# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 13:14:27 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: (4S)-5'-chloro-2',3',7,8,9,10,11,12-octahydro-3H,5H,14H-spiro[1,19-etheno-16lambda~6~-[1,4]oxazepino[3,4-i][1,4,5,10]oxathiadiazacyclohexadecine-4,1'-indene]-16,16,18(15H,17H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2c(CC[C@]23COc4ccc5cc4[N@](CCCCCCOCC[S](=O)(=O)NC5=O)C3)c1
#
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
 N0P  N0P  (4S)-5'-chloro-2',3',7,8,9,10,11,12-octahydro-3H,5H,14H-spiro[1,19-etheno-16lambda~6~-[1,4]oxazepino[3,4-i][1,4,5,10]oxathiadiazacyclohexadecine-4,1'-indene]-16,16,18(15H,17H)-trione  ligand  66  35  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N0P
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
 N0P  C1   C   CR16   0  -0.215   6.2567   1.7108   1.8053
 N0P  C2   C   CR6    0  -0.043   7.0505   0.5854   1.6421
 N0P  C3   C   CR16   0  -0.285   6.6633  -0.4778   0.8360
 N0P  O5   O   O2     0  -0.503  -4.5952  -2.0872  -0.2433
 N0P  C7   C   CR16   0  -0.358  -1.1712   0.8065  -0.1219
 N0P  C8   C   CR6    0  -0.034  -2.0397   1.7990  -0.5658
 N0P  C9   C   CR16   0  -0.285  -1.5761   2.7851  -1.4293
 N0P  C10  C   CR16   0  -0.343  -0.2615   2.7413  -1.8560
 N0P  C11  C   CH2    0  -0.173   2.9635   1.8619  -1.1596
 N0P  C12  C   CH2    0  -0.276   2.2579   0.1358   0.5210
 N0P  C13  C   CR6    0   0.304   0.1601   0.7457  -0.5358
 N0P  C14  C   CR6    0   0.334   0.5977   1.7310  -1.4408
 N0P  C15  C   CR5    0  -0.203   3.3587   0.5752  -0.4600
 N0P  C16  C   C      0   0.565  -3.4431   1.8668  -0.0897
 N0P  C19  C   CH2    0  -0.451  -0.3650  -2.2255  -0.7299
 N0P  C20  C   CH2    0  -0.427  -1.4865  -3.1018  -0.1900
 N0P  C21  C   CH2    0  -0.505   4.7968  -1.3903  -0.7301
 N0P  C22  C   CH2    0  -0.439   3.7218  -0.5570  -1.4415
 N0P  C24  C   CH2    0  -0.435  -2.2133  -3.8531  -1.3058
 N0P  N1   N   NT     0  -0.506   1.0188  -0.2700  -0.1195
 N0P  O1   O   O2     0  -0.490   1.8300   1.6942  -2.0004
 N0P  O2   O   O      0  -0.425  -4.0728   2.8989  -0.0310
 N0P  N2   N   NC1    0  -0.850  -3.9762   0.6562   0.3069
 N0P  C17  C   CH2   -1  -0.312   0.4066  -1.4962   0.3679
 N0P  C4   C   CR56   0   0.084   5.4490  -0.3872   0.1774
 N0P  C5   C   CR56   0   0.175   4.6406   0.7375   0.3243
 N0P  C6   C   CR16   0  -0.340   5.0356   1.7829   1.1430
 N0P  CL1  CL  CL     0  -0.134   8.5768   0.5033   2.4663
 N0P  S1   S   S      0   1.370  -5.4781   0.5404   1.0622
 N0P  C23  C   CH2    0  -0.668  -5.3321  -1.0908   1.7905
 N0P  O3   O   OS     0  -0.643  -6.5458   0.5444   0.0778
 N0P  C18  C   CH2    0  -0.147  -5.5142  -2.2257   0.8083
 N0P  C25  C   CH2    0  -0.170  -4.6651  -3.1240  -1.2133
 N0P  C26  C   CH2    0  -0.457  -3.6587  -4.2457  -0.9984
 N0P  H1   H   HCR6   0   0.277   6.5836   2.5243   2.4386
 N0P  H2   H   HCR6   0   0.272   7.2998  -1.3464   0.7271
 N0P  H4   H   HCR6   0   0.264  -2.2338   3.5679  -1.7812
 N0P  H5   H   HCR6   0   0.271   0.1079   3.4819  -2.5541
