# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 10:55:41 2020
#   Inital geometry file: a 160 line input string
#   Ligand name: (3~{S},14~{E})-8-(azetidin-3-yl)-19-chloranyl-~{N}-(1-cyanocyclopropyl)-5-oxidanylidene-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(21),6(11),7,9,14,18(22),19-heptaene-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1cc2C[C@H](NC(=O)c3cc(ccc3OC\C=C\COc1cc2)C4CNC4)C(=O)NC5(CC5)C#N
#
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
 C7T  C7T  (3~{S},14~{E})-8-(azetidin-3-yl)-19-chloranyl-~{N}-(1-cyanocyclopropyl)-5-oxidanylidene-12,17-dioxa-4-azatricyclo[16.2.2.0^{6,11}]docosa-1(21),6(11),7,9,14,18(22),19-heptaene-3-carboxamide  ligand  63  36  .  2022-09-16  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_C7T
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
 C7T  C1   C   CH2   0  -0.470  -4.4145   5.2815   0.5140
 C7T  C2   C   CT    0   0.086  -4.2525   3.7845   0.5778
 C7T  C4   C   CR16  0  -0.315   3.2971   2.3291   0.9642
 C7T  C7   C   CR16  0  -0.288   1.9543   1.5724  -1.3344
 C7T  C8   C   CR6   0   0.148   1.2730   2.2827  -0.3560
 C7T  C12  C   CH2   0  -0.538  -0.1801   2.6218  -0.5326
 C7T  C14  C   C     0   0.571  -2.5447   2.1413   0.1189
 C7T  C21  C   CR6   0  -0.168  -0.6140  -1.9615   0.6045
 C7T  C22  C   CR16  0  -0.318  -1.7064  -2.5935   0.0301
 C7T  C23  C   CR16  0  -0.366   0.6503  -3.9963   0.3958
 C7T  C24  C   CR6   0   0.376   0.5809  -2.6635   0.7881
 C7T  C3   C   CH2   0  -0.450  -4.5888   4.4768  -0.7201
 C7T  C5   C   CR6   0   0.409   3.9800   1.6100  -0.0104
 C7T  C6   C   CR6   0  -0.104   3.2888   1.2412  -1.1594
 C7T  C9   C   CR16  0  -0.287   1.9635   2.6604   0.7926
 C7T  CL   CL  CL    0  -0.112   4.1124   0.3546  -2.3946
 C7T  O11  O   O2    0  -0.488   5.2889   1.2831   0.1232
 C7T  C13  C   CH1   0  -0.224  -1.0874   1.7587   0.3634
 C7T  O15  O   O     0  -0.449  -3.2676   1.5204  -0.6336
 C7T  N16  N   NH1   0  -0.666  -2.9483   3.2592   0.7639
 C7T  N17  N   NH1   0  -0.606  -0.8901   0.3601   0.1123
 C7T  C18  C   CH2   0  -0.234   5.5740   0.2868   1.1191
 C7T  C19  C   C     0   0.528  -0.7249  -0.5500   1.0897
 C7T  O20  O   O     0  -0.473  -0.6876  -0.2732   2.2765
 C7T  O25  O   O2    0  -0.456   1.5926  -1.9680   1.3249
 C7T  C26  C   CH2   0  -0.236   2.9071  -2.5096   1.3313
 C7T  C27  C   C1    0  -0.197   3.8030  -1.3597   1.6469
 C7T  C28  C   C1    0  -0.258   4.7879  -0.9548   0.8565
 C7T  C29  C   CSP   0   0.115  -5.3071   3.0254   1.2067
 C7T  N30  N   NS    0  -0.264  -6.1470   2.4179   1.7076
 C7T  C31  C   CR16  0  -0.323  -0.4618  -4.6116  -0.1625
 C7T  C32  C   CR6   0   0.195  -1.6597  -3.9313  -0.3567
 C7T  C33  C   C     0  -0.413  -2.8622  -4.5951  -0.9470
 C7T  C34  C   C     0  -0.251  -2.7509  -5.3573  -2.2841
 C7T  N35  N   N     0  -0.614  -3.6459  -6.3914  -1.7450
 C7T  C36  C   C     0  -0.251  -3.3535  -5.9419  -0.3762
 C7T  H1   H   HCH2  0   0.292  -5.2884   5.7050   0.9893
 C7T  H2   H   HCH2  0   0.294  -3.5053   5.8556   0.6356
