# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 14:34:53 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: (3~{R})-2-[(11~{S})-7,8-bis(fluoranyl)-6,11-dihydrobenzo[c][1]benzothiepin-11-yl]-11-oxidanyl-5-oxa-1,2,8-triazatricyclo[8.4.0.0^{3,8}]tetradeca-10,13-diene-9,12-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C2N(C=CC1=O)N([C@@H]3COCCN3C2=O)[C@H]4c5ccc(F)c(F)c5CSc6ccccc46
#
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
 E4Z  E4Z  (3~{R})-2-[(11~{S})-7,8-bis(fluoranyl)-6,11-dihydrobenzo[c][1]benzothiepin-11-yl]-11-oxidanyl-5-oxa-1,2,8-triazatricyclo[8.4.0.0^{3,8}]tetradeca-10,13-diene-9,12-dione  ligand  53  34  .  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_E4Z
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
 E4Z  C1   C  CR6   0   0.363  -4.4026   0.5513   0.2467
 E4Z  N1   N  NR6   0  -0.358  -1.7619  -0.1549   0.7896
 E4Z  O1   O  O     0  -0.524  -5.5673   0.8257  -0.0863
 E4Z  C2   C  CR16  0  -0.496  -3.7383   0.9632   1.4297
 E4Z  O2   O  OH1   0  -0.595  -4.3092  -0.7877  -1.6814
 E4Z  O3   O  O     0  -0.458  -2.0353  -2.1940  -2.1205
 E4Z  C4   C  CR6   0   0.114  -2.3442  -0.6773  -0.3478
 E4Z  O4   O  O2    0  -0.475   1.3649  -3.6198   1.0819
 E4Z  C5   C  CR6   0   0.183  -3.6335  -0.3323  -0.6342
 E4Z  C6   C  C     0   0.601  -1.6111  -1.7525  -1.0677
 E4Z  C7   C  CH1   0   0.142  -0.1480  -1.7834   0.8921
 E4Z  C13  C  CR6   0  -0.086   2.4317   0.5952  -0.5293
 E4Z  C14  C  CH2   0  -0.654   1.7404   0.7942  -1.8574
 E4Z  C15  C  CR6   0  -0.166  -0.4563   2.1260  -0.8985
 E4Z  C16  C  CR6   0   0.177  -0.1783   2.0483   0.4662
 E4Z  C17  C  CR16  0  -0.247  -1.0670   3.2557  -1.4296
 E4Z  C18  C  CR16  0  -0.254  -1.3817   4.3307  -0.6107
 E4Z  C19  C  CR16  0  -0.238  -1.0670   4.2817   0.7386
 E4Z  C20  C  CR16  0  -0.292  -0.4724   3.1456   1.2679
 E4Z  C21  C  CR16  0  -0.292   2.7439   0.5417   1.8632
 E4Z  C22  C  CR16  0  -0.405   4.1085   0.3533   1.7374
 E4Z  C23  C  CR6   0   0.409   4.6322   0.2753   0.4694
 E4Z  C24  C  CR6   0   0.419   3.8050   0.4075  -0.6300
 E4Z  F2   F  F     0  -0.298   5.9381   0.0896   0.2748
 E4Z  C12  C  CR6   0   0.074   1.8902   0.6424   0.7652
 E4Z  F1   F  F     0  -0.301   4.3726   0.3639  -1.8414
 E4Z  S3   S  S2    0   0.058  -0.0576   0.7768  -1.9581
 E4Z  C11  C  CH1   0  -0.239   0.4259   0.8217   1.1197
 E4Z  N2   N  NT    0  -0.346  -0.4157  -0.3754   0.9438
 E4Z  C8   C  CH2   0  -0.205   1.2770  -2.2254   1.2158
 E4Z  C9   C  CH2   0  -0.213   1.2328  -3.9743  -0.2780
