# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 07:38:01 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (11aS)-6-(4-fluorobenzyl)-5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Cn2c3CN4[C@@H](Cc3c5ccccc25)C(=O)NC4=O)cc1
#
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
 4O3  4O3  (11aS)-6-(4-fluorobenzyl)-5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indole-1,3(2H)-dione  ligand  42  26  .  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_4O3
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
 4O3  C15  C  CH2   0  -0.305  -0.9599  -0.9113   0.9921
 4O3  C17  C  CR5   0   0.561  -4.2973  -0.8477  -0.6071
 4O3  O1   O  O     0  -0.481  -2.0152  -3.3964  -0.1528
 4O3  C16  C  CR5   0   0.722  -2.6115  -2.3427  -0.1677
 4O3  N2   N  NR15  0  -0.714  -3.8726  -2.1341  -0.7251
 4O3  O    O  O     0  -0.432  -5.3306  -0.3780  -1.0186
 4O3  C18  C  CR15  0  -0.223  -3.1995  -0.1117   0.1334
 4O3  C19  C  CH2   0  -0.510  -2.6148   1.0631  -0.6504
 4O3  C13  C  CR5   0  -0.031  -1.2748   1.3739  -0.0714
 4O3  C8   C  CR56  0   0.047  -0.5009   2.5736  -0.1336
 4O3  C9   C  CR16  0  -0.379  -0.6949   3.8216  -0.7330
 4O3  C10  C  CR16  0  -0.269   0.2894   4.7830  -0.6064
 4O3  C11  C  CR16  0  -0.281   1.4680   4.5190   0.1082
 4O3  C12  C  CR16  0  -0.313   1.6856   3.2941   0.7123
 4O3  C7   C  CR56  0   0.346   0.6882   2.3288   0.5890
 4O3  N1   N  NR5   0  -0.516  -2.2189  -1.1556   0.3354
 4O3  C14  C  CR5   0   0.310  -0.5484   0.4816   0.6598
 4O3  N    N  NR5   0  -0.592   0.6286   1.0474   1.0778
 4O3  C6   C  CH2   0  -0.395   1.6746   0.3510   1.7859
 4O3  C5   C  CR6   0   0.083   2.4570  -0.5979   0.9096
 4O3  C2   C  CR16  0  -0.262   2.7818  -0.2663  -0.4027
 4O3  C1   C  CR16  0  -0.396   3.5216  -1.1316  -1.1943
 4O3  C4   C  CR16  0  -0.287   2.8835  -1.8205   1.4168
 4O3  C3   C  CR16  0  -0.398   3.6294  -2.6986   0.6422
 4O3  C    C  CR6   0   0.516   3.9350  -2.3344  -0.6538
 4O3  F    F  F     0  -0.315   4.6542  -3.1748  -1.4153
 4O3  H1   H  HCH2  0   0.276  -1.0474  -1.0497   2.0763
 4O3  H2   H  HCH2  0   0.281  -0.2270  -1.6392   0.6356
 4O3  H3   H  HNR5  0   0.428  -4.3902  -2.8683  -1.1876
 4O3  H4   H  HCR5  0   0.318  -3.5880   0.2450   1.0941
 4O3  H5   H  HCH2  0   0.263  -2.5347   0.8106  -1.7124
 4O3  H6   H  HCH2  0   0.266  -3.2914   1.9162  -0.5776
 4O3  H7   H  HCR6  0   0.244  -1.6004   4.0320  -1.2893
 4O3  H8   H  HCR6  0   0.248   0.1549   5.7533  -1.0668
 4O3  H9   H  HCR6  0   0.252   2.2241   5.2889   0.1880
 4O3  H10  H  HCR6  0   0.263   2.6031   3.1019   1.2543
 4O3  H11  H  HCH2  0   0.295   2.3360   1.0969   2.2296
 4O3  H12  H  HCH2  0   0.285   1.2414  -0.1923   2.6280
 4O3  H13  H  HCR6  0   0.266   2.4565   0.6757  -0.8266
 4O3  H14  H  HCR6  0   0.282   3.7724  -0.8737  -2.2146
 4O3  H15  H  HCR6  0   0.267   2.6312  -2.0998   2.4326
 4O3  H16  H  HCR6  0   0.282   3.9570  -3.6503   1.0390

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