 C7T  H3   H   HCR6  0   0.275   3.8182   2.6402   1.8614
 C7T  H4   H   HCR6  0   0.271   1.4452   1.2689  -2.2405
 C7T  H5   H   HCH2  0   0.278  -0.3505   3.6729  -0.2904
 C7T  H6   H   HCH2  0   0.276  -0.4726   2.4899  -1.5775
 C7T  H7   H   HCR6  0   0.257  -2.6240  -2.0317  -0.1097
 C7T  H8   H   HCR6  0   0.283   1.5584  -4.5704   0.5235
 C7T  H9   H   HCH2  0   0.288  -5.5864   4.3360  -1.1133
 C7T  H10  H   HCH2  0   0.290  -3.8014   4.4871  -1.4612
 C7T  H11  H   HCR6  0   0.257   1.4578   3.2267   1.5656
 C7T  H12  H   HCH1  0   0.296  -0.8304   1.9452   1.4079
 C7T  H13  H   HNH1  0   0.419  -2.3739   3.6585   1.4908
 C7T  H14  H   HNH1  0   0.407  -0.9214   0.0390  -0.8429
 C7T  H15  H   HCH2  0   0.256   6.6476   0.1147   1.0439
 C7T  H16  H   HCH2  0   0.233   5.3617   0.6719   2.1215
 C7T  H17  H   HCH2  0   0.240   2.9852  -3.3037   2.0826
 C7T  H18  H   HCH2  0   0.240   3.1631  -2.9388   0.3573
 C7T  H19  H   H     0   0.256   3.5829  -0.8158   2.5614
 C7T  H20  H   H     0   0.255   5.0014  -1.4857  -0.0667
 C7T  H21  H   HCR6  0   0.251  -0.3751  -5.6533  -0.4482
 C7T  H22  H   H     0   0.260  -3.6874  -3.8818  -0.9899
 C7T  H23  H   H     0   0.225  -3.1146  -4.8447  -3.1779
 C7T  H24  H   H     0   0.212  -1.7293  -5.7032  -2.4768
 C7T  H25  H   H     0   0.344  -3.3604  -7.3409  -1.9451
 C7T  H27  H   H     0   0.212  -2.5461  -6.4969   0.1144
 C7T  H28  H   H     0   0.226  -4.2101  -5.9102   0.3011

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
 C7T  N30  C29  triple    1.151  0.020  1.151
 C7T  C36  C33  single    1.543  0.020  1.543
 C7T  C36  N35  single    1.470  0.020  1.470
 C7T  O15  C14  double    1.214  0.020  1.214
 C7T  CL   C6   single    1.729  0.020  1.729
 C7T  C29  C2   single    1.444  0.020  1.444
 C7T  C33  C34  single    1.543  0.020  1.543
 C7T  C33  C32  single    1.495  0.020  1.495
 C7T  C7   C6   aromatic  1.386  0.020  1.386
 C7T  C7   C8   aromatic  1.388  0.020  1.388
 C7T  N35  C34  single    1.470  0.020  1.470
 C7T  C12  C8   single    1.503  0.020  1.503
 C7T  C12  C13  single    1.540  0.020  1.540
 C7T  C14  C13  single    1.526  0.020  1.526
 C7T  C14  N16  single    1.352  0.020  1.352
 C7T  C1   C2   single    1.507  0.020  1.507
 C7T  C1   C3   single    1.484  0.020  1.484
 C7T  C2   N16  single    1.418  0.020  1.418
 C7T  C2   C3   single    1.509  0.020  1.509
 C7T  C6   C5   aromatic  1.391  0.020  1.391
 C7T  C32  C22  aromatic  1.393  0.020  1.393
 C7T  C32  C31  aromatic  1.391  0.020  1.391
 C7T  N17  C13  single    1.435  0.020  1.435
 C7T  N17  C19  single    1.346  0.020  1.346
 C7T  C22  C21  single    1.387  0.020  1.387
 C7T  C8   C9   aromatic  1.392  0.020  1.392
 C7T  C31  C23  aromatic  1.388  0.020  1.388
 C7T  C21  C19  single    1.497  0.020  1.497
 C7T  C21  C24  aromatic  1.398  0.020  1.398
 C7T  C19  O20  double    1.219  0.020  1.219
 C7T  C5   O11  single    1.356  0.020  1.356
 C7T  C5   C4   aromatic  1.390  0.020  1.390
 C7T  C9   C4   aromatic  1.385  0.020  1.385
 C7T  C23  C24  single    1.391  0.020  1.391
