# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 04:49:23 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 6-phenylmethoxy-9H-purin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc2[nH]cnc2c(OCc3ccccc3)n1
#
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
 OBG  OBG  6-phenylmethoxy-9H-purin-2-amine  ligand  29  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_OBG
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
 OBG  C1    C  CR6   0   0.537  -2.6042  -1.6999  -0.0291
 OBG  N1    N  NH2   0  -0.821  -2.9755  -2.9993  -0.0843
 OBG  O1    O  O2    0  -0.451   0.4540   0.0329  -0.0061
 OBG  C2    C  CR6   0   0.514  -0.8401  -0.2315  -0.0119
 OBG  N2    N  N     0  -0.526  -1.2745  -1.4698  -0.0229
 OBG  C3    C  CH2   0  -0.249   1.3748  -1.0677  -0.0172
 OBG  N3    N  N     0  -0.440  -1.6220   2.2021   0.0090
 OBG  C4    C  CR6   0   0.085   2.7516  -0.4785  -0.0168
 OBG  N4    N  NR15  0  -0.652  -3.7733   1.6278   0.0013
 OBG  C5    C  CR16  0  -0.290   3.3873  -0.1714   1.1829
 OBG  N5    N  N     0  -0.493  -3.5652  -0.7823  -0.0207
 OBG  C6    C  CR16  0  -0.242   4.6508   0.4030   1.1847
 OBG  C7    C  CR16  0  -0.261   5.2908   0.6788  -0.0170
 OBG  C8    C  CR16  0  -0.242   4.6636   0.3754  -1.2185
 OBG  C9    C  CR16  0  -0.291   3.3998  -0.1990  -1.2162
 OBG  C10   C  CR56  0  -0.037  -1.7476   0.8340  -0.0056
 OBG  C11   C  CR15  0   0.093  -2.8474   2.6331   0.0130
 OBG  C12   C  CR56  0   0.482  -3.0874   0.4559  -0.0102
 OBG  HN1   H  HNH2  0   0.393  -2.2908  -3.6943   0.1582
 OBG  HN1A  H  HNH2  0   0.393  -3.9313  -3.2244   0.1319
 OBG  H3    H  HCH2  0   0.250   1.2127  -1.6963   0.8610
 OBG  H3A   H  HCH2  0   0.250   1.2081  -1.6833  -0.9037
 OBG  HN4   H  HNR5  0   0.423  -4.7753   1.7409   0.0056
 OBG  H5    H  HCR6  0   0.255   2.8946  -0.3875   2.1234
 OBG  H6    H  HCR6  0   0.259   5.1368   0.6324   2.1241
 OBG  H7    H  HCR6  0   0.259   6.2769   1.1253  -0.0166
 OBG  H8    H  HCR6  0   0.259   5.1590   0.5836  -2.1578
 OBG  H9    H  HCR6  0   0.255   2.9167  -0.4364  -2.1567
 OBG  H11   H  HCR5  0   0.287  -3.1472   3.6696   0.0246

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
 OBG  C1   N1    single    1.352  0.020  1.352
 OBG  C1   N2    aromatic  1.349  0.020  1.349
 OBG  C1   N5    aromatic  1.329  0.020  1.329
 OBG  O1   C2    single    1.321  0.020  1.321
 OBG  O1   C3    single    1.435  0.020  1.435
 OBG  C2   N2    aromatic  1.312  0.020  1.312
 OBG  C2   C10   aromatic  1.400  0.020  1.400
 OBG  C3   C4    single    1.497  0.020  1.497
 OBG  N3   C10   aromatic  1.374  0.020  1.374
 OBG  N3   C11   aromatic  1.299  0.020  1.299
 OBG  C4   C5    aromatic  1.392  0.020  1.392
 OBG  C4   C9    aromatic  1.392  0.020  1.392
 OBG  N4   C11   aromatic  1.367  0.020  1.367
 OBG  N4   C12   aromatic  1.358  0.020  1.358