 E4Z  C10  C  CH2   0  -0.305  -0.1508  -3.6430  -0.7899
 E4Z  N3   N  NT    0  -0.518  -0.5242  -2.2768  -0.4402
 E4Z  C3   C  CR16  0   0.045  -2.4462   0.5942   1.6626
 E4Z  H1   H  HCR6  0   0.280  -4.2498   1.5759   2.1582
 E4Z  H3   H  HCH1  0   0.265  -0.7924  -2.2709   1.6389
 E4Z  H5   H  HCH2  0   0.308   2.0380   0.0040  -2.5494
 E4Z  H6   H  HCR6  0   0.270  -1.2818   3.2970  -2.4895
 E4Z  H7   H  HCR6  0   0.266  -1.8562   5.2073  -1.0311
 E4Z  H8   H  HCR6  0   0.266  -1.2942   5.1195   1.3842
 E4Z  H9   H  HCR6  0   0.267  -0.2494   3.1048   2.3277
 E4Z  H10  H  HCR6  0   0.283   2.3224   0.5947   2.8586
 E4Z  H11  H  HCR6  0   0.299   4.7483   0.2664   2.6049
 E4Z  H12  H  HCH1  0   0.289   0.4424   1.0537   2.1894
 E4Z  H13  H  HCH2  0   0.273   1.5117  -1.9651   2.2480
 E4Z  H14  H  HCH2  0   0.222   2.0059  -1.7504   0.5554
 E4Z  H15  H  HCH2  0   0.217   1.9972  -3.4641  -0.8797
 E4Z  H16  H  HCH2  0   0.257   1.4016  -5.0478  -0.3624
 E4Z  H17  H  HCH2  0   0.270  -0.1686  -3.7606  -1.8715
 E4Z  H18  H  HCH2  0   0.245  -0.8791  -4.3442  -0.3669
 E4Z  H19  H  HCR6  0   0.329  -1.9118   0.9006   2.5496
 E4Z  H20  H  HOH1  0   0.464  -5.1964  -0.3872  -1.5980
 E4Z  H4   H  HCH2  0   0.308   2.0920   1.7323  -2.2923

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
 E4Z  C9   O4   single    1.411  0.020  1.411
 E4Z  C9   C10  single    1.512  0.020  1.512
 E4Z  O4   C8   single    1.404  0.020  1.404
 E4Z  C10  N3   single    1.459  0.020  1.459
 E4Z  C8   C7   single    1.527  0.020  1.527
 E4Z  O3   C6   double    1.218  0.020  1.218
 E4Z  N3   C6   single    1.360  0.020  1.360
 E4Z  N3   C7   single    1.470  0.020  1.470
 E4Z  C6   C4   single    1.487  0.020  1.487
 E4Z  C7   N2   single    1.434  0.020  1.434
 E4Z  O2   C5   single    1.327  0.020  1.327
 E4Z  C4   C5   double    1.365  0.020  1.365
 E4Z  C4   N1   single    1.381  0.020  1.381
 E4Z  C5   C1   single    1.466  0.020  1.466
 E4Z  N2   N1   single    1.373  0.020  1.373
 E4Z  N2   C11  single    1.474  0.020  1.474
 E4Z  N1   C3   single    1.338  0.020  1.338
 E4Z  C1   O1   double    1.242  0.020  1.242
 E4Z  C1   C2   single    1.418  0.020  1.418
 E4Z  C3   C2   double    1.364  0.020  1.364
 E4Z  C11  C12  single    1.517  0.020  1.517
 E4Z  C11  C16  single    1.515  0.020  1.515
 E4Z  C21  C22  aromatic  1.383  0.020  1.383
 E4Z  C21  C12  aromatic  1.394  0.020  1.394
 E4Z  C22  C23  aromatic  1.374  0.020  1.374
 E4Z  C12  C13  aromatic  1.404  0.020  1.404
