# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 09:13:40 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-hydroxy-8,9-dimethoxy-6H-isoindolo[2,1-a]indol-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc2C(=O)n3c4ccc(O)cc4cc3c2cc1OC
#
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
 79X  79X  2-hydroxy-8,9-dimethoxy-6H-isoindolo[2,1-a]indol-6-one  ligand  35  22  .  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_79X
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
 79X  C1    C  CR16  0  -0.487   4.1763  -1.2742  -0.0740
 79X  N1    N  N     0  -0.729   1.1561   0.5970  -0.0326
 79X  O1    O  OH1   0  -0.638   6.4854  -0.6149  -0.0932
 79X  C2    C  CR56  0   0.068   2.8459  -0.8646  -0.0578
 79X  O2    O  O     0  -0.408   0.4018   2.7825  -0.0029
 79X  C3    C  CR56  0   0.374   2.5364   0.5098  -0.0479
 79X  O3    O  O2    0  -0.454  -4.2654  -1.7179   0.0304
 79X  C4    C  CR16  0  -0.282   3.5216   1.4813  -0.0532
 79X  O4    O  O2    0  -0.457  -4.7300   0.7866   0.0554
 79X  C5    C  CR16  0  -0.357   4.8416   1.0593  -0.0690
 79X  C6    C  CR6   0   0.363   5.1703  -0.3036  -0.0791
 79X  C7    C  CR15  0  -0.462   1.6013  -1.6006  -0.0482
 79X  C8    C  CR55  0   0.539   0.6103  -0.6782  -0.0327
 79X  C10   C  CR5   0   0.534   0.1927   1.5933  -0.0097
 79X  C11   C  CR56  0  -0.056  -1.0879   0.8519   0.0028
 79X  C12   C  CR56  0   0.028  -0.8321  -0.5135  -0.0110
 79X  C13   C  CR16  0  -0.526  -1.8715  -1.4300  -0.0028
 79X  C14   C  CR6   0   0.344  -3.1746  -0.9465   0.0200
 79X  C15   C  CR6   0   0.317  -3.4324   0.4509   0.0343
 79X  C16   C  CR16  0  -0.428  -2.3803   1.3530   0.0256
 79X  C21   C  CH3   0  -0.445  -4.1015  -3.1247   0.0081
 79X  C23   C  CH3   0  -0.443  -5.0636   2.1611   0.0646
 79X  H1    H  HCR6  0   0.273   4.4267  -2.3291  -0.0813
 79X  HO1   H  HOH1  0   0.474   6.6025  -1.5713  -0.0942
 79X  H4    H  HCR6  0   0.273   3.2846   2.5359  -0.0452
 79X  H5    H  HCR6  0   0.268   5.6379   1.7924  -0.0723
 79X  H7    H  HCR5  0   0.264   1.4883  -2.6732  -0.0512
 79X  H13   H  HCR6  0   0.288  -1.6675  -2.4918  -0.0134
 79X  H16   H  HCR6  0   0.293  -2.5458   2.4220   0.0368
 79X  H21   H  HCH3  0   0.236  -3.5792  -3.4568  -0.8923
 79X  H21A  H  HCH3  0   0.236  -3.5591  -3.4823   0.8867
 79X  H21B  H  HCH3  0   0.268  -5.1015  -3.5495   0.0135
 79X  H23   H  HCH3  0   0.233  -4.6753   2.6679   0.9519
 79X  H23A  H  HCH3  0   0.233  -4.6945   2.6745  -0.8271
 79X  H23B  H  HCH3  0   0.266  -6.1490   2.2145   0.0768

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
 79X  C1   C2    aromatic  1.392  0.020  1.392
 79X  C1   C6    aromatic  1.389  0.020  1.389
 79X  C1   H1    single    0.930  0.020  1.080
 79X  C8   N1    aromatic  1.387  0.020  1.387
 79X  C3   N1    aromatic  1.383  0.020  1.383
 79X  N1   C10   single    1.386  0.020  1.386
 79X  O1   C6    single    1.351  0.020  1.351
 79X  O1   HO1   single    0.850  0.020  0.980
 79X  C7   C2    aromatic  1.446  0.020  1.446
 79X  C2   C3    aromatic  1.409  0.020  1.409
 79X  C10  O2    double    1.207  0.020  1.207
 79X  C3   C4    aromatic  1.384  0.020  1.384
 79X  C21  O3    single    1.416  0.020  1.416
 79X  O3   C14   single    1.336  0.020  1.336
 79X  C5   C4    aromatic  1.386  0.020  1.386