 OBG  C5   C6    aromatic  1.388  0.020  1.388
 OBG  N5   C12   aromatic  1.327  0.020  1.327
 OBG  C6   C7    aromatic  1.389  0.020  1.389
 OBG  C7   C8    aromatic  1.389  0.020  1.389
 OBG  C8   C9    aromatic  1.388  0.020  1.388
 OBG  C10  C12   aromatic  1.392  0.020  1.392
 OBG  N1   HN1   single    0.890  0.020  1.040
 OBG  N1   HN1A  single    0.890  0.020  1.040
 OBG  C3   H3    single    0.970  0.020  1.090
 OBG  C3   H3A   single    0.970  0.020  1.090
 OBG  N4   HN4   single    0.860  0.020  1.020
 OBG  C5   H5    single    0.930  0.020  1.080
 OBG  C6   H6    single    0.930  0.020  1.080
 OBG  C7   H7    single    0.930  0.020  1.080
 OBG  C8   H8    single    0.930  0.020  1.080
 OBG  C9   H9    single    0.930  0.020  1.080
 OBG  C11  H11   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
 OBG  N5    C1   N2   126.50  3.000
 OBG  N5    C1   N1   117.72  3.000
 OBG  N2    C1   N1   115.76  3.000
 OBG  HN1A  N1   HN1  116.15  3.000
 OBG  HN1A  N1   C1   117.86  3.000
 OBG  HN1   N1   C1   117.87  3.000
 OBG  C3    O1   C2   118.37  3.000
 OBG  C10   C2   N2   120.25  3.000
 OBG  C10   C2   O1   118.87  3.000
 OBG  N2    C2   O1   120.88  3.000
 OBG  C2    N2   C1   119.15  3.000
 OBG  H3A   C3   H3   107.80  3.000
 OBG  H3A   C3   C4   111.24  3.000
 OBG  H3    C3   C4   111.27  3.000
 OBG  H3A   C3   O1   109.91  3.000
 OBG  H3    C3   O1   109.88  3.000
 OBG  C4    C3   O1   106.75  3.000
 OBG  C11   N3   C10  104.13  3.000
 OBG  C9    C4   C5   119.06  3.000
 OBG  C9    C4   C3   120.47  3.000
 OBG  C5    C4   C3   120.46  3.000
 OBG  HN4   N4   C12  126.78  3.000
 OBG  HN4   N4   C11  126.20  3.000
 OBG  C12   N4   C11  107.02  3.000
 OBG  H5    C5   C6   119.69  3.000
 OBG  H5    C5   C4   119.77  3.000
 OBG  C6    C5   C4   120.54  3.000
 OBG  C12   N5   C1   112.58  3.000
 OBG  H6    C6   C7   120.12  3.000
 OBG  H6    C6   C5   119.85  3.000
 OBG  C7    C6   C5   120.03  3.000
 OBG  H7    C7   C8   120.12  3.000
 OBG  H7    C7   C6   120.09  3.000
 OBG  C8    C7   C6   119.79  3.000
 OBG  H8    C8   C9   119.85  3.000
 OBG  H8    C8   C7   120.14  3.000
 OBG  C9    C8   C7   120.01  3.000
 OBG  H9    C9   C8   119.68  3.000
 OBG  H9    C9   C4   119.76  3.000
 OBG  C8    C9   C4   120.57  3.000
 OBG  C12   C10  N3   111.01  3.000
 OBG  C12   C10  C2   114.66  3.000
 OBG  N3    C10  C2   134.34  3.000
 OBG  H11   C11  N4   121.23  3.000
 OBG  H11   C11  N3   125.51  3.000
 OBG  N4    C11  N3   113.27  3.000
 OBG  C10   C12  N5   126.86  3.000
 OBG  C10   C12  N4   104.57  3.000
 OBG  N5    C12  N4   128.56  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
 OBG  CONST_01  C10   C2   N2   C1      0.00   0.0  0
 OBG  CONST_02  N4    C12  N5   C1    180.00   0.0  0
 OBG  CONST_03  C10   C12  N5   C1      0.00   0.0  0
 OBG  CONST_04  N5    C1   N2   C2      0.00   0.0  0