 E4Z  C23  F2   single    1.333  0.020  1.333
 E4Z  C23  C24  aromatic  1.382  0.020  1.382
 E4Z  C13  C24  aromatic  1.390  0.020  1.390
 E4Z  C13  C14  single    1.510  0.020  1.510
 E4Z  C24  F1   single    1.338  0.020  1.338
 E4Z  C14  S3   single    1.801  0.020  1.801
 E4Z  C16  C20  aromatic  1.390  0.020  1.390
 E4Z  C16  C15  aromatic  1.395  0.020  1.395
 E4Z  C20  C19  aromatic  1.387  0.020  1.387
 E4Z  S3   C15  single    1.761  0.020  1.761
 E4Z  C15  C17  aromatic  1.390  0.020  1.390
 E4Z  C19  C18  aromatic  1.386  0.020  1.386
 E4Z  C17  C18  aromatic  1.388  0.020  1.388
 E4Z  C2   H1   single    0.930  0.020  1.080
 E4Z  C7   H3   single    0.970  0.020  1.090
 E4Z  C14  H4   single    0.970  0.020  1.090
 E4Z  C14  H5   single    0.970  0.020  1.090
 E4Z  C17  H6   single    0.930  0.020  1.080
 E4Z  C18  H7   single    0.930  0.020  1.080
 E4Z  C19  H8   single    0.930  0.020  1.080
 E4Z  C20  H9   single    0.930  0.020  1.080
 E4Z  C21  H10  single    0.930  0.020  1.080
 E4Z  C22  H11  single    0.930  0.020  1.080
 E4Z  C11  H12  single    0.970  0.020  1.090
 E4Z  C8   H13  single    0.970  0.020  1.090
 E4Z  C8   H14  single    0.970  0.020  1.090
 E4Z  C9   H15  single    0.970  0.020  1.090
 E4Z  C9   H16  single    0.970  0.020  1.090
 E4Z  C10  H17  single    0.970  0.020  1.090
 E4Z  C10  H18  single    0.970  0.020  1.090
 E4Z  C3   H19  single    0.930  0.020  1.080
 E4Z  O2   H20  single    0.850  0.020  0.980

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
 E4Z  C5   C1   C2   115.52  3.000
 E4Z  C2   C1   O1   126.78  3.000
 E4Z  C5   C1   O1   117.65  3.000
 E4Z  C3   N1   N2   121.20  3.000
 E4Z  C3   N1   C4   122.24  3.000
 E4Z  N2   N1   C4   116.45  3.000
 E4Z  H1   C2   C3   119.12  3.000
 E4Z  H1   C2   C1   120.36  3.000
 E4Z  C3   C2   C1   120.51  3.000
 E4Z  H20  O2   C5   104.74  3.000
 E4Z  C6   C4   C5   123.15  3.000
 E4Z  C5   C4   N1   118.40  3.000
 E4Z  C6   C4   N1   117.67  3.000
 E4Z  C9   O4   C8   109.61  3.000
 E4Z  C4   C5   O2   124.04  3.000
 E4Z  C4   C5   C1   121.46  3.000
 E4Z  O2   C5   C1   114.46  3.000
 E4Z  N3   C6   C4   116.70  3.000
 E4Z  C4   C6   O3   120.58  3.000
 E4Z  N3   C6   O3   122.51  3.000
 E4Z  H3   C7   N3   108.46  3.000
 E4Z  H3   C7   C8   105.93  3.000
 E4Z  N3   C7   C8   109.51  3.000
 E4Z  H3   C7   N2   107.53  3.000
 E4Z  N3   C7   N2   108.33  3.000
 E4Z  C8   C7   N2   116.80  3.000
 E4Z  C12  C13  C24  116.90  3.000
 E4Z  C24  C13  C14  113.97  3.000
 E4Z  C12  C13  C14  129.04  3.000
