# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jul  7 06:52:57 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: (1R,2R,5S)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-2'-[(2S)-2-hydroxypropyl]-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: C[C@H](O)CN1C(=O)C2=C3CCN(Cc4ccc(F)c(Cl)c4)C(=O)C3=C(O)C(=O)N2[C@@]15CC[C@H]6C[C@@H]56
#
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
 X2P  X2P  (1R,2R,5S)-8'-(3-chloro-4-fluorobenzyl)-6'-hydroxy-2'-[(2S)-2-hydroxypropyl]-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  60  35  .  2022-07-22  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_X2P
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
 X2P  N1   N   N     0  -0.665  -2.4070  -0.7599  -0.2347
 X2P  C4   C   CH2   0  -0.531   0.0783   1.8077  -1.4942
 X2P  C5   C   CR56  0   0.193  -1.8541   0.4245  -0.6608
 X2P  C6   C   CR6   0   0.502  -1.7177  -1.9211  -0.2127
 X2P  C7   C   CR6   0   0.205  -0.3278  -1.8383  -0.6848
 X2P  C8   C   C     0   0.436  -3.8103  -0.5828   0.2179
 X2P  C10  C   CH2   0  -0.366  -5.2804   1.5115  -0.0806
 X2P  C13  C   CH2   0  -0.506  -3.9828  -0.8699   1.7277
 X2P  C15  C   CR15  0  -0.228  -5.0904  -2.6493   0.5133
 X2P  C17  C   CH2   0  -0.494  -6.1433  -1.7046   0.0559
 X2P  C20  C   CR16  0  -0.283   5.0226   2.0647  -0.4701
 X2P  C21  C   CR16  0  -0.404   5.8493   2.1545   0.6415
 X2P  C22  C   CR6   0   0.601   6.1643   1.0059   1.3347
 X2P  C24  C   CR16  0  -0.248   4.8478  -0.3087  -0.1762
 X2P  F    F   F     0  -0.294   6.9569   1.0703   2.4067
 X2P  C23  C   CR6   0  -0.213   5.6707  -0.2260   0.9332
 X2P  CL   CL  CL    0  -0.092   6.0973  -1.6380   1.8243
 X2P  C19  C   CR6   0   0.123   4.5135   0.8408  -0.8881
 X2P  N    N   NT    0  -0.470   2.1957   0.6101  -1.6668
 X2P  C1   C   C     0   0.596   1.6318  -0.6163  -1.6053
 X2P  O4   O   O     0  -0.478   2.2147  -1.6316  -1.9578
 X2P  C2   C   CR6   0  -0.063   0.2285  -0.6601  -1.0983
 X2P  O    O   OH1   0  -0.575   0.3040  -2.9969  -0.6452
 X2P  O1   O   O     0  -0.496  -2.1525  -3.0086   0.1565
 X2P  C16  C   CR15  0  -0.282  -4.7336  -1.5672  -0.4618
 X2P  C14  C   CH2   0  -0.420  -4.4754  -2.3179   1.8592
 X2P  N2   N   NR5   0  -0.537  -4.0119   0.8172  -0.1393
 X2P  C11  C   CH1   0   0.022  -5.5362   2.2862   1.2178
 X2P  O3   O   OH1   0  -0.658  -4.4237   3.0573   1.6054
 X2P  C12  C   CH3   0  -0.683  -6.7990   3.1213   1.0653
 X2P  C9   C   CR5   0   0.532  -2.9131   1.4384  -0.6139
 X2P  O2   O   O     0  -0.476  -2.8388   2.6000  -0.9773
 X2P  C3   C   CR6   0   0.007  -0.5695   0.5272  -1.0683
 X2P  C    C   CH2   0  -0.298   1.5407   1.7777  -1.1017
 X2P  H1   H   HCH2  0   0.269  -0.0060   1.9306  -2.5781
 X2P  H2   H   HCH2  0   0.277  -0.4020   2.6673  -1.0353
 X2P  H3   H   HCH2  0   0.266  -5.3076   2.2071  -0.9232
 X2P  H4   H   HCH2  0   0.284  -6.0868   0.8019  -0.2527
