# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 10:52:26 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: (1~{R},3~{S})-3-(1-adamantyl)-1-(aminomethyl)-3,4-dihydro-1~{H}-isochromene-5,6-diol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1O[C@@H](Cc2c(O)c(O)ccc12)C34CC5CC(CC(C5)C3)C4
#
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
 G3O  G3O  (1~{R},3~{S})-3-(1-adamantyl)-1-(aminomethyl)-3,4-dihydro-1~{H}-isochromene-5,6-diol  ligand  51  24  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_G3O
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
 G3O  C10  C  CR16  0   0.024  20.8540  14.4932   9.0517
 G3O  N12  N  NH2   0  -0.797  20.8552  12.2185   9.9833
 G3O  C13  C  CT    0  -0.141  24.0786  15.8512  10.1266
 G3O  C15  C  CR16  0  -0.242  26.3287  16.9790  10.3127
 G3O  C17  C  CR16  0  -0.245  25.3041  15.9129  12.3243
 G3O  C20  C  CR16  0  -0.248  26.1827  14.4956  10.4678
 G3O  C21  C  CH2   0  -0.398  24.8093  14.5384   9.7950
 G3O  C22  C  C     0  -0.413  27.0318  15.6656   9.9705
 G3O  C01  C  CR6   0   0.209  19.7676  18.1151   8.7056
 G3O  C02  C  CR6   0   0.291  18.4991  17.9930   8.1339
 G3O  C03  C  CR16  0  -0.348  18.0166  16.7297   7.8318
 G3O  C04  C  CR16  0  -0.324  18.7751  15.6071   8.1257
 G3O  C05  C  CR66  0  -0.007  20.0256  15.7188   8.7236
 G3O  C06  C  CR66  0   0.008  20.5425  16.9914   8.9857
 G3O  C07  C  C     0  -0.571  21.9403  17.1737   9.5187
 G3O  C08  C  CR16  0   0.115  22.7304  15.8769   9.3956
 G3O  C11  C  CH2   0  -0.306  20.0508  13.4109   9.7678
 G3O  C14  C  CH2   0  -0.419  24.9529  17.0191   9.6441
 G3O  C16  C  C     0  -0.415  26.1513  17.0860  11.8283
 G3O  C18  C  CH2   0  -0.411  23.9286  15.9473  11.6532
 G3O  C19  C  C     0  -0.415  26.0075  14.5983  11.9835
 G3O  O09  O  O     0  -0.493  21.9370  14.8200   9.8819
 G3O  O23  O  OH1   0  -0.635  17.7407  19.0753   7.8554
 G3O  O24  O  OH1   0  -0.645  20.1877  19.3874   8.9316
 G3O  H1   H  HCR6  0   0.212  21.2313  14.0677   8.1041
 G3O  H2   H  HNH2  0   0.349  20.3370  11.5690  10.5605
 G3O  H3   H  HNH2  0   0.339  20.9939  11.7450   9.0986
 G3O  H5   H  HCR6  0   0.220  26.9246  17.8224   9.9508
 G3O  H6   H  HCR6  0   0.219  25.1723  15.9882  13.4081
 G3O  H7   H  HCR6  0   0.218  26.6740  13.5506  10.2166
 G3O  H8   H  HCH2  0   0.225  24.2112  13.6825  10.1191
 G3O  H9   H  HCH2  0   0.215  24.9268  14.4497   8.7085
 G3O  H10  H  H     0   0.219  28.0244  15.6372  10.4311
 G3O  H11  H  H     0   0.218  27.1818  15.5892   8.8887
 G3O  H12  H  HCR6  0   0.257  17.0390  16.6282   7.3771
 G3O  H13  H  HCR6  0   0.244  18.3709  14.6343   7.8774
 G3O  H14  H  H     0   0.258  22.4487  17.9575   8.9506
 G3O  H15  H  H     0   0.260  21.9132  17.5103  10.5614
 G3O  H16  H  HCR6  0   0.207  22.9394  15.7149   8.3233
 G3O  H17  H  HCH2  0   0.226  19.7319  13.8030  10.7373