 C7T  O11  C18  single    1.437  0.020  1.437
 C7T  C24  O25  single    1.340  0.020  1.340
 C7T  C27  C28  double    1.326  0.020  1.326
 C7T  C27  C26  single    1.491  0.020  1.491
 C7T  C18  C28  single    1.493  0.020  1.493
 C7T  O25  C26  single    1.422  0.020  1.422
 C7T  C1   H1   single    0.970  0.020  1.090
 C7T  C1   H2   single    0.970  0.020  1.090
 C7T  C4   H3   single    0.930  0.020  1.080
 C7T  C7   H4   single    0.930  0.020  1.080
 C7T  C12  H5   single    0.970  0.020  1.090
 C7T  C12  H6   single    0.970  0.020  1.090
 C7T  C22  H7   single    0.930  0.020  1.080
 C7T  C23  H8   single    0.930  0.020  1.080
 C7T  C3   H9   single    0.970  0.020  1.090
 C7T  C3   H10  single    0.970  0.020  1.090
 C7T  C9   H11  single    0.930  0.020  1.080
 C7T  C13  H12  single    0.970  0.020  1.090
 C7T  N16  H13  single    0.860  0.020  1.020
 C7T  N17  H14  single    0.860  0.020  1.020
 C7T  C18  H15  single    0.970  0.020  1.090
 C7T  C18  H16  single    0.970  0.020  1.090
 C7T  C26  H17  single    0.970  0.020  1.090
 C7T  C26  H18  single    0.970  0.020  1.090
 C7T  C27  H19  single    0.930  0.020  1.080
 C7T  C28  H20  single    0.930  0.020  1.080
 C7T  C31  H21  single    0.930  0.020  1.080
 C7T  C33  H22  single    0.970  0.020  1.090
 C7T  C34  H23  single    0.970  0.020  1.090
 C7T  C34  H24  single    0.970  0.020  1.090
 C7T  N35  H25  single    0.890  0.020  1.040
 C7T  C36  H27  single    0.970  0.020  1.090
 C7T  C36  H28  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
 C7T  H2   C1   H1   114.96  3.000
 C7T  H2   C1   C3   118.68  3.000
 C7T  H1   C1   C3   118.89  3.000
 C7T  H2   C1   C2   115.59  3.000
 C7T  H1   C1   C2   117.22  3.000
 C7T  C3   C1   C2    60.60  3.000
 C7T  C29  C2   N16  114.83  3.000
 C7T  N16  C2   C3   119.19  3.000
 C7T  C29  C2   C3   116.94  3.000
 C7T  C3   C2   C1    58.93  3.000
 C7T  N16  C2   C1   118.18  3.000
 C7T  C29  C2   C1   117.53  3.000
 C7T  H3   C4   C9   119.82  3.000
 C7T  H3   C4   C5   119.53  3.000
 C7T  C9   C4   C5   120.65  3.000
 C7T  H4   C7   C6   119.43  3.000
 C7T  H4   C7   C8   120.17  3.000
 C7T  C6   C7   C8   120.39  3.000
 C7T  C9   C8   C12  121.02  3.000
 C7T  C9   C8   C7   118.49  3.000
 C7T  C12  C8   C7   120.49  3.000
 C7T  H6   C12  H5   106.64  3.000
 C7T  H6   C12  C13  109.32  3.000
 C7T  H5   C12  C13  108.58  3.000
 C7T  H6   C12  C8   110.12  3.000
 C7T  H5   C12  C8   110.00  3.000
 C7T  C13  C12  C8   112.02  3.000
 C7T  N16  C14  O15  122.73  3.000
 C7T  N16  C14  C13  114.56  3.000
 C7T  O15  C14  C13  122.65  3.000
 C7T  C19  C21  C24  119.63  3.000
 C7T  C24  C21  C22  119.93  3.000
 C7T  C19  C21  C22  120.39  3.000
 C7T  H7   C22  C32  119.32  3.000
 C7T  H7   C22  C21  118.92  3.000
 C7T  C32  C22  C21  121.75  3.000
 C7T  H8   C23  C31  118.99  3.000
 C7T  H8   C23  C24  121.13  3.000
 C7T  C31  C23  C24  119.88  3.000
 C7T  O25  C24  C23  124.93  3.000
 C7T  O25  C24  C21  115.93  3.000
 C7T  C23  C24  C21  119.12  3.000
 C7T  H10  C3   H9   115.08  3.000
 C7T  H10  C3   C2   115.56  3.000