 X2P  H5   H   HCH2  0   0.277  -3.0653  -0.6660   2.2787
 X2P  H6   H   HCH2  0   0.266  -4.7329  -0.1843   2.1189
 X2P  H7   H   HCR5  0   0.260  -5.1271  -3.6820   0.1922
 X2P  H8   H   HCH2  0   0.272  -6.8682  -2.0535  -0.6680
 X2P  H9   H   HCH2  0   0.247  -6.5507  -1.0001   0.7720
 X2P  H10  H   HCR6  0   0.271   4.7780   2.9673  -1.0161
 X2P  H11  H   HCR6  0   0.292   6.2460   3.1071   0.9670
 X2P  H12  H   HCR6  0   0.285   4.4707  -1.2740  -0.4867
 X2P  H13  H   HCH2  0   0.281   3.6629   1.6626  -2.6725
 X2P  H14  H   HCH2  0   0.286   3.8510  -0.0799  -2.7156
 X2P  H15  H   HOH1  0   0.475  -0.3284  -3.6462  -0.2849
 X2P  H16  H   HCR5  0   0.277  -4.5580  -1.7733  -1.5110
 X2P  H17  H   HCH2  0   0.248  -3.6560  -2.9963   2.0793
 X2P  H18  H   HCH2  0   0.239  -5.2021  -2.4097   2.6693
 X2P  H19  H   HCH1  0   0.232  -5.6896   1.5773   2.0360
 X2P  H20  H   HOH1  0   0.442  -4.1913   3.6491   0.8812
 X2P  H21  H   HCH3  0   0.231  -7.6633   2.4918   0.8489
 X2P  H22  H   HCH3  0   0.244  -7.0091   3.6708   1.9828
 X2P  H23  H   HCH3  0   0.227  -6.6977   3.8408   0.2496
 X2P  H24  H   HCH2  0   0.268   2.0390   2.6649  -1.4907
 X2P  H25  H   HCH2  0   0.256   1.6502   1.7996  -0.0126
 X2P  C18  C   CH2   0  -0.428   3.5829   0.7548  -2.0718

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
 X2P  O    C7   single    1.320  0.020  1.320
 X2P  O1   C6   double    1.228  0.020  1.228
 X2P  C14  C15  single    1.516  0.020  1.516
 X2P  C14  C13  single    1.535  0.020  1.535
 X2P  C15  C17  single    1.487  0.020  1.487
 X2P  C15  C16  single    1.500  0.020  1.500
 X2P  C6   C7   single    1.470  0.020  1.470
 X2P  C6   N1   single    1.351  0.020  1.351
 X2P  C7   C2   double    1.367  0.020  1.367
 X2P  O4   C1   double    1.223  0.020  1.223
 X2P  CL   C23  single    1.723  0.020  1.723
 X2P  C17  C16  single    1.508  0.020  1.508
 X2P  C16  C8   single    1.511  0.020  1.511
 X2P  C13  C8   single    1.547  0.020  1.547
 X2P  N1   C8   single    1.485  0.020  1.485
 X2P  N1   C5   single    1.375  0.020  1.375
 X2P  C1   C2   single    1.493  0.020  1.493
 X2P  C1   N    single    1.351  0.020  1.351
 X2P  C2   C3   single    1.431  0.020  1.431
 X2P  C8   N2   single    1.459  0.020  1.459
 X2P  C24  C23  aromatic  1.384  0.020  1.384
 X2P  C24  C19  aromatic  1.393  0.020  1.393
 X2P  C23  C22  aromatic  1.387  0.020  1.387
 X2P  C5   C3   double    1.352  0.020  1.352
 X2P  C5   C9   single    1.467  0.020  1.467
 X2P  N    C18  single    1.452  0.020  1.452
 X2P  N    C    single    1.453  0.020  1.453
 X2P  C3   C4   single    1.497  0.020  1.497
 X2P  C18  C19  single    1.508  0.020  1.508
 X2P  C19  C20  aromatic  1.390  0.020  1.390
 X2P  N2   C9   single    1.348  0.020  1.348
 X2P  N2   C10  single    1.447  0.020  1.447
 X2P  C22  F    single    1.335  0.020  1.335
 X2P  C22  C21  aromatic  1.378  0.020  1.378