 G3O  H18  H  HCH2  0   0.212  19.1360  13.2121   9.1980
 G3O  H19  H  HCH2  0   0.222  25.0646  16.9731   8.5546
 G3O  H20  H  HCH2  0   0.232  24.4763  17.9765   9.8747
 G3O  H21  H  H     0   0.220  27.1258  17.0854  12.3274
 G3O  H22  H  H     0   0.218  25.6672  18.0343  12.0839
 G3O  H23  H  HCH2  0   0.221  23.4147  16.8725  11.9332
 G3O  H24  H  HCH2  0   0.226  23.3192  15.1201  12.0273
 G3O  H25  H  H     0   0.219  25.4217  13.7503  12.3533
 G3O  H26  H  H     0   0.219  26.9811  14.5506  12.4826
 G3O  H27  H  HOH1  0   0.467  18.1762  19.8757   8.1725
 G3O  H28  H  HOH1  0   0.486  20.8899  19.4176   9.5904

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
 G3O  O23  C02  single    1.351  0.020  1.351
 G3O  C03  C02  aromatic  1.386  0.020  1.386
 G3O  C03  C04  aromatic  1.386  0.020  1.386
 G3O  C02  C01  aromatic  1.397  0.020  1.397
 G3O  C04  C05  aromatic  1.391  0.020  1.391
 G3O  C01  O24  single    1.359  0.020  1.359
 G3O  C01  C06  aromatic  1.393  0.020  1.393
 G3O  C05  C06  aromatic  1.398  0.020  1.398
 G3O  C05  C10  single    1.515  0.020  1.515
 G3O  C06  C07  single    1.507  0.020  1.507
 G3O  C10  O09  single    1.403  0.020  1.403
 G3O  C10  C11  single    1.526  0.020  1.526
 G3O  C08  C07  single    1.523  0.020  1.523
 G3O  C08  O09  single    1.408  0.020  1.408
 G3O  C08  C13  single    1.534  0.020  1.534
 G3O  C21  C13  single    1.539  0.020  1.539
 G3O  C21  C20  single    1.530  0.020  1.530
 G3O  C14  C13  single    1.537  0.020  1.537
 G3O  C14  C15  single    1.530  0.020  1.530
 G3O  C13  C18  single    1.537  0.020  1.537
 G3O  C22  C20  single    1.529  0.020  1.529
 G3O  C22  C15  single    1.529  0.020  1.529
 G3O  C11  N12  single    1.454  0.020  1.454
 G3O  C20  C19  single    1.529  0.020  1.529
 G3O  C15  C16  single    1.530  0.020  1.530
 G3O  C18  C17  single    1.531  0.020  1.531
 G3O  C19  C17  single    1.529  0.020  1.529
 G3O  C16  C17  single    1.530  0.020  1.530
 G3O  C10  H1   single    0.970  0.020  1.090
 G3O  N12  H2   single    0.890  0.020  1.040
 G3O  N12  H3   single    0.890  0.020  1.040
 G3O  C15  H5   single    0.970  0.020  1.090
 G3O  C17  H6   single    0.970  0.020  1.090
 G3O  C20  H7   single    0.970  0.020  1.090
 G3O  C21  H8   single    0.970  0.020  1.090
 G3O  C21  H9   single    0.970  0.020  1.090
 G3O  C22  H10  single    0.970  0.020  1.090
 G3O  C22  H11  single    0.970  0.020  1.090
 G3O  C03  H12  single    0.930  0.020  1.080
 G3O  C04  H13  single    0.930  0.020  1.080
 G3O  C07  H14  single    0.970  0.020  1.090
 G3O  C07  H15  single    0.970  0.020  1.090
 G3O  C08  H16  single    0.970  0.020  1.090
 G3O  C11  H17  single    0.970  0.020  1.090
 G3O  C11  H18  single    0.970  0.020  1.090
 G3O  C14  H19  single    0.970  0.020  1.090
 G3O  C14  H20  single    0.970  0.020  1.090