 C7T  H9   C3   C2   117.30  3.000
 C7T  H10  C3   C1   118.64  3.000
 C7T  H9   C3   C1   118.78  3.000
 C7T  C2   C3   C1    60.47  3.000
 C7T  O11  C5   C6   119.83  3.000
 C7T  O11  C5   C4   121.99  3.000
 C7T  C6   C5   C4   118.18  3.000
 C7T  CL   C6   C5   119.30  3.000
 C7T  C5   C6   C7   121.30  3.000
 C7T  CL   C6   C7   119.40  3.000
 C7T  H11  C9   C8   119.92  3.000
 C7T  H11  C9   C4   119.09  3.000
 C7T  C8   C9   C4   120.99  3.000
 C7T  C18  O11  C5   115.27  3.000
 C7T  H12  C13  N17  107.55  3.000
 C7T  H12  C13  C14  109.58  3.000
 C7T  N17  C13  C14  110.34  3.000
 C7T  H12  C13  C12  108.80  3.000
 C7T  N17  C13  C12  111.32  3.000
 C7T  C14  C13  C12  109.20  3.000
 C7T  H13  N16  C14  120.07  3.000
 C7T  H13  N16  C2   118.13  3.000
 C7T  C14  N16  C2   121.20  3.000
 C7T  H14  N17  C19  118.46  3.000
 C7T  H14  N17  C13  118.17  3.000
 C7T  C19  N17  C13  123.31  3.000
 C7T  H16  C18  H15  108.05  3.000
 C7T  H16  C18  C28  110.59  3.000
 C7T  H15  C18  C28  112.03  3.000
 C7T  H16  C18  O11  110.63  3.000
 C7T  H15  C18  O11  104.89  3.000
 C7T  C28  C18  O11  110.50  3.000
 C7T  O20  C19  N17  123.86  3.000
 C7T  O20  C19  C21  121.83  3.000
 C7T  N17  C19  C21  114.30  3.000
 C7T  C26  O25  C24  120.14  3.000
 C7T  H18  C26  H17  108.00  3.000
 C7T  H18  C26  C27  110.49  3.000
 C7T  H17  C26  C27  111.76  3.000
 C7T  H18  C26  O25  111.20  3.000
 C7T  H17  C26  O25  110.18  3.000
 C7T  C27  C26  O25  105.23  3.000
 C7T  H19  C27  C28  119.95  3.000
 C7T  H19  C27  C26  116.25  3.000
 C7T  C28  C27  C26  123.74  3.000
 C7T  H20  C28  C27  120.22  3.000
 C7T  H20  C28  C18  116.91  3.000
 C7T  C27  C28  C18  122.69  3.000
 C7T  N30  C29  C2   180.00  3.000
 C7T  H21  C31  C32  120.15  3.000
 C7T  H21  C31  C23  117.90  3.000
 C7T  C32  C31  C23  121.95  3.000
 C7T  C33  C32  C31  122.04  3.000
 C7T  C31  C32  C22  117.36  3.000
 C7T  C33  C32  C22  120.59  3.000
 C7T  H22  C33  C36  110.13  3.000
 C7T  H22  C33  C34  110.07  3.000
 C7T  C36  C33  C34   84.97  3.000
 C7T  H22  C33  C32  109.48  3.000
 C7T  C34  C33  C32  120.23  3.000
 C7T  C36  C33  C32  119.84  3.000
 C7T  H24  C34  H23  108.34  3.000
 C7T  H24  C34  N35  114.21  3.000
 C7T  H23  C34  N35  115.30  3.000
 C7T  H24  C34  C33  112.06  3.000
 C7T  H23  C34  C33  116.94  3.000
 C7T  N35  C34  C33   89.18  3.000
 C7T  H25  N35  C36  114.52  3.000
 C7T  H25  N35  C34  114.58  3.000
 C7T  C36  N35  C34   90.30  3.000
 C7T  H28  C36  H27  108.35  3.000
 C7T  H28  C36  N35  115.48  3.000
 C7T  H27  C36  N35  114.12  3.000
 C7T  H28  C36  C33  116.98  3.000
 C7T  H27  C36  C33  111.91  3.000
 C7T  N35  C36  C33   89.19  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
 C7T  CONST_01  C7   C6   C5   C4      0.00   0.0  0
 C7T  CONST_02  C7   C8   C9   C4      0.00   0.0  0
 C7T  CONST_03  C5   C6   C7   C8      0.00   0.0  0
 C7T  CONST_04  C5   C4   C9   C8      0.00   0.0  0
 C7T  CONST_05  C31  C32  C22  C21     0.00   0.0  0
 C7T  CONST_06  C31  C23  C24  C21     0.00   0.0  0