 X2P  C9   O2   double    1.219  0.020  1.219
 X2P  C    C4   single    1.515  0.020  1.515
 X2P  C10  C11  single    1.533  0.020  1.533
 X2P  O3   C11  single    1.408  0.020  1.408
 X2P  C20  C21  aromatic  1.388  0.020  1.388
 X2P  C11  C12  single    1.522  0.020  1.522
 X2P  C4   H1   single    0.970  0.020  1.090
 X2P  C4   H2   single    0.970  0.020  1.090
 X2P  C10  H3   single    0.970  0.020  1.090
 X2P  C10  H4   single    0.970  0.020  1.090
 X2P  C13  H5   single    0.970  0.020  1.090
 X2P  C13  H6   single    0.970  0.020  1.090
 X2P  C15  H7   single    0.970  0.020  1.090
 X2P  C17  H8   single    0.970  0.020  1.090
 X2P  C17  H9   single    0.970  0.020  1.090
 X2P  C20  H10  single    0.930  0.020  1.080
 X2P  C21  H11  single    0.930  0.020  1.080
 X2P  C24  H12  single    0.930  0.020  1.080
 X2P  C18  H13  single    0.970  0.020  1.090
 X2P  C18  H14  single    0.970  0.020  1.090
 X2P  O    H15  single    0.850  0.020  0.980
 X2P  C16  H16  single    0.970  0.020  1.090
 X2P  C14  H17  single    0.970  0.020  1.090
 X2P  C14  H18  single    0.970  0.020  1.090
 X2P  C11  H19  single    0.970  0.020  1.090
 X2P  O3   H20  single    0.850  0.020  0.980
 X2P  C12  H21  single    0.970  0.020  1.090
 X2P  C12  H22  single    0.970  0.020  1.090
 X2P  C12  H23  single    0.970  0.020  1.090
 X2P  C    H24  single    0.970  0.020  1.090
 X2P  C    H25  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
 X2P  C8   N1   C6   125.44  3.000
 X2P  C8   N1   C5   111.82  3.000
 X2P  C6   N1   C5   122.72  3.000
 X2P  H2   C4   H1   107.19  3.000
 X2P  H2   C4   C    109.46  3.000
 X2P  H1   C4   C    109.47  3.000
 X2P  H2   C4   C3   111.43  3.000
 X2P  H1   C4   C3   110.16  3.000
 X2P  C    C4   C3   109.10  3.000
 X2P  C3   C5   C9   130.04  3.000
 X2P  C9   C5   N1   107.17  3.000
 X2P  C3   C5   N1   122.76  3.000
 X2P  O1   C6   C7   118.76  3.000
 X2P  C7   C6   N1   115.39  3.000
 X2P  O1   C6   N1   125.85  3.000
 X2P  O    C7   C2   124.80  3.000
 X2P  C2   C7   C6   122.04  3.000
 X2P  O    C7   C6   113.16  3.000
 X2P  N2   C8   C16  115.51  3.000
 X2P  N2   C8   C13  113.69  3.000
 X2P  C16  C8   C13  104.48  3.000
 X2P  N2   C8   N1    99.82  3.000
 X2P  C13  C8   N1   112.38  3.000
 X2P  C16  C8   N1   111.26  3.000
 X2P  H4   C10  H3   105.95  3.000
 X2P  H4   C10  C11  109.87  3.000
 X2P  H3   C10  C11  109.09  3.000
 X2P  H4   C10  N2   109.29  3.000
 X2P  H3   C10  N2   107.21  3.000
 X2P  C11  C10  N2   115.02  3.000
 X2P  H6   C13  H5   106.29  3.000
 X2P  H6   C13  C14  110.00  3.000
 X2P  H5   C13  C14  113.79  3.000
 X2P  H6   C13  C8   108.10  3.000
 X2P  H5   C13  C8   111.41  3.000
 X2P  C14  C13  C8   107.13  3.000
 X2P  H7   C15  C14  119.06  3.000
 X2P  H7   C15  C16  120.25  3.000
 X2P  C14  C15  C16  108.84  3.000
 X2P  H7   C15  C17  119.41  3.000
 X2P  C16  C15  C17   60.66  3.000
 X2P  C14  C15  C17  114.92  3.000
