0.020  1.760
 89F  S1   C8   single    1.801  0.020  1.801
 89F  C6   H1   single    0.970  0.020  1.090
 89F  C9   H2   single    0.930  0.020  1.080
 89F  C4   H3   single    0.930  0.020  1.080
 89F  C3   H6   single    0.930  0.020  1.080
 89F  C5   H7   single    0.970  0.020  1.090
 89F  C5   H8   single    0.970  0.020  1.090
 89F  C5   H9   single    0.970  0.020  1.090
 89F  C8   H10  single    0.970  0.020  1.090
 89F  C8   H11  single    0.970  0.020  1.090
 89F  C8   H12  single    0.970  0.020  1.090
 89F  C11  H13  single    0.970  0.020  1.090
 89F  C11  H14  single    0.970  0.020  1.090
 89F  C13  H15  single    0.930  0.020  1.080
 89F  C14  H16  single    0.970  0.020  1.090
 89F  C14  H17  single    0.970  0.020  1.090
 89F  C15  H18  single    0.930  0.020  1.080
 89F  C16  H19  single    0.930  0.020  1.080
 89F  C17  H20  single    0.970  0.020  1.090
 89F  C17  H21  single    0.970  0.020  1.090
 89F  C18  H22  single    0.970  0.020  1.090
 89F  C18  H23  single    0.970  0.020  1.090
 89F  C19  H24  single    0.930  0.020  1.080
 89F  C20  H25  single    0.970  0.020  1.090
 89F  C20  H26  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
 89F  S2   C7   C13  119.93  3.000
 89F  S2   C7   C10  118.72  3.000
 89F  C13  C7   C10  121.31  3.000
 89F  H1   C6   C20  106.17  3.000
 89F  H1   C6   N1   105.72  3.000
 89F  C20  C6   N1   113.06  3.000
 89F  H1   C6   C2   105.51  3.000
 89F  N1   C6   C2   107.88  3.000
 89F  C20  C6   C2   117.57  3.000
 89F  C20  C10  C16  121.80  3.000
 89F  C20  C10  C7   120.06  3.000
 89F  C16  C10  C7   118.14  3.000
 89F  H2   C9   C12  119.51  3.000
 89F  H2   C9   C2   117.49  3.000
 89F  C12  C9   C2   122.97  3.000
 89F  H3   C4   C12  121.92  3.000
 89F  H3   C4   C3   119.00  3.000
 89F  C12  C4   C3   119.08  3.000
 89F  C1   C2   C9   117.49  3.000
 89F  C9   C2   C6   114.21  3.000
 89F  C1   C2   C6   128.30  3.000
 89F  C17  N1   C14  111.38  3.000
 89F  C17  N1   C6   115.56  3.000
 89F  C14  N1   C6   115.48  3.000
 89F  C18  N2   C11  110.50  3.000
 89F  C11  N2   C5   111.75  3.000
 89F  C18  N2   C5   111.92  3.000
 89F  S2   C1   C3   114.29  3.000
 89F  C3   C1   C2   119.61  3.000
 89F  S2   C1   C2   126.07  3.000
 89F  H6   C3   C1   119.15  3.000
 89F  H6   C3   C4   118.83  3.000
 89F  C1   C3   C4   122.02  3.000
 89F  H9   C5   H8   107.62  3.000
 89F  H9   C5   H7   107.70  3.000
 89F  H8   C5   H7   107.87  3.000
 89F  H9   C5   N2   113.39  3.000
 89F  H8   C5   N2   110.00  3.000
 89F  H7   C5   N2   110.08  3.000
 89F  H12  C8   H11  108.66  3.000
 89F  H12  C8   H10  108.52  3.000
 89F  H11  C8   H10  110.02  3.000
 89F  H12  C8   S1   105.91  3.000
 89F  H11  C8   S1   111.73  3.000
 89F  H10  C8   S1   111.83  3.000
 89F  H14  C11  H13  107.22  3.000
 89F  H14  C11  C17  109.17  3.000
 89F  H13  C11  C17  108.78  3.000
 89F  H14  C11  N2   109.16  3.000
 89F  H13  C11  N2   111.72  3.000
 89F  C17  C11  N2   110.71  3.000
 89F  S1   C12  C4   124.26  3.000
 89F  S1   C12  C9   116.92  3.000
 89F  C4   C12  C9   118.82  3.000
 89F  H15  C13  C15  120.32  3.000
 89F  H15  C13  C7   119.99  3.000
 89F  C15  C13  C7   119.69  3.000
 89F  H17  C14  H16  107.19  3.000
 89F  H17  C14  C18  108.67  3.000
 89F  H16  C14  C18  109.02  3.000
 89F  H17  C14  N1   112.53  3.000
 89F  H16  C14  N1   109.63  3.000
 89F  C18  C14  N1   109.71  3.000
 89F  H18  C15  C19  120.34  3.000