 C7T  CONST_07  C23  C31  C32  C22     0.00   0.0  0
 C7T  CONST_08  C23  C24  C21  C22     0.00   0.0  0
 C7T  CONST_09  C32  C22  C21  C24     0.00   0.0  0
 C7T  CONST_10  C32  C31  C23  C24     0.00   0.0  0
 C7T  CONST_11  C9   C8   C7   C6      0.00   0.0  0
 C7T  CONST_12  C9   C4   C5   C6      0.00   0.0  0
 C7T  CONST_13  C33  C32  C22  C21   180.00   0.0  0
 C7T  CONST_14  C33  C32  C31  C23   180.00   0.0  0
 C7T  CONST_15  C13  N17  C19  C21   180.00   0.0  0
 C7T  CONST_16  CL   C6   C5   C4    180.00   0.0  0
 C7T  CONST_17  CL   C6   C7   C8    180.00   0.0  0
 C7T  CONST_18  O11  C5   C6   CL      0.00   0.0  0
 C7T  CONST_19  O20  C19  N17  C13     0.00   0.0  0
 C7T  CONST_20  H11  C9   C8   C7    180.00   0.0  0
 C7T  CONST_21  H3   C4   C9   C8    180.00   0.0  0
 C7T  CONST_22  H4   C7   C8   C12     0.00   0.0  0
 C7T  CONST_23  H8   C23  C24  C21   180.00   0.0  0
 C7T  CONST_24  H21  C31  C32  C22   180.00   0.0  0
 C7T  CONST_25  H7   C22  C21  C24   180.00   0.0  0
 C7T  CONST_26  H14  N17  C19  C21     0.00   0.0  0
 C7T  CONST_27  C13  C14  N16  C2    180.00   0.0  0
 C7T  CONST_28  O15  C14  N16  C2      0.00   0.0  0
 C7T  CONST_29  H13  N16  C14  C13     0.00   0.0  0
 C7T  Var_01    C26  C27  C28  C18   173.10   0.0  0
 C7T  Var_02    C13  C12  C8   C7    106.16  30.0  1
 C7T  Var_03    N17  C19  C21  C22   -67.77  30.0  1
 C7T  Var_04    C27  C26  O25  C24   165.17  30.0  1
 C7T  Var_05    C28  C18  O11  C5     55.92  30.0  1
 C7T  Var_06    C27  C28  C18  O11  -111.44  30.0  1
 C7T  Var_07    C28  C27  C26  O25  -121.72  30.0  1
 C7T  Var_08    C34  N35  C36  C33    19.35  30.0  1
 C7T  Var_09    C29  C2   C3   C1    107.40  30.0  1
 C7T  Var_10    H20  C28  C27  C26    -1.91   0.0  0
 C7T  Var_11    C14  N16  C2   C1   -141.30  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
 C7T  chir_02  C13  C12  C14  N17  negativ
 C7T  chir_03  C33  C36  C34  C32  positiv
 C7T  chir_04  C2   C1   N16  C3   both

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
 C7T  plan-1  C4   0.020
 C7T  plan-1  C7   0.020
 C7T  plan-1  C8   0.020
 C7T  plan-1  C12  0.020
 C7T  plan-1  C5   0.020
 C7T  plan-1  C6   0.020
 C7T  plan-1  C9   0.020
 C7T  plan-1  CL   0.020
 C7T  plan-1  O11  0.020
 C7T  plan-1  H3   0.020
 C7T  plan-1  H4   0.020
 C7T  plan-1  H11  0.020
 C7T  plan-2  C21  0.020
 C7T  plan-2  C22  0.020
 C7T  plan-2  C23  0.020
 C7T  plan-2  C24  0.020
 C7T  plan-2  C19  0.020
 C7T  plan-2  O25  0.020
 C7T  plan-2  C31  0.020
 C7T  plan-2  C32  0.020
 C7T  plan-2  C33  0.020
 C7T  plan-2  H7   0.020
 C7T  plan-2  H8   0.020
 C7T  plan-2  H21  0.020
 C7T  plan-3  C2   0.020
 C7T  plan-3  C14  0.020
 C7T  plan-3  C13  0.020
 C7T  plan-3  O15  0.020
 C7T  plan-3  N16  0.020
 C7T  plan-3  H13  0.020
 C7T  plan-4  C21  0.020
 C7T  plan-4  C13  0.020
 C7T  plan-4  N17  0.020
 C7T  plan-4  C19  0.020
 C7T  plan-4  O20  0.020
 C7T  plan-4  H14  0.020
 C7T  plan-5  C18  0.020
 C7T  plan-5  C26  0.020
 C7T  plan-5  C27  0.020
 C7T  plan-5  C28  0.020
 C7T  plan-5  H19  0.020
 C7T  plan-5  H20  0.020