 79X  C4   H4    single    0.930  0.020  1.080
 79X  C15  O4    single    1.340  0.020  1.340
 79X  O4   C23   single    1.414  0.020  1.414
 79X  C6   C5    aromatic  1.402  0.020  1.402
 79X  C5   H5    single    0.930  0.020  1.080
 79X  C7   C8    aromatic  1.354  0.020  1.354
 79X  C7   H7    single    0.930  0.020  1.080
 79X  C8   C12   aromatic  1.452  0.020  1.452
 79X  C11  C10   single    1.480  0.020  1.480
 79X  C12  C11   aromatic  1.389  0.020  1.389
 79X  C11  C16   aromatic  1.386  0.020  1.386
 79X  C13  C12   aromatic  1.386  0.020  1.386
 79X  C13  C14   aromatic  1.390  0.020  1.390
 79X  C13  H13   single    0.930  0.020  1.080
 79X  C14  C15   aromatic  1.421  0.020  1.421
 79X  C15  C16   aromatic  1.386  0.020  1.386
 79X  C16  H16   single    0.930  0.020  1.080
 79X  C21  H21   single    0.970  0.020  1.090
 79X  C21  H21A  single    0.970  0.020  1.090
 79X  C21  H21B  single    0.970  0.020  1.090
 79X  C23  H23   single    0.970  0.020  1.090
 79X  C23  H23A  single    0.970  0.020  1.090
 79X  C23  H23B  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
 79X  H1    C1   C6    120.96  3.000
 79X  H1    C1   C2    120.47  3.000
 79X  C6    C1   C2    118.57  3.000
 79X  C10   N1   C8    112.79  3.000
 79X  C10   N1   C3    137.65  3.000
 79X  C8    N1   C3    109.55  3.000
 79X  HO1   O1   C6    110.31  3.000
 79X  C7    C2   C3    107.90  3.000
 79X  C3    C2   C1    119.81  3.000
 79X  C7    C2   C1    132.29  3.000
 79X  C4    C3   C2    121.90  3.000
 79X  C4    C3   N1    131.79  3.000
 79X  C2    C3   N1    106.31  3.000
 79X  C21   O3   C14   118.61  3.000
 79X  H4    C4   C5    120.39  3.000
 79X  H4    C4   C3    121.93  3.000
 79X  C5    C4   C3    117.68  3.000
 79X  C23   O4   C15   118.15  3.000
 79X  H5    C5   C6    119.07  3.000
 79X  H5    C5   C4    119.64  3.000
 79X  C6    C5   C4    121.29  3.000
 79X  C5    C6   O1    116.88  3.000
 79X  C5    C6   C1    120.75  3.000
 79X  O1    C6   C1    122.36  3.000
 79X  H7    C7   C8    126.94  3.000
 79X  H7    C7   C2    126.61  3.000
 79X  C8    C7   C2    106.45  3.000
 79X  C12   C8   C7    143.57  3.000
 79X  C12   C8   N1    106.65  3.000
 79X  C7    C8   N1    109.78  3.000
 79X  C11   C10  O2    130.04  3.000
 79X  C11   C10  N1    103.97  3.000
 79X  O2    C10  N1    125.99  3.000
 79X  C16   C11  C12   121.81  3.000
 79X  C16   C11  C10   128.74  3.000
 79X  C12   C11  C10   109.45  3.000
 79X  C13   C12  C11   120.78  3.000
 79X  C13   C12  C8    132.08  3.000
 79X  C11   C12  C8    107.13  3.000
 79X  H13   C13  C14   121.24  3.000
 79X  H13   C13  C12   120.52  3.000
 79X  C14   C13  C12   118.24  3.000
 79X  C15   C14  C13   120.82  3.000
 79X  C15   C14  O3    114.81  3.000
 79X  C13   C14  O3    124.38  3.000
 79X  C16   C15  C14   120.15  3.000
 79X  C16   C15  O4    124.89  3.000
 79X  C14   C15  O4    114.96  3.000
 79X  H16   C16  C15   121.80  3.000
 79X  H16   C16  C11   120.00  3.000
 79X  C15   C16  C11   118.20  3.000
 79X  H21B  C21  H21A  108.96  3.000
 79X  H21B  C21  H21   108.98  3.000
 79X  H21A  C21  H21   109.02  3.000
 79X  H21B  C21  O3    106.36  3.000
 79X  H21A  C21  O3    111.71  3.000
 79X  H21   C21  O3    111.73  3.000
 79X  H23B  C23  H23A  108.86  3.000
