# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Mon Jun  1 20:08:05 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: (1R,2S,5R)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-1-(hydroxymethyl)-2'-methyl-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C2=C3CCN(Cc4ccc(F)c(Cl)c4)C(=O)C3=C(O)C(=O)N2[C@]15CC[C@@H]6C[C@]56CO
#
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
 4RT  4RT  (1R,2S,5R)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-1-(hydroxymethyl)-2'-methyl-9',10'-dihydro-2'H-spiro[bicyclo[3.1.0]hexane-2,3'-imidazo[5,1-a][2,6]naphthyridine]-1',5',7'(8'H)-trione  ligand  57  34  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4RT
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
 4RT  N1   N   N     0  -0.658  -2.7581   0.0586  -0.4686
 4RT  C4   C   CH2   0  -0.529   0.0337   2.5937  -0.1273
 4RT  C5   C   CR56  0   0.183  -2.0649   1.2022  -0.1504
 4RT  C6   C   CR6   0   0.488  -2.2080  -0.9715  -1.1472
 4RT  C7   C   CR6   0   0.209  -0.8107  -0.7797  -1.5553
 4RT  C8   C   C     0   0.409  -4.1607   0.1067   0.0095
 4RT  C13  C   CR15  0  -0.237  -5.4081  -1.9877   0.2268
 4RT  C20  C   CR16  0  -0.403   5.8965   1.3204   1.4216
 4RT  C21  C   CR6   0   0.601   6.0388  -0.0498   1.4388
 4RT  C22  C   CR6   0  -0.212   5.3414  -0.8502   0.5461
 4RT  F    F   F     0  -0.294   6.8592  -0.6238   2.3212
 4RT  C19  C   CR16  0  -0.284   5.0399   1.8962   0.4930
 4RT  CL   CL  CL    0  -0.092   5.5554  -2.5593   0.6023
 4RT  C23  C   CR16  0  -0.248   4.4909  -0.2698  -0.3778
 4RT  C18  C   CR6   0   0.118   4.3330   1.1136  -0.4116
 4RT  N    N   NT    0  -0.470   1.9965   1.4975  -1.0648
 4RT  C1   C   C     0   0.596   1.2913   0.5426  -1.7094
 4RT  O4   O   O     0  -0.479   1.7539  -0.1204  -2.6264
 4RT  C2   C   CR6   0  -0.068  -0.1175   0.3583  -1.2470
 4RT  O    O   OH1   0  -0.575  -0.3084  -1.8074  -2.2149
 4RT  O1   O   O     0  -0.494  -2.7804  -2.0208  -1.4287
 4RT  C14  C   CR5   0  -0.053  -4.4923  -1.0447   0.9476
 4RT  O3   O   OH1   0  -0.667  -3.9192  -2.4683   2.7682
 4RT  C16  C   CH2   0  -0.482  -5.9447  -1.1486   1.3369
 4RT  C12  C   CH2   0  -0.410  -5.6932  -1.4531  -1.1614
 4RT  C11  C   CH2   0  -0.503  -5.1794  -0.0072  -1.1476
 4RT  N2   N   NR5   0  -0.525  -4.1577   1.4118   0.6553
 4RT  C9   C   CR5   0   0.525  -2.9861   2.0771   0.5865
 4RT  O2   O   O     0  -0.464  -2.7509   3.1805   1.0456
 4RT  C3   C   CR6   0   0.007  -0.7708   1.3857  -0.4940
 4RT  C    C   CH2   0  -0.300   1.4679   2.1703   0.1094
 4RT  H1   H   HCH2  0   0.270  -0.0036   3.3312  -0.9347
 4RT  H2   H   HCH2  0   0.279  -0.3565   3.0737   0.7658
 4RT  H3   H   HCH3  0   0.252  -6.1967   1.9029   0.7503
 4RT  H4   H   HCH3  0   0.261  -5.4805   1.4058   2.2916
 4RT  H5   H   HCH3  0   0.275  -5.0983   2.9847   1.5991