 G3O  C16  H21  single    0.970  0.020  1.090
 G3O  C16  H22  single    0.970  0.020  1.090
 G3O  C18  H23  single    0.970  0.020  1.090
 G3O  C18  H24  single    0.970  0.020  1.090
 G3O  C19  H25  single    0.970  0.020  1.090
 G3O  C19  H26  single    0.970  0.020  1.090
 G3O  O23  H27  single    0.850  0.020  0.980
 G3O  O24  H28  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
 G3O  H1   C10  O09  109.48  3.000
 G3O  H1   C10  C11  108.00  3.000
 G3O  O09  C10  C11  107.08  3.000
 G3O  H1   C10  C05  108.21  3.000
 G3O  C11  C10  C05  112.80  3.000
 G3O  O09  C10  C05  111.20  3.000
 G3O  H3   N12  H2   105.57  3.000
 G3O  H3   N12  C11  109.24  3.000
 G3O  H2   N12  C11  109.12  3.000
 G3O  C18  C13  C14  108.66  3.000
 G3O  C18  C13  C08  112.74  3.000
 G3O  C14  C13  C08  109.74  3.000
 G3O  C18  C13  C21  108.29  3.000
 G3O  C14  C13  C21  108.10  3.000
 G3O  C08  C13  C21  109.21  3.000
 G3O  H5   C15  C16  109.69  3.000
 G3O  H5   C15  C14  108.96  3.000
 G3O  C16  C15  C14  109.07  3.000
 G3O  H5   C15  C22  109.74  3.000
 G3O  C16  C15  C22  109.58  3.000
 G3O  C14  C15  C22  109.77  3.000
 G3O  H6   C17  C19  109.59  3.000
 G3O  H6   C17  C18  108.93  3.000
 G3O  C19  C17  C18  109.57  3.000
 G3O  H6   C17  C16  109.58  3.000
 G3O  C19  C17  C16  109.40  3.000
 G3O  C18  C17  C16  109.77  3.000
 G3O  H7   C20  C19  109.69  3.000
 G3O  H7   C20  C22  109.69  3.000
 G3O  C19  C20  C22  109.55  3.000
 G3O  H7   C20  C21  109.04  3.000
 G3O  C19  C20  C21  109.34  3.000
 G3O  C22  C20  C21  109.52  3.000
 G3O  H9   C21  H8   106.80  3.000
 G3O  H9   C21  C20  109.71  3.000
 G3O  H8   C21  C20  109.80  3.000
 G3O  H9   C21  C13  109.48  3.000
 G3O  H8   C21  C13  110.14  3.000
 G3O  C20  C21  C13  110.82  3.000
 G3O  H11  C22  H10  106.84  3.000
 G3O  H11  C22  C20  110.13  3.000
 G3O  H10  C22  C20  110.30  3.000
 G3O  H11  C22  C15  110.13  3.000
 G3O  H10  C22  C15  110.19  3.000
 G3O  C20  C22  C15  109.23  3.000
 G3O  O24  C01  C06  123.35  3.000
 G3O  C06  C01  C02  121.12  3.000
 G3O  O24  C01  C02  115.52  3.000
 G3O  O23  C02  C03  119.35  3.000
 G3O  C03  C02  C01  119.03  3.000
 G3O  O23  C02  C01  121.62  3.000
 G3O  H12  C03  C04  120.47  3.000
 G3O  H12  C03  C02  119.43  3.000
 G3O  C04  C03  C02  120.10  3.000
 G3O  H13  C04  C05  120.45  3.000
 G3O  H13  C04  C03  118.35  3.000
 G3O  C05  C04  C03  121.21  3.000
 G3O  C06  C05  C04  119.09  3.000
 G3O  C06  C05  C10  119.57  3.000
 G3O  C04  C05  C10  121.31  3.000
 G3O  C07  C06  C05  121.28  3.000
 G3O  C07  C06  C01  119.30  3.000
 G3O  C05  C06  C01  119.39  3.000
 G3O  H15  C07  H14  106.60  3.000
 G3O  H15  C07  C08  110.56  3.000
 G3O  H14  C07  C08  109.09  3.000
 G3O  H15  C07  C06  110.53  3.000
 G3O  H14  C07  C06  109.52  3.000
 G3O  C08  C07  C06  110.45  3.000
 G3O  H16  C08  O09  109.38  3.000