 79X  H23B  C23  H23   108.83  3.000
 79X  H23A  C23  H23   108.93  3.000
 79X  H23B  C23  O4    106.46  3.000
 79X  H23A  C23  O4    111.81  3.000
 79X  H23   C23  O4    111.84  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
 79X  CONST_01  C8   C7   C2   C1   180.00   0.0  0
 79X  CONST_02  N1   C3   C2   C1   180.00   0.0  0
 79X  CONST_03  C4   C3   C2   C1     0.00   0.0  0
 79X  CONST_04  C4   C5   C6   C1     0.00   0.0  0
 79X  CONST_05  C2   C7   C8   N1     0.00   0.0  0
 79X  CONST_06  C11  C12  C8   N1     0.00   0.0  0
 79X  CONST_07  C13  C12  C8   N1   180.00   0.0  0
 79X  CONST_08  C7   C2   C3   N1     0.00   0.0  0
 79X  CONST_09  C5   C4   C3   N1   180.00   0.0  0
 79X  CONST_10  C5   C6   C1   C2     0.00   0.0  0
 79X  CONST_11  C12  C8   C7   C2   180.00   0.0  0
 79X  CONST_12  C8   N1   C3   C2     0.00   0.0  0
 79X  CONST_13  C5   C4   C3   C2     0.00   0.0  0
 79X  CONST_14  C7   C8   N1   C3     0.00   0.0  0
 79X  CONST_15  C12  C8   N1   C3   180.00   0.0  0
 79X  CONST_16  C6   C1   C2   C3     0.00   0.0  0
 79X  CONST_17  C8   C7   C2   C3     0.00   0.0  0
 79X  CONST_18  C6   C5   C4   C3     0.00   0.0  0
 79X  CONST_19  C8   N1   C3   C4   180.00   0.0  0
 79X  CONST_20  C7   C2   C3   C4   180.00   0.0  0
 79X  CONST_21  C7   C2   C1   C6   180.00   0.0  0
 79X  CONST_22  C11  C12  C8   C7   180.00   0.0  0
 79X  CONST_23  C13  C12  C8   C7     0.00   0.0  0
 79X  CONST_24  C16  C11  C12  C8   180.00   0.0  0
 79X  CONST_25  C14  C13  C12  C8   180.00   0.0  0
 79X  CONST_26  C14  C13  C12  C11    0.00   0.0  0
 79X  CONST_27  C14  C15  C16  C11    0.00   0.0  0
 79X  CONST_28  C15  C16  C11  C12    0.00   0.0  0
 79X  CONST_29  C15  C14  C13  C12    0.00   0.0  0
 79X  CONST_30  C16  C11  C12  C13    0.00   0.0  0
 79X  CONST_31  C16  C15  C14  C13    0.00   0.0  0
 79X  CONST_32  C2   C1   C6   O1   180.00   0.0  0
 79X  CONST_33  C4   C5   C6   O1   180.00   0.0  0
 79X  CONST_34  C12  C13  C14  O3   180.00   0.0  0
 79X  CONST_35  C16  C15  C14  O3   180.00   0.0  0
 79X  CONST_36  C13  C14  C15  O4   180.00   0.0  0
 79X  CONST_37  C11  C16  C15  O4   180.00   0.0  0
 79X  CONST_38  H7   C7   C2   C1     0.00   0.0  0
 79X  CONST_39  H5   C5   C6   C1   180.00   0.0  0
 79X  CONST_40  H4   C4   C3   N1     0.00   0.0  0
 79X  CONST_41  H1   C1   C2   C3   180.00   0.0  0
 79X  CONST_42  H13  C13  C12  C8     0.00   0.0  0
 79X  CONST_43  H16  C16  C11  C10    0.00   0.0  0
 79X  Var_01    H21  C21  O3   C14  -60.76  30.0  3
 79X  Var_02    H23  C23  O4   C15  -61.51  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
 79X  plan-1  C1   0.020
 79X  plan-1  N1   0.020
 79X  plan-1  O1   0.020
 79X  plan-1  C2   0.020
 79X  plan-1  O2   0.020
 79X  plan-1  C3   0.020
 79X  plan-1  O3   0.020
 79X  plan-1  C4   0.020
 79X  plan-1  O4   0.020
 79X  plan-1  C5   0.020
 79X  plan-1  C6   0.020
 79X  plan-1  C7   0.020
 79X  plan-1  C8   0.020
 79X  plan-1  C10  0.020
 79X  plan-1  C11  0.020
 79X  plan-1  C12  0.020
 79X  plan-1  C13  0.020
 79X  plan-1  C14  0.020
 79X  plan-1  C15  0.020
 79X  plan-1  C16  0.020
 79X  plan-1  H1   0.020
 79X  plan-1  H4   0.020
 79X  plan-1  H5   0.020
 79X  plan-1  H7   0.020
 79X  plan-1  H13  0.020
 79X  plan-1  H16  0.020