 OBG  CONST_05  C11   N3   C10  C2    180.00   0.0  0
 OBG  CONST_06  N4    C12  C10  C2    180.00   0.0  0
 OBG  CONST_07  N5    C12  C10  C2      0.00   0.0  0
 OBG  CONST_08  C12   N5   C1   N2      0.00   0.0  0
 OBG  CONST_09  N3    C10  C2   N2    180.00   0.0  0
 OBG  CONST_10  C12   C10  C2   N2      0.00   0.0  0
 OBG  CONST_11  N4    C12  C10  N3      0.00   0.0  0
 OBG  CONST_12  N5    C12  C10  N3    180.00   0.0  0
 OBG  CONST_13  C12   N4   C11  N3      0.00   0.0  0
 OBG  CONST_14  C7    C6   C5   C4      0.00   0.0  0
 OBG  CONST_15  C7    C8   C9   C4      0.00   0.0  0
 OBG  CONST_16  C10   N3   C11  N4      0.00   0.0  0
 OBG  CONST_17  C8    C9   C4   C5      0.00   0.0  0
 OBG  CONST_18  C8    C7   C6   C5      0.00   0.0  0
 OBG  CONST_19  C11   N4   C12  N5    180.00   0.0  0
 OBG  CONST_20  C9    C4   C5   C6      0.00   0.0  0
 OBG  CONST_21  C9    C8   C7   C6      0.00   0.0  0
 OBG  CONST_22  C11   N4   C12  C10     0.00   0.0  0
 OBG  CONST_23  C12   C10  N3   C11     0.00   0.0  0
 OBG  CONST_24  O1    C2   N2   C1    180.00   0.0  0
 OBG  CONST_25  C2    N2   C1   N1    180.00   0.0  0
 OBG  CONST_26  C12   N5   C1   N1    180.00   0.0  0
 OBG  CONST_27  N3    C10  C2   O1      0.00   0.0  0
 OBG  CONST_28  C12   C10  C2   O1    180.00   0.0  0
 OBG  CONST_29  C6    C5   C4   C3    180.00   0.0  0
 OBG  CONST_30  C8    C9   C4   C3    180.00   0.0  0
 OBG  CONST_31  HN4   N4   C11  N3    180.00   0.0  0
 OBG  CONST_32  H6    C6   C5   C4    180.00   0.0  0
 OBG  CONST_33  H8    C8   C9   C4    180.00   0.0  0
 OBG  CONST_34  H9    C9   C4   C5    180.00   0.0  0
 OBG  CONST_35  H7    C7   C6   C5    180.00   0.0  0
 OBG  CONST_36  H5    C5   C6   C7    180.00   0.0  0
 OBG  CONST_37  H11   C11  N3   C10   180.00   0.0  0
 OBG  CONST_39  HN1A  N1   C1   N2    180.00   0.0  0
 OBG  Var_01    C5    C4   C3   O1     88.00  30.0  2
 OBG  Var_02    C4    C3   O1   C2    179.62  30.0  3
 OBG  Var_03    C10   C2   O1   C3   -179.80  30.0  2

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
 OBG  plan-1  C3    0.020
 OBG  plan-1  C4    0.020
 OBG  plan-1  C5    0.020
 OBG  plan-1  C6    0.020
 OBG  plan-1  C7    0.020
 OBG  plan-1  C8    0.020
 OBG  plan-1  C9    0.020
 OBG  plan-1  H5    0.020
 OBG  plan-1  H6    0.020
 OBG  plan-1  H7    0.020
 OBG  plan-1  H8    0.020
 OBG  plan-1  H9    0.020
 OBG  plan-2  C1    0.020
 OBG  plan-2  N1    0.020
 OBG  plan-2  O1    0.020
 OBG  plan-2  C2    0.020
 OBG  plan-2  N2    0.020
 OBG  plan-2  N3    0.020
 OBG  plan-2  N4    0.020
 OBG  plan-2  N5    0.020
 OBG  plan-2  C10   0.020
 OBG  plan-2  C11   0.020
 OBG  plan-2  C12   0.020
 OBG  plan-2  HN4   0.020
 OBG  plan-2  H11   0.020
 OBG  plan-3  C1    0.020
 OBG  plan-3  N1    0.020
 OBG  plan-3  HN1   0.020
 OBG  plan-3  HN1A  0.020