 E4Z  H5   C14  H4   106.35  3.000
 E4Z  H5   C14  S3   103.28  3.000
 E4Z  H4   C14  S3   107.90  3.000
 E4Z  H5   C14  C13  109.71  3.000
 E4Z  H4   C14  C13  108.42  3.000
 E4Z  S3   C14  C13  120.32  3.000
 E4Z  S3   C15  C17  119.49  3.000
 E4Z  C17  C15  C16  120.45  3.000
 E4Z  S3   C15  C16  120.05  3.000
 E4Z  C11  C16  C20  118.32  3.000
 E4Z  C20  C16  C15  118.56  3.000
 E4Z  C11  C16  C15  123.12  3.000
 E4Z  H6   C17  C18  120.23  3.000
 E4Z  H6   C17  C15  119.51  3.000
 E4Z  C18  C17  C15  120.26  3.000
 E4Z  H7   C18  C19  120.42  3.000
 E4Z  H7   C18  C17  119.86  3.000
 E4Z  C19  C18  C17  119.71  3.000
 E4Z  H8   C19  C20  119.77  3.000
 E4Z  H8   C19  C18  120.38  3.000
 E4Z  C20  C19  C18  119.84  3.000
 E4Z  H9   C20  C19  119.48  3.000
 E4Z  H9   C20  C16  119.38  3.000
 E4Z  C19  C20  C16  121.13  3.000
 E4Z  H10  C21  C12  118.83  3.000
 E4Z  H10  C21  C22  118.33  3.000
 E4Z  C12  C21  C22  122.83  3.000
 E4Z  H11  C22  C23  120.68  3.000
 E4Z  H11  C22  C21  121.44  3.000
 E4Z  C23  C22  C21  117.88  3.000
 E4Z  F2   C23  C24  118.91  3.000
 E4Z  C24  C23  C22  120.03  3.000
 E4Z  F2   C23  C22  121.05  3.000
 E4Z  F1   C24  C23  117.58  3.000
 E4Z  F1   C24  C13  119.28  3.000
 E4Z  C23  C24  C13  123.14  3.000
 E4Z  C11  C12  C21  114.55  3.000
 E4Z  C21  C12  C13  119.17  3.000
 E4Z  C11  C12  C13  126.27  3.000
 E4Z  C15  S3   C14  100.66  3.000
 E4Z  H12  C11  N2   107.30  3.000
 E4Z  H12  C11  C12  103.82  3.000
 E4Z  N2   C11  C12  115.29  3.000
 E4Z  H12  C11  C16  104.82  3.000
 E4Z  C12  C11  C16  112.31  3.000
 E4Z  N2   C11  C16  112.23  3.000
 E4Z  C11  N2   C7   134.04  3.000
 E4Z  C11  N2   N1   116.29  3.000
 E4Z  C7   N2   N1   109.67  3.000
 E4Z  H14  C8   H13  108.97  3.000
 E4Z  H14  C8   C7   111.63  3.000
 E4Z  H13  C8   C7   109.43  3.000
 E4Z  H14  C8   O4   109.42  3.000
 E4Z  H13  C8   O4   108.31  3.000
 E4Z  C7   C8   O4   109.01  3.000
 E4Z  H16  C9   H15  107.89  3.000
 E4Z  H16  C9   C10  109.34  3.000
 E4Z  H15  C9   C10  110.46  3.000
 E4Z  H16  C9   O4   107.91  3.000
 E4Z  H15  C9   O4   110.24  3.000
 E4Z  C10  C9   O4   110.91  3.000
 E4Z  H18  C10  H17  107.68  3.000
 E4Z  H18  C10  N3   109.66  3.000
 E4Z  H17  C10  N3   109.59  3.000
 E4Z  H18  C10  C9   109.71  3.000
 E4Z  H17  C10  C9   109.14  3.000
 E4Z  N3   C10  C9   110.99  3.000
 E4Z  C10  N3   C7   117.79  3.000
 E4Z  C7   N3   C6   119.57  3.000
 E4Z  C10  N3   C6   117.06  3.000
 E4Z  H19  C3   C2   122.16  3.000
 E4Z  H19  C3   N1   116.20  3.000