 N0P  H6   H   HCH2   0   0.231   2.7757   2.6592  -0.4303
 N0P  H7   H   HCH2   0   0.253   3.7710   2.1952  -1.8134
 N0P  H8   H   HCH2   0   0.255   2.6270  -0.7176   1.0904
 N0P  H9   H   HCH2   0   0.242   2.0913   0.9384   1.2523
 N0P  H10  H   HCH2   0   0.236   0.3344  -2.8151  -1.3295
 N0P  H11  H   HCH2   0   0.231  -0.8102  -1.5029  -1.4193
 N0P  H12  H   HCH2   0   0.223  -1.0956  -3.8153   0.5417
 N0P  H13  H   HCH2   0   0.213  -2.1888  -2.4696   0.3589
 N0P  H14  H   HCH2   0   0.253   4.3565  -2.2007  -0.1406
 N0P  H15  H   HCH2   0   0.261   5.4963  -1.8571  -1.4247
 N0P  H16  H   HCH2   0   0.250   2.8504  -1.1389  -1.7398
 N0P  H17  H   HCH2   0   0.246   4.1492  -0.1266  -2.3508
 N0P  H18  H   HCH2   0   0.213  -2.2151  -3.2397  -2.2144
 N0P  H19  H   HCH2   0   0.232  -1.6396  -4.7479  -1.5608
 N0P  H20  H   HNC1   0   0.443  -3.6590  -0.2083  -0.1240
 N0P  H21  H   HCH2   0   0.221  -0.2393  -1.3212   1.2412
 N0P  H22  H   HCH2   0   0.256   1.2090  -2.1390   0.7293
 N0P  H23  H   HCR6   0   0.257   4.4161   2.6617   1.2748
 N0P  H24  H   HCH2   0   0.321  -4.3728  -1.1218   2.3092
 N0P  H25  H   HCH2   0   0.340  -6.1229  -1.1264   2.5428
 N0P  H26  H   HCH2   0   0.238  -6.5421  -2.2288   0.4293
 N0P  H27  H   HCH2   0   0.249  -5.3711  -3.1598   1.3643
 N0P  H28  H   HCH2   0   0.226  -5.6814  -3.5333  -1.2402
 N0P  H29  H   HCH2   0   0.232  -4.4846  -2.6573  -2.1852
 N0P  H30  H   HCH2   0   0.237  -3.9584  -5.0543  -1.6710
 N0P  H31  H   HCH2   0   0.228  -3.7470  -4.6523   0.0144
 N0P  H3   H   HCR6   0   0.261  -1.5274   0.0766   0.5919
 N0P  O4   O   OS     0  -0.646  -5.5020   1.5270   2.1261

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
 N0P  O3   S1   double    1.452  0.020  1.452
 N0P  O4   S1   double    1.451  0.020  1.451
 N0P  S1   N2   single    1.685  0.020  1.685
 N0P  S1   C23  single    1.792  0.020  1.792
 N0P  N2   C16  single    1.381  0.020  1.381
 N0P  C24  C20  single    1.529  0.020  1.529
 N0P  C24  C26  single    1.529  0.020  1.529
 N0P  C22  C21  single    1.535  0.020  1.535
 N0P  C22  C15  single    1.542  0.020  1.542
 N0P  C17  N1   single    1.455  0.020  1.455
 N0P  C17  C19  single    1.527  0.020  1.527
 N0P  C20  C19  single    1.522  0.020  1.522
 N0P  C16  O2   double    1.210  0.020  1.210
 N0P  C16  C8   single    1.484  0.020  1.484
 N0P  C23  C18  single    1.512  0.020  1.512
 N0P  C18  O5   single    1.403  0.020  1.403
 N0P  O5   C25  single    1.422  0.020  1.422
 N0P  C21  C4   single    1.502  0.020  1.502
 N0P  C7   C8   aromatic  1.392  0.020  1.392
 N0P  C7   C13  aromatic  1.396  0.020  1.396
 N0P  C8   C9   single    1.390  0.020  1.390
 N0P  N1   C13  single    1.394  0.020  1.394
 N0P  N1   C12  single    1.453  0.020  1.453
 N0P  C13  C14  single    1.408  0.020  1.408
 N0P  C25  C26  single    1.522  0.020  1.522
 N0P  C11  C15  single    1.517  0.020  1.517
 N0P  C11  O1   single    1.421  0.020  1.421
 N0P  C15  C12  single    1.539  0.020  1.539
 N0P  C15  C5   single    1.512  0.020  1.512
 N0P  C9   C10  aromatic  1.383  0.020  1.383
