# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:29:53 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: 2'-(2-fluorophenyl)-1-methyl-6',8',9',11'-tetrahydrospiro[azetidine-3,10'-pyrido[3',4':4,5]pyrrolo[2,3-f]isoquinolin]-7'(5'H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CC2(CNC(=O)c3c4CCc5cnc(cc5c4[nH]c23)c6ccccc6F)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
 L8I  L8I  2'-(2-fluorophenyl)-1-methyl-6',8',9',11'-tetrahydrospiro[azetidine-3,10'-pyrido[3',4':4,5]pyrrolo[2,3-f]isoquinolin]-7'(5'H)-one  ligand  50  29  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L8I
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
 L8I  F1    F  F     0  -0.302  -5.3179  -0.4143   1.5314
 L8I  C2    C  CR6   0   0.521  -5.1487   0.5976   0.6687
 L8I  C3    C  CR6   0  -0.155  -3.9885   0.6542  -0.0949
 L8I  C4    C  CR16  0  -0.275  -3.8393   1.7529  -0.9421
 L8I  C6    C  CR16  0  -0.257  -4.8114   2.7379  -1.0279
 L8I  C8    C  CR16  0  -0.244  -5.9606   2.6415  -0.2553
 L8I  C10   C  CR16  0  -0.405  -6.1314   1.5660   0.6048
 L8I  C12   C  CR6   0   0.228  -2.9471  -0.3939  -0.0232
 L8I  N13   N  N     0  -0.427  -3.3465  -1.6618  -0.0640
 L8I  C14   C  CR16  0  -0.133  -2.4180  -2.6112  -0.0168
 L8I  C16   C  CR66  0  -0.053  -1.0571  -2.3752   0.0700
 L8I  C17   C  CR66  0   0.221  -0.6382  -1.0352   0.0972
 L8I  C18   C  CR16  0  -0.400  -1.6050  -0.0361   0.0555
 L8I  C20   C  CR56  0   0.271   0.7849  -0.8127   0.1357
 L8I  N21   N  NR15  0  -0.737   1.4478   0.3736   0.3440
 L8I  C23   C  CR56  0   0.459   2.7710   0.1668   0.2366
 L8I  C24   C  CR56  0  -0.215   2.9810  -1.1653  -0.0709
 L8I  C25   C  CR56  0   0.029   1.7138  -1.7926  -0.1294
 L8I  C26   C  C     0  -0.513   1.2866  -3.1833  -0.4636
 L8I  C29   C  C     0  -0.531  -0.0510  -3.4845   0.2155
 L8I  C32   C  CR6   0   0.465   4.3167  -1.6736  -0.3655
 L8I  N33   N  NR16  0  -0.656   5.3057  -0.7690  -0.1515
 L8I  C35   C  C     0  -0.284   5.1367   0.4176   0.6683
 L8I  C38   C  C     0  -0.227   3.8568   1.1687   0.3473
 L8I  C39   C  C     0  -0.264   3.5329   2.3846   1.2335
 L8I  N42   N  N     0  -0.397   3.0366   3.0741   0.0441
 L8I  C43   C  C     0  -0.248   3.8302   2.1949  -0.8136
 L8I  C46   C  CH3   0  -0.524   3.2339   4.4955  -0.0587
 L8I  O50   O  O     0  -0.488   4.5300  -2.7938  -0.8162
 L8I  H4    H  HCR6  0   0.269  -2.9499   1.8225  -1.5561
 L8I  H6    H  HCR6  0   0.264  -4.6742   3.5733  -1.7008
 L8I  H8    H  HCR6  0   0.271  -6.7272   3.4021  -0.3166
 L8I  H10   H  HCR6  0   0.280  -7.0132   1.4808   1.2265
 L8I  H14   H  HCR6  0   0.256  -2.7810  -3.6344  -0.0492
 L8I  H18   H  HCR6  0   0.261  -1.3302   1.0110   0.0852
 L8I  HN21  H  HNR5  0   0.416   1.0260   1.2679   0.5446