 X2P  H9   C17  H8   113.56  3.000
 X2P  H9   C17  C16  121.26  3.000
 X2P  H8   C17  C16  115.20  3.000
 X2P  H9   C17  C15  118.42  3.000
 X2P  H8   C17  C15  118.38  3.000
 X2P  C16  C17  C15   60.10  3.000
 X2P  H10  C20  C19  119.97  3.000
 X2P  H10  C20  C21  118.97  3.000
 X2P  C19  C20  C21  121.06  3.000
 X2P  H11  C21  C22  119.91  3.000
 X2P  H11  C21  C20  121.07  3.000
 X2P  C22  C21  C20  119.01  3.000
 X2P  C23  C22  F    119.14  3.000
 X2P  F    C22  C21  119.97  3.000
 X2P  C23  C22  C21  120.90  3.000
 X2P  H12  C24  C19  120.40  3.000
 X2P  H12  C24  C23  119.39  3.000
 X2P  C19  C24  C23  120.21  3.000
 X2P  CL   C23  C24  120.85  3.000
 X2P  C24  C23  C22  119.80  3.000
 X2P  CL   C23  C22  119.34  3.000
 X2P  C18  C19  C24  120.14  3.000
 X2P  C18  C19  C20  120.82  3.000
 X2P  C24  C19  C20  119.02  3.000
 X2P  C    N    C1   121.57  3.000
 X2P  C    N    C18  117.31  3.000
 X2P  C1   N    C18  120.11  3.000
 X2P  C2   C1   O4   121.45  3.000
 X2P  C2   C1   N    115.75  3.000
 X2P  O4   C1   N    122.80  3.000
 X2P  C3   C2   C1   120.47  3.000
 X2P  C3   C2   C7   118.81  3.000
 X2P  C1   C2   C7   120.70  3.000
 X2P  H15  O    C7   106.56  3.000
 X2P  H16  C16  C17  117.81  3.000
 X2P  H16  C16  C15  122.07  3.000
 X2P  C17  C16  C15   59.25  3.000
 X2P  H16  C16  C8   117.41  3.000
 X2P  C17  C16  C8   118.43  3.000
 X2P  C15  C16  C8   108.84  3.000
 X2P  H18  C14  H17  107.40  3.000
 X2P  H18  C14  C15  111.72  3.000
 X2P  H17  C14  C15  110.44  3.000
 X2P  H18  C14  C13  110.88  3.000
 X2P  H17  C14  C13  111.37  3.000
 X2P  C15  C14  C13  105.09  3.000
 X2P  C9   N2   C10  120.50  3.000
 X2P  C10  N2   C8   124.86  3.000
 X2P  C9   N2   C8   114.56  3.000
 X2P  H19  C11  C12  108.33  3.000
 X2P  H19  C11  O3   105.06  3.000
 X2P  C12  C11  O3   112.51  3.000
 X2P  H19  C11  C10  109.23  3.000
 X2P  C12  C11  C10  109.32  3.000
 X2P  O3   C11  C10  112.20  3.000
 X2P  H20  O3   C11  108.66  3.000
 X2P  H23  C12  H22  108.32  3.000
 X2P  H23  C12  H21  107.78  3.000
 X2P  H22  C12  H21  107.77  3.000
 X2P  H23  C12  C11  111.06  3.000
 X2P  H22  C12  C11  110.63  3.000
 X2P  H21  C12  C11  111.15  3.000
 X2P  O2   C9   N2   126.39  3.000
 X2P  O2   C9   C5   127.22  3.000
 X2P  N2   C9   C5   106.33  3.000
 X2P  C2   C3   C5   118.25  3.000
 X2P  C5   C3   C4   124.20  3.000
 X2P  C2   C3   C4   117.55  3.000
 X2P  H25  C    H24  107.05  3.000
 X2P  H25  C    N    110.96  3.000
 X2P  H24  C    N    108.02  3.000
 X2P  H25  C    C4   110.73  3.000
 X2P  H24  C    C4   109.45  3.000
 X2P  N    C    C4   110.51  3.000
 X2P  H14  C18  H13  107.12  3.000
 X2P  H14  C18  N    108.91  3.000
 X2P  H13  C18  N    107.84  3.000
 X2P  H14  C18  C19  110.87  3.000
 X2P  H13  C18  C19  109.83  3.000
 X2P  N    C18  C19  112.10  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
 X2P  CONST_01  C23  C24  C19  C20     0.00   0.0  0