 89F  H18  C15  C13  119.94  3.000
 89F  C19  C15  C13  119.72  3.000
 89F  H19  C16  C19  119.75  3.000
 89F  H19  C16  C10  119.26  3.000
 89F  C19  C16  C10  120.97  3.000
 89F  H21  C17  H20  107.01  3.000
 89F  H21  C17  C11  109.08  3.000
 89F  H20  C17  C11  108.82  3.000
 89F  H21  C17  N1   109.11  3.000
 89F  H20  C17  N1   113.14  3.000
 89F  C11  C17  N1   109.58  3.000
 89F  H23  C18  H22  107.16  3.000
 89F  H23  C18  C14  109.01  3.000
 89F  H22  C18  C14  109.18  3.000
 89F  H23  C18  N2   111.83  3.000
 89F  H22  C18  N2   109.01  3.000
 89F  C14  C18  N2   110.56  3.000
 89F  H24  C19  C16  119.74  3.000
 89F  H24  C19  C15  120.12  3.000
 89F  C16  C19  C15  120.14  3.000
 89F  H26  C20  H25  106.73  3.000
 89F  H26  C20  C10  109.70  3.000
 89F  H25  C20  C10  108.83  3.000
 89F  H26  C20  C6   110.29  3.000
 89F  H25  C20  C6   107.26  3.000
 89F  C10  C20  C6   113.76  3.000
 89F  C12  S1   C8   103.56  3.000
 89F  C1   S2   C7   101.79  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
 89F  CONST_01  C19  C15  C13  C7      0.00   0.0  0
 89F  CONST_02  C19  C16  C10  C7      0.00   0.0  0
 89F  CONST_03  C15  C19  C16  C10     0.00   0.0  0
 89F  CONST_04  C15  C13  C7   C10     0.00   0.0  0
 89F  CONST_05  C3   C1   C2   C9      0.00   0.0  0
 89F  CONST_06  C3   C4   C12  C9      0.00   0.0  0
 89F  CONST_07  C2   C1   C3   C4      0.00   0.0  0
 89F  CONST_08  C2   C9   C12  C4      0.00   0.0  0
 89F  CONST_09  C12  C9   C2   C1      0.00   0.0  0
 89F  CONST_10  C12  C4   C3   C1      0.00   0.0  0
 89F  CONST_11  C16  C19  C15  C13     0.00   0.0  0
 89F  CONST_12  C16  C10  C7   C13     0.00   0.0  0
 89F  CONST_13  S1   C12  C9   C2    180.00   0.0  0
 89F  CONST_14  S1   C12  C4   C3    180.00   0.0  0
 89F  CONST_15  H18  C15  C13  C7    180.00   0.0  0
 89F  CONST_16  H19  C16  C10  C7    180.00   0.0  0
 89F  CONST_17  H2   C9   C2   C6      0.00   0.0  0
 89F  CONST_18  H24  C19  C16  C10   180.00   0.0  0
 89F  CONST_19  H15  C13  C7   C10   180.00   0.0  0
 89F  CONST_20  H3   C4   C12  C9    180.00   0.0  0
 89F  CONST_21  H6   C3   C1   C2    180.00   0.0  0
 89F  Var_01    C6   C20  C10  C7    -79.10  30.0  1
 89F  Var_02    C2   C1   S2   C7    -52.45  30.0  1
 89F  Var_03    C18  C14  N1   C6   -167.44  30.0  1
 89F  Var_04    C11  C17  N1   C6    167.56  30.0  1
 89F  Var_05    N2   C18  C14  N1    -57.30  30.0  1
 89F  Var_06    N2   C11  C17  N1     57.34  30.0  1
 89F  Var_07    C13  C7   S2   C1   -116.40  30.0  1
 89F  Var_08    C14  C18  N2   C11    57.44  30.0  1
 89F  Var_09    C18  N2   C11  C17   -57.52  30.0  1
 89F  Var_10    H7   C5   N2   C11  -177.80  30.0  3
 89F  Var_11    H10  C8   S1   C12   -62.83  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
 89F  chir_01  C6  C20  N1  C2  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
 89F  plan-1  C6   0.020
 89F  plan-1  C9   0.020
 89F  plan-1  C4   0.020
 89F  plan-1  C2   0.020
 89F  plan-1  C1   0.020
 89F  plan-1  C3   0.020
 89F  plan-1  C12  0.020
 89F  plan-1  S1   0.020
 89F  plan-1  S2   0.020
 89F  plan-1  H2   0.020
 89F  plan-1  H3   0.020
 89F  plan-1  H6   0.020
 89F  plan-2  C7   0.020
 89F  plan-2  C10  0.020
 89F  plan-2  C13  0.020
 89F  plan-2  C15  0.020
 89F  plan-2  C16  0.020
 89F  plan-2  C19  0.020
 89F  plan-2  C20  0.020
 89F  plan-2  S2   0.020
 89F  plan-2  H15  0.020
 89F  plan-2  H18  0.020
 89F  plan-2  H19  0.020
 89F  plan-2  H24  0.020