 L8I  H26   H  H     0   0.248   1.1924  -3.2880  -1.5499
 L8I  H26A  H  H     0   0.256   2.0335  -3.9117  -0.1499
 L8I  H29   H  H     0   0.257   0.1298  -3.6352   1.2859
 L8I  H29A  H  H     0   0.259  -0.4657  -4.4202  -0.1623
 L8I  HN33  H  HNR6  0   0.397   6.2493  -1.1050  -0.2725
 L8I  H35   H  H     0   0.246   5.1220   0.1541   1.7332
 L8I  H35A  H  H     0   0.263   5.9973   1.0658   0.5105
 L8I  H39   H  H     0   0.242   2.8167   2.2564   2.0486
 L8I  H39A  H  H     0   0.229   4.4554   2.8250   1.6405
 L8I  H43   H  H     0   0.220   4.8392   2.5800  -1.0206
 L8I  H43A  H  H     0   0.239   3.3622   1.8965  -1.7542
 L8I  H46   H  HCH3  0   0.195   4.2847   4.7958   0.0693
 L8I  H46A  H  HCH3  0   0.236   2.8996   4.8473  -1.0355
 L8I  H46B  H  HCH3  0   0.236   2.6416   5.0092   0.6995

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
 L8I  F1   C2    single    1.340  0.020  1.340
 L8I  C2   C3    aromatic  1.390  0.020  1.390
 L8I  C2   C10   aromatic  1.381  0.020  1.381
 L8I  C3   C4    aromatic  1.395  0.020  1.395
 L8I  C3   C12   single    1.479  0.020  1.479
 L8I  C4   C6    aromatic  1.387  0.020  1.387
 L8I  C6   C8    aromatic  1.388  0.020  1.388
 L8I  C8   C10   aromatic  1.388  0.020  1.388
 L8I  C12  N13   aromatic  1.330  0.020  1.330
 L8I  C12  C18   aromatic  1.391  0.020  1.391
 L8I  N13  C14   aromatic  1.329  0.020  1.329
 L8I  C14  C16   aromatic  1.384  0.020  1.384
 L8I  C16  C17   aromatic  1.404  0.020  1.404
 L8I  C16  C29   single    1.505  0.020  1.505
 L8I  C17  C18   aromatic  1.391  0.020  1.391
 L8I  C17  C20   aromatic  1.441  0.020  1.441
 L8I  C20  N21   aromatic  1.375  0.020  1.375
 L8I  C20  C25   aromatic  1.376  0.020  1.376
 L8I  N21  C23   aromatic  1.344  0.020  1.344
 L8I  C23  C24   aromatic  1.383  0.020  1.383
 L8I  C23  C38   single    1.482  0.020  1.482
 L8I  C24  C25   aromatic  1.415  0.020  1.415
 L8I  C24  C32   single    1.459  0.020  1.459
 L8I  C25  C26   single    1.493  0.020  1.493
 L8I  C26  C29   single    1.530  0.020  1.530
 L8I  C32  N33   single    1.357  0.020  1.357
 L8I  C32  O50   double    1.226  0.020  1.226
 L8I  N33  C35   single    1.452  0.020  1.452
 L8I  C35  C38   single    1.518  0.020  1.518
 L8I  C38  C39   single    1.539  0.020  1.539
 L8I  C38  C43   single    1.550  0.020  1.550
 L8I  C39  N42   single    1.462  0.020  1.462
 L8I  N42  C43   single    1.462  0.020  1.462
 L8I  N42  C46   single    1.439  0.020  1.439
 L8I  C4   H4    single    0.930  0.020  1.080
 L8I  C6   H6    single    0.930  0.020  1.080
 L8I  C8   H8    single    0.930  0.020  1.080
 L8I  C10  H10   single    0.930  0.020  1.080
 L8I  C14  H14   single    0.930  0.020  1.080
 L8I  C18  H18   single    0.930  0.020  1.080
 L8I  N21  HN21  single    0.860  0.020  1.020
