# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 09:41:35 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 3-[(11aS)-6-(4-fluorobenzyl)-1,3-dioxo-5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indol-2(3H)-yl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCN1C(=O)[C@@H]2Cc3c(CN2C1=O)n(Cc4ccc(F)cc4)c5ccccc35
#
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
 4O2  4O2  '3-[(11aS)-6-(4-fluorobenzyl)-1,3-dioxo-5,6,11,11a-tetrahydro-1H-imidazo[1',5':1,6]pyrido[3,4-b]indol-2(3H)-yl]propanoic acid'  ligand  51  31  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4O2
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
 4O2  C1   C  CH2   0  -0.289  -4.5888  -0.3230   0.3958
 4O2  C2   C  CH2   0  -0.567  -4.7256  -0.9094  -1.0012
 4O2  C3   C  C     0   0.556  -6.0836  -1.5173  -1.2131
 4O2  C4   C  CR5   0   0.566  -3.0029   1.5964   0.3975
 4O2  C5   C  CR15  0  -0.199  -1.5419   1.7793   0.7430
 4O2  C6   C  CH2   0  -0.493  -0.7016   2.3535  -0.3956
 4O2  C7   C  CH2   0  -0.293   0.2086   0.0857   1.4330
 4O2  C8   C  CR5   0   0.321   1.1169   1.0245   0.7174
 4O2  C10  C  CR56  0   0.058   1.9224   2.6844  -0.5511
 4O2  C11  C  CR16  0  -0.357   2.1816   3.7720  -1.3891
 4O2  C13  C  CR16  0  -0.258   4.5531   3.4333  -1.0335
 4O2  C14  C  CR16  0  -0.289   4.3256   2.3561  -0.1979
 4O2  C17  C  CR6   0   0.083   3.2192  -1.3603   0.8507
 4O2  C19  C  CR16  0  -0.382   3.2658  -2.7101  -1.1519
 4O2  C21  C  CR16  0  -0.382   3.2019  -3.7735   1.0144
 4O2  C20  C  CR6   0   0.531   3.2411  -3.8459  -0.3641
 4O2  C18  C  CR16  0  -0.246   3.2560  -1.4683  -0.5359
 4O2  C22  C  CR16  0  -0.260   3.1882  -2.5221   1.6126
 4O2  N2   N  NR5   0  -0.598   2.4836   0.9931   0.8259
 4O2  N1   N  NR5   0  -0.534  -1.1424   0.4316   1.0736
 4O2  C    C  CR5   0   0.776  -2.1619  -0.4442   0.9940
 4O2  O    O  O     0  -0.471  -2.1500  -1.6336   1.2099
 4O2  C15  C  CR56  0   0.355   3.0023   1.9950   0.0424
 4O2  C12  C  CR16  0  -0.255   3.4928   4.1382  -1.6210
 4O2  C9   C  CR5   0  -0.037   0.7278   2.0420  -0.1013
 4O2  O3   O  O     0  -0.457  -3.7666   2.4505   0.0085
 4O2  N    N  NR5   0  -0.571  -3.2926   0.2840   0.5984
 4O2  O2   O  OH1   0  -0.586  -6.1954  -2.0702  -2.4208
 4O2  O1   O  O     0  -0.406  -6.9730  -1.5141  -0.4054
 4O2  H1   H  HCH2  0   0.266  -5.3443   0.4402   0.5710
 4O2  H2   H  HCH2  0   0.275  -4.7267  -1.0911   1.1543
 4O2  H3   H  HCH2  0   0.274  -4.5671  -0.1406  -1.7622
 4O2  H4   H  HCH2  0   0.283  -3.9653  -1.6742  -1.1759
 4O2  H5   H  HCR5  0   0.301  -1.4683   2.4354   1.6180
 4O2  H6   H  HCH2  0   0.253  -1.0092   1.9230  -1.3537
 4O2  H7   H  HCH2  0   0.254  -0.8722   3.4291  -0.4617
 4O2  H8   H  HCH2  0   0.282   0.3955  -0.9517   1.1452
 4O2  H9   H  HCH2  0   0.256   0.3526   0.1478   2.5185