 N0P  C14  C10  aromatic  1.390  0.020  1.390
 N0P  C14  O1   single    1.354  0.020  1.354
 N0P  C4   C5   aromatic  1.393  0.020  1.393
 N0P  C4   C3   aromatic  1.384  0.020  1.384
 N0P  C5   C6   aromatic  1.385  0.020  1.385
 N0P  C3   C2   aromatic  1.389  0.020  1.389
 N0P  C6   C1   aromatic  1.391  0.020  1.391
 N0P  C2   C1   aromatic  1.387  0.020  1.387
 N0P  C2   CL1  single    1.737  0.020  1.737
 N0P  C1   H1   single    0.930  0.020  1.080
 N0P  C3   H2   single    0.930  0.020  1.080
 N0P  C7   H3   single    0.930  0.020  1.080
 N0P  C9   H4   single    0.930  0.020  1.080
 N0P  C10  H5   single    0.930  0.020  1.080
 N0P  C11  H6   single    0.970  0.020  1.090
 N0P  C11  H7   single    0.970  0.020  1.090
 N0P  C12  H8   single    0.970  0.020  1.090
 N0P  C12  H9   single    0.970  0.020  1.090
 N0P  C19  H10  single    0.970  0.020  1.090
 N0P  C19  H11  single    0.970  0.020  1.090
 N0P  C20  H12  single    0.970  0.020  1.090
 N0P  C20  H13  single    0.970  0.020  1.090
 N0P  C21  H14  single    0.970  0.020  1.090
 N0P  C21  H15  single    0.970  0.020  1.090
 N0P  C22  H16  single    0.970  0.020  1.090
 N0P  C22  H17  single    0.970  0.020  1.090
 N0P  C24  H18  single    0.970  0.020  1.090
 N0P  C24  H19  single    0.970  0.020  1.090
 N0P  N2   H20  single    0.890  0.020  1.040
 N0P  C17  H21  single    0.970  0.020  1.090
 N0P  C17  H22  single    0.970  0.020  1.090
 N0P  C6   H23  single    0.930  0.020  1.080
 N0P  C23  H24  single    0.970  0.020  1.090
 N0P  C23  H25  single    0.970  0.020  1.090
 N0P  C18  H26  single    0.970  0.020  1.090
 N0P  C18  H27  single    0.970  0.020  1.090
 N0P  C25  H28  single    0.970  0.020  1.090
 N0P  C25  H29  single    0.970  0.020  1.090
 N0P  C26  H30  single    0.970  0.020  1.090
 N0P  C26  H31  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
 N0P  H1   C1   C6   120.34  3.000
 N0P  H1   C1   C2   120.42  3.000
 N0P  C6   C1   C2   119.24  3.000
 N0P  CL1  C2   C3   118.96  3.000
 N0P  CL1  C2   C1   119.05  3.000
 N0P  C3   C2   C1   121.99  3.000
 N0P  H2   C3   C4   121.36  3.000
 N0P  H2   C3   C2   120.57  3.000
 N0P  C4   C3   C2   118.07  3.000
 N0P  C25  O5   C18  114.03  3.000
 N0P  H3   C7   C13  118.73  3.000
 N0P  H3   C7   C8   119.11  3.000
 N0P  C13  C7   C8   122.13  3.000
 N0P  C16  C8   C9   118.84  3.000
 N0P  C9   C8   C7   119.73  3.000
 N0P  C16  C8   C7   121.37  3.000
 N0P  H4   C9   C10  120.05  3.000
 N0P  H4   C9   C8   120.85  3.000
 N0P  C10  C9   C8   119.09  3.000
 N0P  H5   C10  C14  118.62  3.000
 N0P  H5   C10  C9   120.11  3.000
 N0P  C14  C10  C9   121.23  3.000
 N0P  H7   C11  H6   107.65  3.000
 N0P  H7   C11  O1   105.77  3.000
 N0P  H6   C11  O1   110.03  3.000
 N0P  H7   C11  C15  110.04  3.000
 N0P  H6   C11  C15  110.77  3.000
 N0P  O1   C11  C15  112.36  3.000
 N0P  H9   C12  H8   106.00  3.000
 N0P  H9   C12  N1   111.61  3.000
 N0P  H8   C12  N1   107.48  3.000
 N0P  H9   C12  C15  108.93  3.000
 N0P  H8   C12  C15  108.32  3.000