 4O3  F    C    single    1.343  0.020  1.343
 4O3  C3   C    aromatic  1.380  0.020  1.380
 4O3  C3   C4   aromatic  1.388  0.020  1.388
 4O3  C    C1   aromatic  1.382  0.020  1.382
 4O3  C4   C5   aromatic  1.391  0.020  1.391
 4O3  C1   C2   aromatic  1.387  0.020  1.387
 4O3  C5   C2   aromatic  1.392  0.020  1.392
 4O3  C5   C6   single    1.510  0.020  1.510
 4O3  C6   N    single    1.442  0.020  1.442
 4O3  O1   C16  double    1.211  0.020  1.211
 4O3  C15  N1   single    1.441  0.020  1.441
 4O3  C15  C14  single    1.490  0.020  1.490
 4O3  N    C14  aromatic  1.371  0.020  1.371
 4O3  N    C7   aromatic  1.373  0.020  1.373
 4O3  C16  N1   single    1.348  0.020  1.348
 4O3  C16  N2   single    1.394  0.020  1.394
 4O3  N1   C18  single    1.446  0.020  1.446
 4O3  C14  C13  aromatic  1.363  0.020  1.363
 4O3  C7   C12  aromatic  1.393  0.020  1.393
 4O3  C7   C8   aromatic  1.413  0.020  1.413
 4O3  N2   C17  single    1.360  0.020  1.360
 4O3  C12  C11  aromatic  1.383  0.020  1.383
 4O3  C18  C17  single    1.515  0.020  1.515
 4O3  C18  C19  single    1.528  0.020  1.528
 4O3  C13  C8   aromatic  1.429  0.020  1.429
 4O3  C13  C19  single    1.492  0.020  1.492
 4O3  C17  O    double    1.207  0.020  1.207
 4O3  C8   C9   aromatic  1.398  0.020  1.398
 4O3  C11  C10  aromatic  1.403  0.020  1.403
 4O3  C9   C10  aromatic  1.382  0.020  1.382
 4O3  C15  H1   single    0.970  0.020  1.090
 4O3  C15  H2   single    0.970  0.020  1.090
 4O3  N2   H3   single    0.860  0.020  1.020
 4O3  C18  H4   single    0.970  0.020  1.090
 4O3  C19  H5   single    0.970  0.020  1.090
 4O3  C19  H6   single    0.970  0.020  1.090
 4O3  C9   H7   single    0.930  0.020  1.080
 4O3  C10  H8   single    0.930  0.020  1.080
 4O3  C11  H9   single    0.930  0.020  1.080
 4O3  C12  H10  single    0.930  0.020  1.080
 4O3  C6   H11  single    0.970  0.020  1.090
 4O3  C6   H12  single    0.970  0.020  1.090
 4O3  C2   H13  single    0.930  0.020  1.080
 4O3  C1   H14  single    0.930  0.020  1.080
 4O3  C4   H15  single    0.930  0.020  1.080
 4O3  C3   H16  single    0.930  0.020  1.080

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
 4O3  H2   C15  H1   106.98  3.000
 4O3  H2   C15  C14  111.39  3.000
 4O3  H1   C15  C14  111.13  3.000
 4O3  H2   C15  N1   108.93  3.000
 4O3  H1   C15  N1   111.07  3.000
 4O3  C14  C15  N1   107.35  3.000
 4O3  C18  C17  O    126.71  3.000
 4O3  O    C17  N2   127.28  3.000
 4O3  C18  C17  N2   106.00  3.000
 4O3  N1   C16  N2   106.32  3.000
 4O3  N2   C16  O1   125.48  3.000
 4O3  N1   C16  O1   128.20  3.000
 4O3  H3   N2   C16  122.52  3.000
 4O3  H3   N2   C17  124.55  3.000
 4O3  C16  N2   C17  112.91  3.000
 4O3  H4   C18  N1   110.65  3.000
 4O3  H4   C18  C19  109.57  3.000
 4O3  N1   C18  C19  111.53  3.000
 4O3  H4   C18  C17  109.25  3.000
 4O3  C19  C18  C17  113.57  3.000
 4O3  N1   C18  C17  102.06  3.000
 4O3  H6   C19  H5   106.88  3.000
 4O3  H6   C19  C13  111.59  3.000