 X2P  CONST_02  C23  C22  C21  C20     0.00   0.0  0
 X2P  CONST_03  C24  C23  C22  C21     0.00   0.0  0
 X2P  CONST_04  C24  C19  C20  C21     0.00   0.0  0
 X2P  CONST_05  C19  C24  C23  C22     0.00   0.0  0
 X2P  CONST_06  C19  C20  C21  C22     0.00   0.0  0
 X2P  CONST_07  C7   C6   N1   C5      0.00   0.0  0
 X2P  CONST_08  C8   N2   C9   C5      0.00   0.0  0
 X2P  CONST_09  C8   N1   C6   C7    180.00   0.0  0
 X2P  CONST_10  C    N    C1   C2      0.00   0.0  0
 X2P  CONST_11  F    C22  C21  C20   180.00   0.0  0
 X2P  CONST_12  CL   C23  C22  C21   180.00   0.0  0
 X2P  CONST_13  C18  C19  C20  C21   180.00   0.0  0
 X2P  CONST_14  F    C22  C23  C24   180.00   0.0  0
 X2P  CONST_15  C18  C19  C24  C23   180.00   0.0  0
 X2P  CONST_16  C19  C24  C23  CL    180.00   0.0  0
 X2P  CONST_17  O1   C6   N1   C5    180.00   0.0  0
 X2P  CONST_18  C10  N2   C9   C5    180.00   0.0  0
 X2P  CONST_19  O1   C6   N1   C8      0.00   0.0  0
 X2P  CONST_20  O2   C9   N2   C8    180.00   0.0  0
 X2P  CONST_21  C2   C1   N    C18   180.00   0.0  0
 X2P  CONST_22  C    N    C1   O4    180.00   0.0  0
 X2P  CONST_23  H12  C24  C19  C20   180.00   0.0  0
 X2P  CONST_24  H10  C20  C21  C22   180.00   0.0  0
 X2P  CONST_25  H11  C21  C22  C23   180.00   0.0  0
 X2P  CONST_26  O2   C9   N2   C10     0.00   0.0  0
 X2P  CONST_27  O4   C1   N    C18     0.00   0.0  0
 X2P  Var_01    C1   N    C    C4    -45.77  30.0  1
 X2P  Var_02    C    C4   C3   C5    146.83  30.0  1
 X2P  Var_03    N    C1   C2   C7   -163.90  30.0  1
 X2P  Var_04    C14  C15  C16  C8      3.87  30.0  1
 X2P  Var_05    C15  C14  C13  C8    -21.70  30.0  1
 X2P  Var_06    C3   C4   C    N      55.89  30.0  1
 X2P  Var_07    N    C18  C19  C20  -101.67  30.0  1
 X2P  Var_08    C11  C10  N2   C8     94.54  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
 X2P  chir_01  C8   C13  N1   N2   positiv
 X2P  chir_04  C11  C10  O3   C12  negativ
 X2P  chir_05  C15  C14  C17  C16  both
 X2P  chir_06  C16  C8   C17  C15  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
 X2P  plan-1  C20  0.020
 X2P  plan-1  C21  0.020
 X2P  plan-1  C22  0.020
 X2P  plan-1  C24  0.020
 X2P  plan-1  F    0.020
 X2P  plan-1  C23  0.020
 X2P  plan-1  CL   0.020
 X2P  plan-1  C19  0.020
 X2P  plan-1  H10  0.020
 X2P  plan-1  H11  0.020
 X2P  plan-1  H12  0.020
 X2P  plan-1  C18  0.020
 X2P  plan-2  N    0.020
 X2P  plan-2  C1   0.020
 X2P  plan-2  O4   0.020
 X2P  plan-2  C2   0.020
 X2P  plan-2  C    0.020
 X2P  plan-2  C18  0.020
 X2P  plan-3  N1   0.020
 X2P  plan-3  C4   0.020
 X2P  plan-3  C5   0.020
 X2P  plan-3  C6   0.020
 X2P  plan-3  C7   0.020
 X2P  plan-3  C8   0.020
 X2P  plan-3  C10  0.020
 X2P  plan-3  C1   0.020
 X2P  plan-3  C2   0.020
 X2P  plan-3  O    0.020
 X2P  plan-3  O1   0.020
 X2P  plan-3  N2   0.020
 X2P  plan-3  C9   0.020
 X2P  plan-3  O2   0.020
 X2P  plan-3  C3   0.020