 L8I  C26  H26   single    0.970  0.020  1.090
 L8I  C26  H26A  single    0.970  0.020  1.090
 L8I  C29  H29   single    0.970  0.020  1.090
 L8I  C29  H29A  single    0.970  0.020  1.090
 L8I  N33  HN33  single    0.890  0.020  1.040
 L8I  C35  H35   single    0.970  0.020  1.090
 L8I  C35  H35A  single    0.970  0.020  1.090
 L8I  C39  H39   single    0.970  0.020  1.090
 L8I  C39  H39A  single    0.970  0.020  1.090
 L8I  C43  H43   single    0.970  0.020  1.090
 L8I  C43  H43A  single    0.970  0.020  1.090
 L8I  C46  H46   single    0.970  0.020  1.090
 L8I  C46  H46A  single    0.970  0.020  1.090
 L8I  C46  H46B  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
 L8I  C10   C2   C3    122.68  3.000
 L8I  C10   C2   F1    117.98  3.000
 L8I  C3    C2   F1    119.32  3.000
 L8I  C12   C3   C4    120.80  3.000
 L8I  C12   C3   C2    122.15  3.000
 L8I  C4    C3   C2    117.05  3.000
 L8I  H4    C4   C6    119.68  3.000
 L8I  H4    C4   C3    118.85  3.000
 L8I  C6    C4   C3    121.46  3.000
 L8I  H6    C6   C8    120.33  3.000
 L8I  H6    C6   C4    119.89  3.000
 L8I  C8    C6   C4    119.78  3.000
 L8I  H8    C8   C10   119.53  3.000
 L8I  H8    C8   C6    120.42  3.000
 L8I  C10   C8   C6    120.05  3.000
 L8I  H10   C10  C8    121.16  3.000
 L8I  H10   C10  C2    119.86  3.000
 L8I  C8    C10  C2    118.98  3.000
 L8I  C18   C12  N13   122.46  3.000
 L8I  C18   C12  C3    119.98  3.000
 L8I  N13   C12  C3    117.55  3.000
 L8I  C14   N13  C12   118.05  3.000
 L8I  H14   C14  C16   119.42  3.000
 L8I  H14   C14  N13   116.01  3.000
 L8I  C16   C14  N13   124.58  3.000
 L8I  C29   C16  C17   120.15  3.000
 L8I  C29   C16  C14   122.54  3.000
 L8I  C17   C16  C14   117.21  3.000
 L8I  C20   C17  C18   125.20  3.000
 L8I  C20   C17  C16   116.26  3.000
 L8I  C18   C17  C16   118.52  3.000
 L8I  H18   C18  C17   121.15  3.000
 L8I  H18   C18  C12   119.67  3.000
 L8I  C17   C18  C12   119.18  3.000
 L8I  C25   C20  N21   108.55  3.000
 L8I  C25   C20  C17   123.48  3.000
 L8I  N21   C20  C17   127.84  3.000
 L8I  HN21  N21  C23   124.33  3.000
 L8I  HN21  N21  C20   126.40  3.000
 L8I  C23   N21  C20   109.26  3.000
 L8I  C38   C23  C24   123.82  3.000
 L8I  C38   C23  N21   127.71  3.000
 L8I  C24   C23  N21   108.39  3.000
 L8I  C32   C24  C25   131.07  3.000
 L8I  C32   C24  C23   121.29  3.000
 L8I  C25   C24  C23   107.46  3.000
 L8I  C26   C25  C24   132.73  3.000
 L8I  C26   C25  C20   120.89  3.000
 L8I  C24   C25  C20   106.31  3.000
 L8I  H26A  C26  H26   106.30  3.000
 L8I  H26A  C26  C29   109.87  3.000
 L8I  H26   C26  C29   110.25  3.000
 L8I  H26A  C26  C25   111.24  3.000
 L8I  H26   C26  C25   109.61  3.000
 L8I  C29   C26  C25   109.53  3.000
 L8I  H29A  C29  H29   106.44  3.000