 4O3  H5   C19  C13  111.02  3.000
 4O3  H6   C19  C18  109.24  3.000
 4O3  H5   C19  C18  110.38  3.000
 4O3  C13  C19  C18  107.73  3.000
 4O3  C14  C13  C8   106.51  3.000
 4O3  C8   C13  C19  130.10  3.000
 4O3  C14  C13  C19  123.38  3.000
 4O3  C7   C8   C9   119.39  3.000
 4O3  C9   C8   C13  133.86  3.000
 4O3  C7   C8   C13  106.75  3.000
 4O3  H7   C9   C10  120.49  3.000
 4O3  H7   C9   C8   120.63  3.000
 4O3  C10  C9   C8   118.88  3.000
 4O3  H8   C10  C11  119.31  3.000
 4O3  H8   C10  C9   119.75  3.000
 4O3  C11  C10  C9   120.93  3.000
 4O3  H9   C11  C12  119.21  3.000
 4O3  H9   C11  C10  119.37  3.000
 4O3  C12  C11  C10  121.41  3.000
 4O3  H10  C12  C7   121.86  3.000
 4O3  H10  C12  C11  120.61  3.000
 4O3  C7   C12  C11  117.53  3.000
 4O3  N    C7   C12  130.25  3.000
 4O3  C12  C7   C8   121.85  3.000
 4O3  N    C7   C8   107.89  3.000
 4O3  C18  N1   C16  112.71  3.000
 4O3  C18  N1   C15  122.26  3.000
 4O3  C16  N1   C15  125.03  3.000
 4O3  N    C14  C13  110.54  3.000
 4O3  C13  C14  C15  125.75  3.000
 4O3  N    C14  C15  123.70  3.000
 4O3  C6   N    C14  124.95  3.000
 4O3  C14  N    C7   108.29  3.000
 4O3  C6   N    C7   126.44  3.000
 4O3  H12  C6   H11  105.49  3.000
 4O3  H12  C6   C5   109.91  3.000
 4O3  H11  C6   C5   110.58  3.000
 4O3  H12  C6   N    109.33  3.000
 4O3  H11  C6   N    108.00  3.000
 4O3  C5   C6   N    113.22  3.000
 4O3  C4   C5   C2   118.80  3.000
 4O3  C2   C5   C6   121.22  3.000
 4O3  C4   C5   C6   119.98  3.000
 4O3  H13  C2   C1   118.66  3.000
 4O3  H13  C2   C5   120.41  3.000
 4O3  C1   C2   C5   120.93  3.000
 4O3  H14  C1   C    120.46  3.000
 4O3  H14  C1   C2   120.89  3.000
 4O3  C    C1   C2   118.65  3.000
 4O3  H15  C4   C3   119.03  3.000
 4O3  H15  C4   C5   119.82  3.000
 4O3  C3   C4   C5   121.15  3.000
 4O3  H16  C3   C    120.62  3.000
 4O3  H16  C3   C4   120.96  3.000
 4O3  C    C3   C4   118.42  3.000
 4O3  F    C    C3   119.07  3.000
 4O3  C3   C    C1   122.05  3.000
 4O3  F    C    C1   118.89  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
 4O3  CONST_01  C7   N    C14  C13     0.00   0.0  0
 4O3  CONST_02  N    C7   C8   C13     0.00   0.0  0
 4O3  CONST_03  C12  C7   C8   C13   180.00   0.0  0
 4O3  CONST_04  C10  C9   C8   C13   180.00   0.0  0
 4O3  CONST_05  C14  N    C7   C8      0.00   0.0  0
 4O3  CONST_06  C11  C12  C7   C8      0.00   0.0  0
 4O3  CONST_07  N    C14  C13  C8      0.00   0.0  0
 4O3  CONST_08  C11  C10  C9   C8      0.00   0.0  0
 4O3  CONST_09  N    C7   C8   C9    180.00   0.0  0
 4O3  CONST_10  C12  C7   C8   C9      0.00   0.0  0
 4O3  CONST_11  C14  C13  C8   C9    180.00   0.0  0
 4O3  CONST_12  C12  C11  C10  C9      0.00   0.0  0
 4O3  CONST_13  C7   C12  C11  C10     0.00   0.0  0
 4O3  CONST_14  C7   C8   C9   C10     0.00   0.0  0
 4O3  CONST_15  N    C7   C12  C11   180.00   0.0  0
 4O3  CONST_16  C14  N    C7   C12   180.00   0.0  0
 4O3  CONST_17  C14  C13  C8   C7      0.00   0.0  0