 N0P  N1   C12  C15  114.13  3.000
 N0P  N1   C13  C14  120.71  3.000
 N0P  C14  C13  C7   117.18  3.000
 N0P  N1   C13  C7   122.07  3.000
 N0P  O1   C14  C13  121.98  3.000
 N0P  O1   C14  C10  117.32  3.000
 N0P  C13  C14  C10  120.58  3.000
 N0P  C5   C15  C22  102.09  3.000
 N0P  C5   C15  C12  107.85  3.000
 N0P  C22  C15  C12  111.39  3.000
 N0P  C5   C15  C11  111.66  3.000
 N0P  C12  C15  C11  110.48  3.000
 N0P  C22  C15  C11  113.00  3.000
 N0P  N2   C16  O2   122.19  3.000
 N0P  O2   C16  C8   123.13  3.000
 N0P  N2   C16  C8   114.67  3.000
 N0P  H11  C19  H10  105.72  3.000
 N0P  H11  C19  C17  110.08  3.000
 N0P  H10  C19  C17  109.17  3.000
 N0P  H11  C19  C20  107.71  3.000
 N0P  H10  C19  C20  110.81  3.000
 N0P  C17  C19  C20  113.09  3.000
 N0P  H13  C20  H12  105.72  3.000
 N0P  H13  C20  C24  110.20  3.000
 N0P  H12  C20  C24  109.72  3.000
 N0P  H13  C20  C19  108.58  3.000
 N0P  H12  C20  C19  110.45  3.000
 N0P  C24  C20  C19  111.98  3.000
 N0P  H15  C21  H14  106.50  3.000
 N0P  H15  C21  C4   113.10  3.000
 N0P  H14  C21  C4   110.10  3.000
 N0P  H15  C21  C22  112.73  3.000
 N0P  H14  C21  C22  111.70  3.000
 N0P  C4   C21  C22  102.80  3.000
 N0P  H17  C22  H16  107.17  3.000
 N0P  H17  C22  C21  108.99  3.000
 N0P  H16  C22  C21  113.40  3.000
 N0P  H17  C22  C15  109.42  3.000
 N0P  H16  C22  C15  112.22  3.000
 N0P  C21  C22  C15  105.58  3.000
 N0P  H19  C24  H18  105.40  3.000
 N0P  H19  C24  C26  109.44  3.000
 N0P  H18  C24  C26  107.99  3.000
 N0P  H19  C24  C20  108.84  3.000
 N0P  H18  C24  C20  109.31  3.000
 N0P  C26  C24  C20  115.39  3.000
 N0P  C17  N1   C13  117.07  3.000
 N0P  C13  N1   C12  116.98  3.000
 N0P  C17  N1   C12  116.53  3.000
 N0P  C14  O1   C11  118.57  3.000
 N0P  H20  N2   S1   114.18  3.000
 N0P  H20  N2   C16  120.22  3.000
 N0P  S1   N2   C16  122.21  3.000
 N0P  H22  C17  H21  105.24  3.000
 N0P  H22  C17  N1   107.37  3.000
 N0P  H21  C17  N1   112.28  3.000
 N0P  H22  C17  C19  109.19  3.000
 N0P  H21  C17  C19  110.48  3.000
 N0P  N1   C17  C19  111.98  3.000
 N0P  C5   C4   C21  110.55  3.000
 N0P  C5   C4   C3   120.78  3.000
 N0P  C21  C4   C3   128.66  3.000
 N0P  C6   C5   C4   120.41  3.000
 N0P  C6   C5   C15  129.01  3.000
 N0P  C4   C5   C15  110.54  3.000
 N0P  H23  C6   C5   121.40  3.000
 N0P  H23  C6   C1   119.09  3.000
 N0P  C5   C6   C1   119.51  3.000
 N0P  O3   S1   C23  109.74  3.000
 N0P  C23  S1   N2    99.91  3.000
 N0P  O3   S1   N2   110.56  3.000
 N0P  C23  S1   O4   108.80  3.000
 N0P  N2   S1   O4   107.25  3.000
 N0P  O3   S1   O4   118.88  3.000
 N0P  H25  C23  H24  107.95  3.000
 N0P  H25  C23  C18  109.62  3.000
 N0P  H24  C23  C18  113.17  3.000
 N0P  H25  C23  S1   104.51  3.000
 N0P  H24  C23  S1   106.89  3.000
 N0P  C18  C23  S1   114.17  3.000
 N0P  H27  C18  H26  107.18  3.000
 N0P  H27  C18  C23  107.12  3.000
 N0P  H26  C18  C23  109.87  3.000
 N0P  H27  C18  O5   112.25  3.000
 N0P  H26  C18  O5   110.82  3.000
 N0P  C23  C18  O5   109.50  3.000
 N0P  H29  C25  H28  106.90  3.000