 4O2  H10  H  HCR6  0   0.220   1.3708   4.3227  -1.8494
 4O2  H11  H  HCR6  0   0.236   5.5707   3.7384  -1.2354
 4O2  H12  H  HCR6  0   0.234   5.1579   1.8240   0.2443
 4O2  H13  H  HCR6  0   0.261   3.2912  -2.7923  -2.2301
 4O2  H14  H  HCR6  0   0.262   3.1740  -4.6735   1.6131
 4O2  H15  H  HCR6  0   0.255   3.2715  -0.5818  -1.1575
 4O2  H16  H  HCR6  0   0.237   3.1491  -2.4603   2.6930
 4O2  H19  H  HCR6  0   0.232   3.7085   4.9825  -2.2620
 4O2  H20  H  HOH1  0   0.450  -7.0817  -2.4469  -2.5034
 4O2  C16  C  CH2   0  -0.374   3.2346  -0.0135   1.5316
 4O2  F    F  F     0  -0.302   3.2483  -5.0469  -0.9528
 4O2  H17  H  HCH2  0   0.258   2.8522  -0.1081   2.5512
 4O2  H18  H  HCH2  0   0.272   4.2588   0.3482   1.6346

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
 4O2  F    C20  single    1.338  0.020  1.338
 4O2  C20  C19  aromatic  1.383  0.020  1.383
 4O2  C20  C21  aromatic  1.381  0.020  1.381
 4O2  C19  C18  aromatic  1.386  0.020  1.386
 4O2  C21  C22  aromatic  1.387  0.020  1.387
 4O2  C18  C17  aromatic  1.391  0.020  1.391
 4O2  C22  C17  aromatic  1.390  0.020  1.390
 4O2  C17  C16  single    1.509  0.020  1.509
 4O2  O1   C3   double    1.201  0.020  1.201
 4O2  C3   O2   single    1.333  0.020  1.333
 4O2  C3   C2   single    1.503  0.020  1.503
 4O2  C16  N2   single    1.441  0.020  1.441
 4O2  C7   C8   single    1.489  0.020  1.489
 4O2  C7   N1   single    1.440  0.020  1.440
 4O2  C5   N1   single    1.444  0.020  1.444
 4O2  C5   C4   single    1.512  0.020  1.512
 4O2  C5   C6   single    1.527  0.020  1.527
 4O2  N2   C8   aromatic  1.371  0.020  1.371
 4O2  N2   C15  aromatic  1.374  0.020  1.374
 4O2  C8   C9   aromatic  1.363  0.020  1.363
 4O2  N1   C    single    1.346  0.020  1.346
 4O2  C15  C14  aromatic  1.393  0.020  1.393
 4O2  C15  C10  aromatic  1.412  0.020  1.412
 4O2  C4   O3   double    1.210  0.020  1.210
 4O2  C4   N    single    1.359  0.020  1.359
 4O2  C2   C1   single    1.521  0.020  1.521
 4O2  C    O    double    1.209  0.020  1.209
 4O2  C    N    single    1.402  0.020  1.402
 4O2  C9   C6   single    1.492  0.020  1.492
 4O2  C9   C10  aromatic  1.429  0.020  1.429
 4O2  C14  C13  aromatic  1.382  0.020  1.382
 4O2  N    C1   single    1.446  0.020  1.446
 4O2  C10  C11  aromatic  1.397  0.020  1.397
 4O2  C13  C12  aromatic  1.402  0.020  1.402
 4O2  C11  C12  aromatic  1.381  0.020  1.381
 4O2  C1   H1   single    0.970  0.020  1.090
 4O2  C1   H2   single    0.970  0.020  1.090
 4O2  C2   H3   single    0.970  0.020  1.090
 4O2  C2   H4   single    0.970  0.020  1.090
 4O2  C5   H5   single    0.970  0.020  1.090
 4O2  C6   H6   single    0.970  0.020  1.090
 4O2  C6   H7   single    0.970  0.020  1.090
 4O2  C7   H8   single    0.970  0.020  1.090