 4O3  CONST_18  C    C3   C4   C5      0.00   0.0  0
 4O3  CONST_19  C    C1   C2   C5      0.00   0.0  0
 4O3  CONST_20  C3   C    C1   C2      0.00   0.0  0
 4O3  CONST_21  C3   C4   C5   C2      0.00   0.0  0
 4O3  CONST_22  C4   C3   C    C1      0.00   0.0  0
 4O3  CONST_23  C4   C5   C2   C1      0.00   0.0  0
 4O3  CONST_24  N2   C16  N1   C15   180.00   0.0  0
 4O3  CONST_25  N1   C16  N2   C17     0.00   0.0  0
 4O3  CONST_26  C18  C17  N2   C16     0.00   0.0  0
 4O3  CONST_27  C18  N1   C16  N2      0.00   0.0  0
 4O3  CONST_28  C6   N    C14  C15     0.00   0.0  0
 4O3  CONST_29  C6   N    C14  C13   180.00   0.0  0
 4O3  CONST_30  C6   N    C7   C8    180.00   0.0  0
 4O3  CONST_31  C6   N    C7   C12     0.00   0.0  0
 4O3  CONST_32  C3   C4   C5   C6    180.00   0.0  0
 4O3  CONST_33  C1   C2   C5   C6    180.00   0.0  0
 4O3  CONST_34  F    C    C1   C2    180.00   0.0  0
 4O3  CONST_35  F    C    C3   C4    180.00   0.0  0
 4O3  CONST_36  O1   C16  N1   C15     0.00   0.0  0
 4O3  CONST_37  O1   C16  N2   C17   180.00   0.0  0
 4O3  CONST_38  C18  N1   C16  O1    180.00   0.0  0
 4O3  CONST_39  O    C17  N2   C16   180.00   0.0  0
 4O3  CONST_40  H7   C9   C8   C13     0.00   0.0  0
 4O3  CONST_41  H10  C12  C7   C8    180.00   0.0  0
 4O3  CONST_42  H8   C10  C9   C8    180.00   0.0  0
 4O3  CONST_43  H9   C11  C10  C9    180.00   0.0  0
 4O3  CONST_44  H16  C3   C4   C5    180.00   0.0  0
 4O3  CONST_45  H14  C1   C2   C5    180.00   0.0  0
 4O3  CONST_46  H15  C4   C5   C2    180.00   0.0  0
 4O3  CONST_47  H13  C2   C5   C4    180.00   0.0  0
 4O3  CONST_48  H3   N2   C17  C18   180.00   0.0  0
 4O3  Var_01    C14  C15  N1   C16   146.20  30.0  1
 4O3  Var_02    C14  C13  C19  C18    21.14  30.0  1
 4O3  Var_03    N1   C15  C14  C13     3.26  30.0  1
 4O3  Var_04    C5   C6   N    C7    -99.59  30.0  3
 4O3  Var_05    C4   C5   C6   N    -142.19  30.0  2

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
 4O3  chir_01  C18  N1  C17  C19  positiv

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
 4O3  plan-1  C6   0.020
 4O3  plan-1  C5   0.020
 4O3  plan-1  C2   0.020
 4O3  plan-1  C1   0.020
 4O3  plan-1  C4   0.020
 4O3  plan-1  C3   0.020
 4O3  plan-1  C    0.020
 4O3  plan-1  F    0.020
 4O3  plan-1  H13  0.020
 4O3  plan-1  H14  0.020
 4O3  plan-1  H15  0.020
 4O3  plan-1  H16  0.020
 4O3  plan-2  C15  0.020
 4O3  plan-2  C19  0.020
 4O3  plan-2  C13  0.020
 4O3  plan-2  C8   0.020
 4O3  plan-2  C9   0.020
 4O3  plan-2  C10  0.020
 4O3  plan-2  C11  0.020
 4O3  plan-2  C12  0.020
 4O3  plan-2  C7   0.020
 4O3  plan-2  C14  0.020
 4O3  plan-2  N    0.020
 4O3  plan-2  C6   0.020
 4O3  plan-2  H7   0.020
 4O3  plan-2  H8   0.020
 4O3  plan-2  H9   0.020
 4O3  plan-2  H10  0.020
 4O3  plan-3  C15  0.020
 4O3  plan-3  C17  0.020
 4O3  plan-3  O1   0.020
 4O3  plan-3  C16  0.020
 4O3  plan-3  N2   0.020
 4O3  plan-3  O    0.020
 4O3  plan-3  C18  0.020
 4O3  plan-3  N1   0.020
 4O3  plan-3  H3   0.020