 N0P  H29  C25  C26  109.33  3.000
 N0P  H28  C25  C26  109.96  3.000
 N0P  H29  C25  O5   106.69  3.000
 N0P  H28  C25  O5   109.55  3.000
 N0P  C26  C25  O5   114.12  3.000
 N0P  H31  C26  H30  105.79  3.000
 N0P  H31  C26  C25  110.55  3.000
 N0P  H30  C26  C25  106.07  3.000
 N0P  H31  C26  C24  110.95  3.000
 N0P  H30  C26  C24  108.98  3.000
 N0P  C25  C26  C24  114.04  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
 N0P  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 N0P  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 N0P  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 N0P  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 N0P  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 N0P  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 N0P  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 N0P  CONST_08  C14  C10  C9   C8      0.00   0.0  0
 N0P  CONST_09  C13  C7   C8   C9      0.00   0.0  0
 N0P  CONST_10  S1   N2   C16  C8    180.00   0.0  0
 N0P  CONST_11  CL1  C2   C3   C4    180.00   0.0  0
 N0P  CONST_12  CL1  C2   C1   C6    180.00   0.0  0
 N0P  CONST_13  S1   N2   C16  O2      0.00   0.0  0
 N0P  CONST_14  H2   C3   C2   C1    180.00   0.0  0
 N0P  CONST_15  H23  C6   C1   C2    180.00   0.0  0
 N0P  CONST_16  H1   C1   C2   C3    180.00   0.0  0
 N0P  CONST_17  H4   C9   C8   C7    180.00   0.0  0
 N0P  CONST_18  H5   C10  C9   C8    180.00   0.0  0
 N0P  CONST_19  H3   C7   C8   C9    180.00   0.0  0
 N0P  Var_01    C22  C21  C4   C3   -163.99  30.0  1
 N0P  Var_02    S1   C23  C18  O5     56.26  30.0  1
 N0P  Var_03    C24  C26  C25  O5    -71.61  30.0  1
 N0P  Var_04    N2   C16  C8   C7    -26.70  30.0  1
 N0P  Var_05    C4   C21  C22  C15   -27.59  30.0  1
 N0P  Var_06    C23  S1   N2   C16  -161.71  30.0  1
 N0P  Var_07    C26  C24  C20  C19  -154.34  30.0  1
 N0P  Var_08    C25  C26  C24  C20    81.67  30.0  1
 N0P  Var_09    N1   C17  C19  C20  -154.11  30.0  1
 N0P  Var_10    C17  C19  C20  C24  -178.21  30.0  1
 N0P  Var_11    C18  C23  S1   N2    -76.97  30.0  1
 N0P  Var_12    C26  C25  O5   C18   -96.06  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
 N0P  chir_01  C15  C11  C12  C5   positiv
 N0P  chir_02  N1   C17  C13  C12  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
 N0P  plan-1  C7   0.020
 N0P  plan-1  C8   0.020
 N0P  plan-1  C9   0.020
 N0P  plan-1  C10  0.020
 N0P  plan-1  C13  0.020
 N0P  plan-1  C14  0.020
 N0P  plan-1  C16  0.020
 N0P  plan-1  N1   0.020
 N0P  plan-1  O1   0.020
 N0P  plan-1  H4   0.020
 N0P  plan-1  H5   0.020
 N0P  plan-1  H3   0.020
 N0P  plan-2  C1   0.020
 N0P  plan-2  C2   0.020
 N0P  plan-2  C3   0.020
 N0P  plan-2  C15  0.020
 N0P  plan-2  C21  0.020
 N0P  plan-2  C4   0.020
 N0P  plan-2  C5   0.020
 N0P  plan-2  C6   0.020
 N0P  plan-2  CL1  0.020
 N0P  plan-2  H1   0.020
 N0P  plan-2  H2   0.020
 N0P  plan-2  H23  0.020
 N0P  plan-3  C8   0.020
 N0P  plan-3  C16  0.020
 N0P  plan-3  O2   0.020
 N0P  plan-3  N2   0.020
 N0P  plan-3  S1   0.020
 N0P  plan-3  H20  0.020