 L8I  H29A  C29  C26   110.33  3.000
 L8I  H29   C29  C26   108.44  3.000
 L8I  H29A  C29  C16   110.16  3.000
 L8I  H29   C29  C16   107.82  3.000
 L8I  C26   C29  C16   113.36  3.000
 L8I  O50   C32  N33   122.69  3.000
 L8I  O50   C32  C24   123.48  3.000
 L8I  N33   C32  C24   113.77  3.000
 L8I  HN33  N33  C35   116.66  3.000
 L8I  HN33  N33  C32   116.14  3.000
 L8I  C35   N33  C32   123.28  3.000
 L8I  H35A  C35  H35   107.12  3.000
 L8I  H35A  C35  C38   109.94  3.000
 L8I  H35   C35  C38   108.22  3.000
 L8I  H35A  C35  N33   108.22  3.000
 L8I  H35   C35  N33   110.69  3.000
 L8I  C38   C35  N33   112.52  3.000
 L8I  C43   C38  C39    84.53  3.000
 L8I  C43   C38  C35   120.03  3.000
 L8I  C39   C38  C35   116.52  3.000
 L8I  C43   C38  C23   112.29  3.000
 L8I  C39   C38  C23   115.03  3.000
 L8I  C35   C38  C23   107.40  3.000
 L8I  H39A  C39  H39   108.70  3.000
 L8I  H39A  C39  N42   113.38  3.000
 L8I  H39   C39  N42   116.10  3.000
 L8I  H39A  C39  C38   110.66  3.000
 L8I  H39   C39  C38   118.35  3.000
 L8I  N42   C39  C38    88.60  3.000
 L8I  C46   N42  C43   118.53  3.000
 L8I  C46   N42  C39   118.53  3.000
 L8I  C43   N42  C39    90.54  3.000
 L8I  H43A  C43  H43   109.07  3.000
 L8I  H43A  C43  N42   115.91  3.000
 L8I  H43   C43  N42   113.44  3.000
 L8I  H43A  C43  C38   118.14  3.000
 L8I  H43   C43  C38   110.92  3.000
 L8I  N42   C43  C38    88.17  3.000
 L8I  H46B  C46  H46A  107.71  3.000
 L8I  H46B  C46  H46   108.01  3.000
 L8I  H46A  C46  H46   108.00  3.000
 L8I  H46B  C46  N42   109.94  3.000
 L8I  H46A  C46  N42   109.91  3.000
 L8I  H46   C46  N42   113.09  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
 L8I  CONST_01  C6    C4   C3   C2     0.00   0.0  0
 L8I  CONST_04  C6    C8   C10  C2     0.00   0.0  0
 L8I  CONST_05  C8    C10  C2   C3     0.00   0.0  0
 L8I  CONST_06  C8    C6   C4   C3     0.00   0.0  0
 L8I  CONST_07  C14   N13  C12  C3   180.00   0.0  0
 L8I  CONST_08  C17   C18  C12  C3   180.00   0.0  0
 L8I  CONST_09  C10   C2   C3   C4     0.00   0.0  0
 L8I  CONST_12  C10   C8   C6   C4     0.00   0.0  0
 L8I  CONST_13  C12   C3   C4   C6   180.00   0.0  0
 L8I  CONST_14  C12   C3   C2   C10  180.00   0.0  0
 L8I  CONST_15  C16   C14  N13  C12    0.00   0.0  0
 L8I  CONST_16  C16   C17  C18  C12    0.00   0.0  0
 L8I  CONST_17  C20   C17  C18  C12  180.00   0.0  0
 L8I  CONST_18  C17   C18  C12  N13    0.00   0.0  0
 L8I  CONST_19  C17   C16  C14  N13    0.00   0.0  0
 L8I  CONST_20  C18   C12  N13  C14    0.00   0.0  0
 L8I  CONST_21  C18   C17  C16  C14    0.00   0.0  0
 L8I  CONST_22  C20   C17  C16  C14  180.00   0.0  0
 L8I  CONST_23  N21   C20  C17  C16  180.00   0.0  0
 L8I  CONST_24  C25   C20  C17  C16    0.00   0.0  0
 L8I  CONST_25  C23   N21  C20  C17  180.00   0.0  0