 G3O  H16  C08  C07  107.55  3.000
 G3O  O09  C08  C07  108.59  3.000
 G3O  H16  C08  C13  107.09  3.000
 G3O  O09  C08  C13  108.54  3.000
 G3O  C07  C08  C13  115.56  3.000
 G3O  H18  C11  H17  106.42  3.000
 G3O  H18  C11  N12  112.95  3.000
 G3O  H17  C11  N12  108.90  3.000
 G3O  H18  C11  C10  108.91  3.000
 G3O  H17  C11  C10  108.38  3.000
 G3O  N12  C11  C10  111.09  3.000
 G3O  H20  C14  H19  106.90  3.000
 G3O  H20  C14  C15  108.81  3.000
 G3O  H19  C14  C15  109.97  3.000
 G3O  H20  C14  C13  110.55  3.000
 G3O  H19  C14  C13  109.77  3.000
 G3O  C15  C14  C13  110.76  3.000
 G3O  H22  C16  H21  106.71  3.000
 G3O  H22  C16  C17  110.10  3.000
 G3O  H21  C16  C17  110.17  3.000
 G3O  H22  C16  C15  110.06  3.000
 G3O  H21  C16  C15  110.39  3.000
 G3O  C17  C16  C15  109.39  3.000
 G3O  H24  C18  H23  106.87  3.000
 G3O  H24  C18  C17  109.50  3.000
 G3O  H23  C18  C17  109.19  3.000
 G3O  H24  C18  C13  110.30  3.000
 G3O  H23  C18  C13  110.65  3.000
 G3O  C17  C18  C13  110.26  3.000
 G3O  H26  C19  H25  106.74  3.000
 G3O  H26  C19  C20  110.30  3.000
 G3O  H25  C19  C20  110.12  3.000
 G3O  H26  C19  C17  110.17  3.000
 G3O  H25  C19  C17  110.14  3.000
 G3O  C20  C19  C17  109.35  3.000
 G3O  C08  O09  C10  113.91  3.000
 G3O  H27  O23  C02  110.10  3.000
 G3O  H28  O24  C01  111.62  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
 G3O  CONST_01  C04  C03  C02  C01     0.00   0.0  0
 G3O  CONST_02  C04  C05  C06  C01     0.00   0.0  0
 G3O  CONST_03  C05  C04  C03  C02     0.00   0.0  0
 G3O  CONST_04  C05  C06  C01  C02     0.00   0.0  0
 G3O  CONST_05  C06  C01  C02  C03     0.00   0.0  0
 G3O  CONST_06  C06  C05  C04  C03     0.00   0.0  0
 G3O  CONST_07  O24  C01  C02  C03   180.00   0.0  0
 G3O  CONST_08  O23  C02  C03  C04   180.00   0.0  0
 G3O  CONST_09  O24  C01  C06  C05   180.00   0.0  0
 G3O  CONST_10  O23  C02  C01  C06   180.00   0.0  0
 G3O  CONST_11  O24  C01  C06  C07     0.00   0.0  0
 G3O  CONST_12  H13  C04  C05  C10     0.00   0.0  0
 G3O  CONST_13  H12  C03  C02  C01   180.00   0.0  0
 G3O  Var_01    C08  C13  C14  C15  -177.45  30.0  1
 G3O  Var_02    C08  C07  C06  C01  -164.55  30.0  1
 G3O  Var_03    H2   N12  C11  C10   172.83  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
 G3O  chir_01  C10  C05  O09  C11  negativ
 G3O  chir_02  C15  C14  C22  C16  positiv
 G3O  chir_03  C17  C18  C19  C16  negativ
 G3O  chir_04  C20  C21  C22  C19  negativ
 G3O  chir_05  C08  O09  C13  C07  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
 G3O  plan-1  C10  0.020
 G3O  plan-1  C01  0.020
 G3O  plan-1  C02  0.020
 G3O  plan-1  C03  0.020
 G3O  plan-1  C04  0.020
 G3O  plan-1  C05  0.020
 G3O  plan-1  C06  0.020
 G3O  plan-1  C07  0.020
 G3O  plan-1  O23  0.020
 G3O  plan-1  O24  0.020
 G3O  plan-1  H12  0.020
 G3O  plan-1  H13  0.020