 4O2  C7   H9   single    0.970  0.020  1.090
 4O2  C11  H10  single    0.930  0.020  1.080
 4O2  C13  H11  single    0.930  0.020  1.080
 4O2  C14  H12  single    0.930  0.020  1.080
 4O2  C19  H13  single    0.930  0.020  1.080
 4O2  C21  H14  single    0.930  0.020  1.080
 4O2  C18  H15  single    0.930  0.020  1.080
 4O2  C22  H16  single    0.930  0.020  1.080
 4O2  C16  H17  single    0.970  0.020  1.090
 4O2  C16  H18  single    0.970  0.020  1.090
 4O2  C12  H19  single    0.930  0.020  1.080
 4O2  O2   H20  single    0.850  0.020  0.980

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
 4O2  H2   C1   H1   107.15  3.000
 4O2  H2   C1   N    108.20  3.000
 4O2  H1   C1   N    107.78  3.000
 4O2  H2   C1   C2   110.89  3.000
 4O2  H1   C1   C2   110.85  3.000
 4O2  N    C1   C2   111.79  3.000
 4O2  H4   C2   H3   106.26  3.000
 4O2  H4   C2   C3   108.85  3.000
 4O2  H3   C2   C3   108.50  3.000
 4O2  H4   C2   C1   110.74  3.000
 4O2  H3   C2   C1   110.80  3.000
 4O2  C3   C2   C1   111.51  3.000
 4O2  O1   C3   O2   123.24  3.000
 4O2  O2   C3   C2   111.80  3.000
 4O2  O1   C3   C2   124.96  3.000
 4O2  N    C4   O3   126.49  3.000
 4O2  N    C4   C5   106.79  3.000
 4O2  O3   C4   C5   126.71  3.000
 4O2  H5   C5   N1   110.93  3.000
 4O2  H5   C5   C6   109.46  3.000
 4O2  N1   C5   C6   111.68  3.000
 4O2  H5   C5   C4   108.64  3.000
 4O2  C6   C5   C4   114.00  3.000
 4O2  N1   C5   C4   101.93  3.000
 4O2  H7   C6   H6   106.91  3.000
 4O2  H7   C6   C9   111.56  3.000
 4O2  H6   C6   C9   111.09  3.000
 4O2  H7   C6   C5   109.25  3.000
 4O2  H6   C6   C5   110.49  3.000
 4O2  C9   C6   C5   107.55  3.000
 4O2  H9   C7   H8   106.97  3.000
 4O2  H9   C7   N1   110.89  3.000
 4O2  H8   C7   N1   108.83  3.000
 4O2  H9   C7   C8   111.09  3.000
 4O2  H8   C7   C8   111.57  3.000
 4O2  N1   C7   C8   107.51  3.000
 4O2  C9   C8   N2   110.44  3.000
 4O2  C9   C8   C7   125.81  3.000
 4O2  N2   C8   C7   123.73  3.000
 4O2  C9   C10  C15  106.71  3.000
 4O2  C9   C10  C11  133.93  3.000
 4O2  C15  C10  C11  119.36  3.000
 4O2  H10  C11  C12  120.31  3.000
 4O2  H10  C11  C10  120.79  3.000
 4O2  C12  C11  C10  118.90  3.000
 4O2  H11  C13  C12  119.44  3.000
 4O2  H11  C13  C14  119.19  3.000
 4O2  C12  C13  C14  121.37  3.000
 4O2  H12  C14  C15  122.19  3.000
 4O2  H12  C14  C13  120.24  3.000
 4O2  C15  C14  C13  117.57  3.000
 4O2  C16  C17  C22  119.93  3.000
 4O2  C16  C17  C18  121.24  3.000
 4O2  C22  C17  C18  118.82  3.000
 4O2  H13  C19  C18  120.75  3.000
 4O2  H13  C19  C20  120.40  3.000
 4O2  C18  C19  C20  118.85  3.000
 4O2  H14  C21  C22  120.79  3.000
 4O2  H14  C21  C20  120.65  3.000
 4O2  C22  C21  C20  118.56  3.000
 4O2  F    C20  C21  119.12  3.000
 4O2  C21  C20  C19  121.76  3.000
 4O2  F    C20  C19  119.13  3.000