 L8I  CONST_26  C24   C25  C20  C17  180.00   0.0  0
 L8I  CONST_27  N21   C20  C17  C18    0.00   0.0  0
 L8I  CONST_29  C24   C23  N21  C20    0.00   0.0  0
 L8I  CONST_30  C23   C24  C25  C20    0.00   0.0  0
 L8I  CONST_31  C24   C25  C20  N21    0.00   0.0  0
 L8I  CONST_32  C25   C24  C23  N21    0.00   0.0  0
 L8I  CONST_33  C25   C20  N21  C23    0.00   0.0  0
 L8I  CONST_34  C38   C23  N21  C20  180.00   0.0  0
 L8I  CONST_35  C38   C23  C24  C25  180.00   0.0  0
 L8I  CONST_36  C38   C23  C24  C32    0.00   0.0  0
 L8I  CONST_38  C4    C3   C2   F1   180.00   0.0  0
 L8I  CONST_39  C12   C3   C2   F1     0.00   0.0  0
 L8I  CONST_40  C8    C10  C2   F1   180.00   0.0  0
 L8I  CONST_42  H4    C4   C3   C2   180.00   0.0  0
 L8I  CONST_43  H8    C8   C10  C2   180.00   0.0  0
 L8I  CONST_44  H10   C10  C2   C3   180.00   0.0  0
 L8I  CONST_45  H6    C6   C4   C3   180.00   0.0  0
 L8I  CONST_46  H18   C18  C12  C3     0.00   0.0  0
 L8I  CONST_47  H14   C14  N13  C12  180.00   0.0  0
 L8I  CONST_48  HN21  N21  C20  C17    0.00   0.0  0
 L8I  CONST_49  HN33  N33  C32  C24  180.00   0.0  0
 L8I  Var_01    C26   C29  C16  C14  147.41  30.0  1
 L8I  Var_02    C25   C26  C29  C16   45.50  30.0  1
 L8I  Var_03    C29   C26  C25  C20  -29.04  30.0  1
 L8I  Var_04    C35   C38  C23  N21  159.37  30.0  1
 L8I  Var_05    N33   C32  C24  C23    7.39  30.0  1
 L8I  Var_06    N33   C35  C38  C23   44.94  30.0  1
 L8I  Var_07    N42   C39  C38  C23  -91.25  30.0  3
 L8I  Var_08    N42   C43  C38  C23   94.02  30.0  3
 L8I  Var_09    C38   C35  N33  C32  -46.86  30.0  1
 L8I  Var_10    C43   N42  C39  C38  -22.02  30.0  1
 L8I  Var_11    H46   C46  N42  C39   53.78  30.0  3

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
 L8I  plan-1  F1    0.020
 L8I  plan-1  C2    0.020
 L8I  plan-1  C3    0.020
 L8I  plan-1  C4    0.020
 L8I  plan-1  C6    0.020
 L8I  plan-1  C8    0.020
 L8I  plan-1  C10   0.020
 L8I  plan-1  C12   0.020
 L8I  plan-1  H4    0.020
 L8I  plan-1  H6    0.020
 L8I  plan-1  H8    0.020
 L8I  plan-1  H10   0.020
 L8I  plan-2  C17   0.020
 L8I  plan-2  C20   0.020
 L8I  plan-2  N21   0.020
 L8I  plan-2  C23   0.020
 L8I  plan-2  C24   0.020
 L8I  plan-2  C25   0.020
 L8I  plan-2  C26   0.020
 L8I  plan-2  C32   0.020
 L8I  plan-2  C38   0.020
 L8I  plan-2  HN21  0.020
 L8I  plan-3  C3    0.020
 L8I  plan-3  C12   0.020
 L8I  plan-3  N13   0.020
 L8I  plan-3  C14   0.020
 L8I  plan-3  C16   0.020
 L8I  plan-3  C17   0.020
 L8I  plan-3  C18   0.020
 L8I  plan-3  C20   0.020
 L8I  plan-3  C29   0.020
 L8I  plan-3  H14   0.020
 L8I  plan-3  H18   0.020
 L8I  plan-4  C24   0.020
 L8I  plan-4  C32   0.020
 L8I  plan-4  N33   0.020
 L8I  plan-4  C35   0.020
 L8I  plan-4  O50   0.020
 L8I  plan-4  HN33  0.020