 4RT  H6   H   HCR5  0   0.256  -5.3162  -3.0573   0.3697
 4RT  H7   H   HCH2  0   0.209  -2.5377  -1.8122   1.3831
 4RT  H8   H   HCH2  0   0.200  -3.1089  -0.5743   2.5006
 4RT  H9   H   HCH2  0   0.281   3.5455   2.8217  -1.4284
 4RT  H10  H   HCH2  0   0.287   3.5748   1.3642  -2.4050
 4RT  H11  H   HCR6  0   0.293   6.4473   1.9292   2.1266
 4RT  H12  H   HCR6  0   0.272   4.9280   2.9732   0.4783
 4RT  H13  H   HCR6  0   0.284   3.9567  -0.9003  -1.0769
 4RT  H14  H   HOH1  0   0.476  -1.0081  -2.4836  -2.2682
 4RT  H15  H   HOH1  0   0.461  -3.2093  -2.7388   3.3571
 4RT  H16  H   HCH2  0   0.251  -6.6405  -0.3529   1.0983
 4RT  H17  H   HCH2  0   0.270  -6.1471  -1.6212   2.2882
 4RT  H18  H   HCH2  0   0.247  -5.1775  -2.0455  -1.9123
 4RT  H19  H   HCH2  0   0.236  -6.7602  -1.4863  -1.3914
 4RT  H20  H   HCH2  0   0.264  -5.9955   0.6902  -0.9587
 4RT  H21  H   HCH2  0   0.278  -4.7330   0.3000  -2.0929
 4RT  H22  H   HCH2  0   0.271   2.0838   3.0475   0.3047
 4RT  H23  H   HCH2  0   0.257   1.5340   1.5262   0.9918
 4RT  C10  C   CH3   0  -0.543  -5.2965   1.9434   1.3625
 4RT  C15  C   CH2   0  -0.152  -3.4221  -1.4590   1.9262
 4RT  C17  C   CH2   0  -0.421   3.3862   1.7420  -1.4028

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
 4RT  O    C7   single    1.320  0.020  1.320
 4RT  O1   C6   double    1.228  0.020  1.228
 4RT  C13  C12  single    1.515  0.020  1.515
 4RT  C13  C14  single    1.499  0.020  1.499
 4RT  C13  C16  single    1.491  0.020  1.491
 4RT  C12  C11  single    1.535  0.020  1.535
 4RT  C15  C14  single    1.508  0.020  1.508
 4RT  C15  O3   single    1.405  0.020  1.405
 4RT  C6   C7   single    1.468  0.020  1.468
 4RT  C6   N1   single    1.351  0.020  1.351
 4RT  C7   C2   double    1.368  0.020  1.368
 4RT  O4   C1   double    1.222  0.020  1.222
 4RT  C14  C16  single    1.507  0.020  1.507
 4RT  C14  C8   single    1.522  0.020  1.522
 4RT  CL   C22  single    1.723  0.020  1.723
 4RT  N1   C8   single    1.483  0.020  1.483
 4RT  N1   C5   single    1.375  0.020  1.375
 4RT  C11  C8   single    1.546  0.020  1.546
 4RT  C2   C1   single    1.494  0.020  1.494
 4RT  C2   C3   single    1.432  0.020  1.432
 4RT  C1   N    single    1.351  0.020  1.351
 4RT  C8   N2   single    1.456  0.020  1.456
 4RT  C23  C22  aromatic  1.383  0.020  1.383
 4RT  C23  C18  aromatic  1.393  0.020  1.393
 4RT  C22  C21  aromatic  1.387  0.020  1.387
 4RT  C5   C3   double    1.351  0.020  1.351
 4RT  C5   C9   single    1.469  0.020  1.469
 4RT  C3   C4   single    1.497  0.020  1.497
 4RT  N    C17  single    1.451  0.020  1.451
 4RT  N    C    single    1.453  0.020  1.453
 4RT  C17  C18  single    1.508  0.020  1.508
 4RT  N2   C9   single    1.349  0.020  1.349
 4RT  N2   C10  single    1.442  0.020  1.442