 4O2  H15  C18  C19  118.57  3.000
 4O2  H15  C18  C17  120.59  3.000
 4O2  C19  C18  C17  120.84  3.000
 4O2  H16  C22  C21  118.82  3.000
 4O2  H16  C22  C17  120.00  3.000
 4O2  C21  C22  C17  121.17  3.000
 4O2  C15  N2   C16  126.32  3.000
 4O2  C15  N2   C8   108.33  3.000
 4O2  C16  N2   C8   125.05  3.000
 4O2  C    N1   C7   124.67  3.000
 4O2  C    N1   C5   112.59  3.000
 4O2  C7   N1   C5   122.74  3.000
 4O2  N    C    O    124.71  3.000
 4O2  N    C    N1   106.82  3.000
 4O2  O    C    N1   128.47  3.000
 4O2  N2   C15  C14  130.27  3.000
 4O2  C14  C15  C10  121.84  3.000
 4O2  N2   C15  C10  107.88  3.000
 4O2  H19  C12  C13  119.33  3.000
 4O2  H19  C12  C11  119.72  3.000
 4O2  C13  C12  C11  120.95  3.000
 4O2  C10  C9   C8   106.62  3.000
 4O2  C10  C9   C6   130.16  3.000
 4O2  C8   C9   C6   123.22  3.000
 4O2  C    N    C4   111.81  3.000
 4O2  C    N    C1   123.00  3.000
 4O2  C4   N    C1   125.17  3.000
 4O2  H20  O2   C3   108.42  3.000
 4O2  H18  C16  H17  105.60  3.000
 4O2  H18  C16  N2   107.69  3.000
 4O2  H17  C16  N2   109.58  3.000
 4O2  H18  C16  C17  110.37  3.000
 4O2  H17  C16  C17  109.88  3.000
 4O2  N2   C16  C17  113.41  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
 4O2  CONST_01  C14  C15  N2   C8    180.00   0.0  0
 4O2  CONST_02  C10  C15  N2   C8      0.00   0.0  0
 4O2  CONST_03  C15  C10  C9   C8      0.00   0.0  0
 4O2  CONST_04  C11  C10  C9   C8    180.00   0.0  0
 4O2  CONST_05  C13  C14  C15  C10     0.00   0.0  0
 4O2  CONST_06  N2   C8   C9   C10     0.00   0.0  0
 4O2  CONST_07  C13  C12  C11  C10     0.00   0.0  0
 4O2  CONST_08  N2   C15  C10  C11   180.00   0.0  0
 4O2  CONST_09  C14  C15  C10  C11     0.00   0.0  0
 4O2  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 4O2  CONST_11  N2   C15  C14  C13   180.00   0.0  0
 4O2  CONST_12  C9   C10  C15  C14   180.00   0.0  0
 4O2  CONST_13  C20  C19  C18  C17     0.00   0.0  0
 4O2  CONST_14  C20  C21  C22  C17     0.00   0.0  0
 4O2  CONST_15  C22  C21  C20  C19     0.00   0.0  0
 4O2  CONST_16  C22  C17  C18  C19     0.00   0.0  0
 4O2  CONST_17  C18  C19  C20  C21     0.00   0.0  0
 4O2  CONST_18  C18  C17  C22  C21     0.00   0.0  0
 4O2  CONST_19  C9   C10  C15  N2      0.00   0.0  0
 4O2  CONST_20  C9   C8   N2   C15     0.00   0.0  0
 4O2  CONST_21  C12  C13  C14  C15     0.00   0.0  0
 4O2  CONST_22  C12  C11  C10  C15     0.00   0.0  0
 4O2  CONST_23  C9   C10  C11  C12   180.00   0.0  0
 4O2  CONST_24  N1   C    N    C4      0.00   0.0  0
 4O2  CONST_25  N    C    N1   C5      0.00   0.0  0
 4O2  CONST_26  C    N    C4   C5      0.00   0.0  0
 4O2  CONST_27  N    C    N1   C7    180.00   0.0  0
 4O2  CONST_28  C16  N2   C8   C7      0.00   0.0  0
 4O2  CONST_29  C16  N2   C15  C10   180.00   0.0  0