 E4Z  C2   C3   N1   121.63  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
 E4Z  CONST_01  C22  C23  C24  C13     0.00   0.0  0
 E4Z  CONST_02  C19  C18  C17  C15     0.00   0.0  0
 E4Z  CONST_03  C18  C19  C20  C16     0.00   0.0  0
 E4Z  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 E4Z  CONST_05  C24  C23  C22  C21     0.00   0.0  0
 E4Z  CONST_06  C12  C21  C22  C23     0.00   0.0  0
 E4Z  CONST_08  C7   N3   C6   C4      0.00   0.0  0
 E4Z  CONST_09  F2   C23  C24  C13   180.00   0.0  0
 E4Z  CONST_10  F2   C23  C22  C21   180.00   0.0  0
 E4Z  CONST_11  F1   C24  C23  C22   180.00   0.0  0
 E4Z  CONST_13  C7   N3   C6   O3    180.00   0.0  0
 E4Z  CONST_14  H7   C18  C17  C15   180.00   0.0  0
 E4Z  CONST_15  H8   C19  C20  C16   180.00   0.0  0
 E4Z  CONST_16  H9   C20  C19  C18   180.00   0.0  0
 E4Z  CONST_17  H6   C17  C18  C19   180.00   0.0  0
 E4Z  CONST_18  H10  C21  C22  C23   180.00   0.0  0
 E4Z  CONST_19  H11  C22  C23  C24   180.00   0.0  0
 E4Z  Var_01    N3   C6   C4   N1      9.63  30.0  1
 E4Z  Var_02    C7   N2   N1   C4    -55.92  30.0  1
 E4Z  Var_03    N3   C10  C9   O4     49.19  30.0  1
 E4Z  Var_04    C9   C10  N3   C6    166.64  30.0  1
 E4Z  Var_05    C10  C9   O4   C8    -65.68  30.0  1
 E4Z  Var_06    H13  C8   O4   C9   -172.65  30.0  1

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
 E4Z  chir_01  C7   C8  N3   N2   positiv
 E4Z  chir_02  C11  N2  C12  C16  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
 E4Z  plan-1  C15  0.020
 E4Z  plan-1  C16  0.020
 E4Z  plan-1  C17  0.020
 E4Z  plan-1  C18  0.020
 E4Z  plan-1  C19  0.020
 E4Z  plan-1  C20  0.020
 E4Z  plan-1  S3   0.020
 E4Z  plan-1  C11  0.020
 E4Z  plan-1  H6   0.020
 E4Z  plan-1  H7   0.020
 E4Z  plan-1  H8   0.020
 E4Z  plan-1  H9   0.020
 E4Z  plan-2  C13  0.020
 E4Z  plan-2  C14  0.020
 E4Z  plan-2  C21  0.020
 E4Z  plan-2  C22  0.020
 E4Z  plan-2  C23  0.020
 E4Z  plan-2  C24  0.020
 E4Z  plan-2  F2   0.020
 E4Z  plan-2  C12  0.020
 E4Z  plan-2  F1   0.020
 E4Z  plan-2  C11  0.020
 E4Z  plan-2  H10  0.020
 E4Z  plan-2  H11  0.020
 E4Z  plan-3  C1   0.020
 E4Z  plan-3  N1   0.020
 E4Z  plan-3  O1   0.020
 E4Z  plan-3  C2   0.020
 E4Z  plan-3  O2   0.020
 E4Z  plan-3  C4   0.020
 E4Z  plan-3  C5   0.020
 E4Z  plan-3  C6   0.020
 E4Z  plan-3  N2   0.020
 E4Z  plan-3  C3   0.020
 E4Z  plan-3  H1   0.020
 E4Z  plan-3  H19  0.020
 E4Z  plan-4  O3   0.020
 E4Z  plan-4  C4   0.020
 E4Z  plan-4  C6   0.020
 E4Z  plan-4  C7   0.020
 E4Z  plan-4  C10  0.020
 E4Z  plan-4  N3   0.020