 4RT  C18  C19  aromatic  1.389  0.020  1.389
 4RT  C21  F    single    1.335  0.020  1.335
 4RT  C21  C20  aromatic  1.378  0.020  1.378
 4RT  C9   O2   double    1.218  0.020  1.218
 4RT  C    C4   single    1.514  0.020  1.514
 4RT  C19  C20  aromatic  1.388  0.020  1.388
 4RT  C4   H1   single    0.970  0.020  1.090
 4RT  C4   H2   single    0.970  0.020  1.090
 4RT  C10  H3   single    0.970  0.020  1.090
 4RT  C10  H4   single    0.970  0.020  1.090
 4RT  C10  H5   single    0.970  0.020  1.090
 4RT  C13  H6   single    0.970  0.020  1.090
 4RT  C15  H7   single    0.970  0.020  1.090
 4RT  C15  H8   single    0.970  0.020  1.090
 4RT  C17  H9   single    0.970  0.020  1.090
 4RT  C17  H10  single    0.970  0.020  1.090
 4RT  C20  H11  single    0.930  0.020  1.080
 4RT  C19  H12  single    0.930  0.020  1.080
 4RT  C23  H13  single    0.930  0.020  1.080
 4RT  O    H14  single    0.850  0.020  0.980
 4RT  O3   H15  single    0.850  0.020  0.980
 4RT  C16  H16  single    0.970  0.020  1.090
 4RT  C16  H17  single    0.970  0.020  1.090
 4RT  C12  H18  single    0.970  0.020  1.090
 4RT  C12  H19  single    0.970  0.020  1.090
 4RT  C11  H20  single    0.970  0.020  1.090
 4RT  C11  H21  single    0.970  0.020  1.090
 4RT  C    H22  single    0.970  0.020  1.090
 4RT  C    H23  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
 4RT  C8   N1   C6   124.90  3.000
 4RT  C8   N1   C5   112.05  3.000
 4RT  C6   N1   C5   123.05  3.000
 4RT  H2   C4   H1   107.25  3.000
 4RT  H2   C4   C    109.59  3.000
 4RT  H1   C4   C    109.64  3.000
 4RT  H2   C4   C3   111.40  3.000
 4RT  H1   C4   C3   110.17  3.000
 4RT  C    C4   C3   108.77  3.000
 4RT  C3   C5   C9   130.33  3.000
 4RT  C9   C5   N1   107.19  3.000
 4RT  C3   C5   N1   122.48  3.000
 4RT  O1   C6   C7   119.44  3.000
 4RT  C7   C6   N1   115.32  3.000
 4RT  O1   C6   N1   125.24  3.000
 4RT  O    C7   C2   124.57  3.000
 4RT  C2   C7   C6   121.90  3.000
 4RT  O    C7   C6   113.53  3.000
 4RT  N2   C8   C11  113.54  3.000
 4RT  N2   C8   C14  113.91  3.000
 4RT  C11  C8   C14  105.19  3.000
 4RT  N2   C8   N1    99.80  3.000
 4RT  C11  C8   N1   112.31  3.000
 4RT  C14  C8   N1   112.36  3.000
 4RT  H6   C13  C12  119.04  3.000
 4RT  H6   C13  C16  119.21  3.000
 4RT  C12  C13  C16  114.57  3.000
 4RT  H6   C13  C14  120.40  3.000
 4RT  C16  C13  C14   60.53  3.000
 4RT  C12  C13  C14  109.49  3.000
 4RT  H11  C20  C19  121.10  3.000
 4RT  H11  C20  C21  119.93  3.000
 4RT  C19  C20  C21  118.98  3.000
 4RT  F    C21  C22  119.11  3.000
 4RT  F    C21  C20  119.96  3.000
 4RT  C22  C21  C20  120.93  3.000
 4RT  C23  C22  CL   120.94  3.000
 4RT  C23  C22  C21  119.79  3.000
 4RT  CL   C22  C21  119.26  3.000
 4RT  H12  C19  C18  119.92  3.000
 4RT  H12  C19  C20  119.03  3.000
 4RT  C18  C19  C20  121.05  3.000