 4O2  CONST_30  C16  N2   C15  C14     0.00   0.0  0
 4O2  CONST_31  C16  C17  C18  C19   180.00   0.0  0
 4O2  CONST_32  C16  C17  C22  C21   180.00   0.0  0
 4O2  CONST_33  C18  C19  C20  F     180.00   0.0  0
 4O2  CONST_34  C22  C21  C20  F     180.00   0.0  0
 4O2  CONST_35  C9   C8   N2   C16   180.00   0.0  0
 4O2  CONST_36  C5   C4   N    C1    180.00   0.0  0
 4O2  CONST_37  N1   C    N    C1    180.00   0.0  0
 4O2  CONST_38  O    C    N    C4    180.00   0.0  0
 4O2  CONST_39  O    C    N1   C5    180.00   0.0  0
 4O2  CONST_40  O    C    N1   C7      0.00   0.0  0
 4O2  CONST_41  O3   C4   N    C     180.00   0.0  0
 4O2  CONST_42  H12  C14  C15  C10   180.00   0.0  0
 4O2  CONST_43  H19  C12  C11  C10   180.00   0.0  0
 4O2  CONST_44  H11  C13  C12  C11   180.00   0.0  0
 4O2  CONST_45  H10  C11  C12  C13   180.00   0.0  0
 4O2  CONST_46  H13  C19  C18  C17   180.00   0.0  0
 4O2  CONST_47  H14  C21  C22  C17   180.00   0.0  0
 4O2  CONST_48  H15  C18  C19  C20   180.00   0.0  0
 4O2  CONST_49  H16  C22  C21  C20   180.00   0.0  0
 4O2  CONST_50  O3   C4   N    C1      0.00   0.0  0
 4O2  CONST_51  O    C    N    C1      0.00   0.0  0
 4O2  CONST_52  H20  O2   C3   C2    180.00   0.0  0
 4O2  Var_01    C8   C7   N1   C5    -30.35  30.0  1
 4O2  Var_02    C8   C9   C6   C5     22.53  30.0  1
 4O2  Var_03    N1   C7   C8   N2    179.80  30.0  1
 4O2  Var_04    C17  C16  N2   C8     70.27  30.0  2
 4O2  Var_05    N2   C16  C17  C18    37.05  30.0  2
 4O2  Var_06    C4   N    C1   C2     93.16  30.0  2
 4O2  Var_07    N    C1   C2   C3   -179.00  30.0  3
 4O2  Var_08    O1   C3   C2   C1      2.05  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
 4O2  chir_01  C5  N1  C4  C6  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
 4O2  plan-1  C17  0.020
 4O2  plan-1  C19  0.020
 4O2  plan-1  C21  0.020
 4O2  plan-1  C20  0.020
 4O2  plan-1  C18  0.020
 4O2  plan-1  C22  0.020
 4O2  plan-1  H13  0.020
 4O2  plan-1  H14  0.020
 4O2  plan-1  H15  0.020
 4O2  plan-1  H16  0.020
 4O2  plan-1  C16  0.020
 4O2  plan-1  F    0.020
 4O2  plan-2  C6   0.020
 4O2  plan-2  C7   0.020
 4O2  plan-2  C8   0.020
 4O2  plan-2  C10  0.020
 4O2  plan-2  C11  0.020
 4O2  plan-2  C13  0.020
 4O2  plan-2  C14  0.020
 4O2  plan-2  N2   0.020
 4O2  plan-2  C15  0.020
 4O2  plan-2  C12  0.020
 4O2  plan-2  C9   0.020
 4O2  plan-2  H10  0.020
 4O2  plan-2  H11  0.020
 4O2  plan-2  H12  0.020
 4O2  plan-2  H19  0.020
 4O2  plan-2  C16  0.020
 4O2  plan-3  C1   0.020
 4O2  plan-3  C4   0.020
 4O2  plan-3  C5   0.020
 4O2  plan-3  C7   0.020
 4O2  plan-3  N1   0.020
 4O2  plan-3  C    0.020
 4O2  plan-3  O    0.020
 4O2  plan-3  O3   0.020
 4O2  plan-3  N    0.020
 4O2  plan-4  C2   0.020
 4O2  plan-4  C3   0.020
 4O2  plan-4  O2   0.020
 4O2  plan-4  O1   0.020
 4O2  plan-4  H20  0.020