 4RT  H13  C23  C18  120.46  3.000
 4RT  H13  C23  C22  119.37  3.000
 4RT  C18  C23  C22  120.17  3.000
 4RT  C23  C18  C19  119.08  3.000
 4RT  C19  C18  C17  120.84  3.000
 4RT  C23  C18  C17  120.07  3.000
 4RT  C    N    C1   121.54  3.000
 4RT  C    N    C17  117.31  3.000
 4RT  C1   N    C17  120.53  3.000
 4RT  C2   C1   O4   121.47  3.000
 4RT  C2   C1   N    115.58  3.000
 4RT  O4   C1   N    122.94  3.000
 4RT  C3   C2   C1   120.30  3.000
 4RT  C3   C2   C7   118.97  3.000
 4RT  C1   C2   C7   120.72  3.000
 4RT  H14  O    C7   107.11  3.000
 4RT  C16  C14  C15  119.82  3.000
 4RT  C16  C14  C13   59.48  3.000
 4RT  C15  C14  C13  124.94  3.000
 4RT  C16  C14  C8   114.92  3.000
 4RT  C15  C14  C8   116.94  3.000
 4RT  C13  C14  C8   108.23  3.000
 4RT  H15  O3   C15  107.93  3.000
 4RT  H17  C16  H16  113.24  3.000
 4RT  H17  C16  C14  115.96  3.000
 4RT  H16  C16  C14  120.75  3.000
 4RT  H17  C16  C13  118.44  3.000
 4RT  H16  C16  C13  118.70  3.000
 4RT  C14  C16  C13   59.99  3.000
 4RT  H19  C12  H18  107.55  3.000
 4RT  H19  C12  C11  110.95  3.000
 4RT  H18  C12  C11  111.16  3.000
 4RT  H19  C12  C13  111.48  3.000
 4RT  H18  C12  C13  110.59  3.000
 4RT  C11  C12  C13  105.15  3.000
 4RT  H21  C11  H20  106.07  3.000
 4RT  H21  C11  C12  113.27  3.000
 4RT  H20  C11  C12  110.72  3.000
 4RT  H21  C11  C8   111.01  3.000
 4RT  H20  C11  C8   108.45  3.000
 4RT  C12  C11  C8   107.26  3.000
 4RT  C9   N2   C10  121.94  3.000
 4RT  C10  N2   C8   123.11  3.000
 4RT  C9   N2   C8   114.91  3.000
 4RT  O2   C9   N2   126.53  3.000
 4RT  O2   C9   C5   127.43  3.000
 4RT  N2   C9   C5   106.05  3.000
 4RT  C2   C3   C5   118.24  3.000
 4RT  C5   C3   C4   124.19  3.000
 4RT  C2   C3   C4   117.56  3.000
 4RT  H23  C    H22  107.17  3.000
 4RT  H23  C    N    110.92  3.000
 4RT  H22  C    N    108.18  3.000
 4RT  H23  C    C4   110.36  3.000
 4RT  H22  C    C4   109.78  3.000
 4RT  N    C    C4   110.35  3.000
 4RT  H5   C10  H4   108.56  3.000
 4RT  H5   C10  H3   107.99  3.000
 4RT  H4   C10  H3   108.75  3.000
 4RT  H5   C10  N2   108.43  3.000
 4RT  H4   C10  N2   111.70  3.000
 4RT  H3   C10  N2   111.30  3.000
 4RT  H8   C15  H7   106.75  3.000
 4RT  H8   C15  O3   111.43  3.000
 4RT  H7   C15  O3   110.53  3.000
 4RT  H8   C15  C14  108.65  3.000
 4RT  H7   C15  C14  109.85  3.000
 4RT  O3   C15  C14  109.57  3.000
 4RT  H10  C17  H9   107.26  3.000
 4RT  H10  C17  N    108.80  3.000
 4RT  H9   C17  N    108.17  3.000
 4RT  H10  C17  C18  110.61  3.000
 4RT  H9   C17  C18  109.63  3.000
 4RT  N    C17  C18  112.21  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
 4RT  CONST_01  C23  C22  C21  C20     0.00   0.0  0
 4RT  CONST_02  C23  C18  C19  C20     0.00   0.0  0
 4RT  CONST_03  C18  C23  C22  C21     0.00   0.0  0
 4RT  CONST_04  C18  C19  C20  C21     0.00   0.0  0
 4RT  CONST_05  C19  C18  C23  C22     0.00   0.0  0
 4RT  CONST_06  C19  C20  C21  C22     0.00   0.0  0
 4RT  CONST_07  C7   C6   N1   C5      0.00   0.0  0
 4RT  CONST_08  C8   N2   C9   C5      0.00   0.0  0
 4RT  CONST_09  C8   N1   C6   C7    180.00   0.0  0
 4RT  CONST_10  C    N    C1   C2      0.00   0.0  0
 4RT  CONST_11  C22  C23  C18  C17   180.00   0.0  0
 4RT  CONST_12  C20  C19  C18  C17   180.00   0.0  0
 4RT  CONST_13  CL   C22  C21  C20   180.00   0.0  0
 4RT  CONST_14  C23  C22  C21  F     180.00   0.0  0
 4RT  CONST_15  C19  C20  C21  F     180.00   0.0  0
 4RT  CONST_16  C18  C23  C22  CL    180.00   0.0  0
 4RT  CONST_17  O1   C6   N1   C5    180.00   0.0  0
 4RT  CONST_18  C10  N2   C9   C5    180.00   0.0  0
 4RT  CONST_19  O1   C6   N1   C8      0.00   0.0  0
 4RT  CONST_20  O2   C9   N2   C8    180.00   0.0  0
 4RT  CONST_21  C2   C1   N    C17   180.00   0.0  0
 4RT  CONST_22  C    N    C1   O4    180.00   0.0  0
 4RT  CONST_23  H13  C23  C22  C21   180.00   0.0  0
 4RT  CONST_24  H12  C19  C20  C21   180.00   0.0  0
 4RT  CONST_25  H11  C20  C21  C22   180.00   0.0  0
 4RT  CONST_26  O2   C9   N2   C10     0.00   0.0  0
 4RT  CONST_27  O4   C1   N    C17     0.00   0.0  0
 4RT  Var_01    C1   N    C    C4    -46.17  30.0  1
 4RT  Var_02    C    C4   C3   C5    145.91  30.0  1
 4RT  Var_03    N    C1   C2   C7   -162.56  30.0  1
 4RT  Var_04    C12  C13  C14  C8     -0.85  30.0  1
 4RT  Var_05    C13  C12  C11  C8     20.81  30.0  1
 4RT  Var_06    C3   C4   C    N      56.65  30.0  1
 4RT  Var_07    C11  C12  C13  C14   -12.40  30.0  1
 4RT  Var_08    N    C17  C18  C19  -107.33  30.0  2
 4RT  Var_09    O3   C15  C14  C8    176.20  30.0  1
 4RT  Var_10    H3   C10  N2   C8    -51.79  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
 4RT  chir_01  C8   N1   C11  N2   positiv
 4RT  chir_02  C13  C12  C14  C16  both
 4RT  chir_03  C14  C16  C15  C13  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
 4RT  plan-1  C20  0.020
 4RT  plan-1  C21  0.020
 4RT  plan-1  C22  0.020
 4RT  plan-1  F    0.020
 4RT  plan-1  C19  0.020
 4RT  plan-1  CL   0.020
 4RT  plan-1  C23  0.020
 4RT  plan-1  C18  0.020
 4RT  plan-1  H11  0.020
 4RT  plan-1  H12  0.020
 4RT  plan-1  H13  0.020
 4RT  plan-1  C17  0.020
 4RT  plan-2  N    0.020
 4RT  plan-2  C1   0.020
 4RT  plan-2  O4   0.020
 4RT  plan-2  C2   0.020
 4RT  plan-2  C    0.020
 4RT  plan-2  C17  0.020
 4RT  plan-3  N1   0.020
 4RT  plan-3  C4   0.020
 4RT  plan-3  C5   0.020
 4RT  plan-3  C6   0.020
 4RT  plan-3  C7   0.020
 4RT  plan-3  C8   0.020
 4RT  plan-3  C1   0.020
 4RT  plan-3  C2   0.020
 4RT  plan-3  O    0.020
 4RT  plan-3  O1   0.020
 4RT  plan-3  N2   0.020
 4RT  plan-3  C9   0.020
 4RT  plan-3  O2   0.020
 4RT  plan-3  C3   0.020
 4RT  plan-3  C10  0.020

