# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 12:10:31 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1OC[C@H]2CCCN2c3ncnc4nc[nH]c34
#
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
 7BH  7BH  6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine  ligand  42  23  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7BH
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
 7BH  C1   C  CR15  0  -0.072  -0.0680  -1.6764  -1.6583
 7BH  C2   C  CH2   0  -0.485   0.3615  -3.1159  -1.3359
 7BH  C3   C  CH2   0  -0.459  -0.6827  -3.6260  -0.3514
 7BH  C8   C  CR6   0   0.369   2.7044   0.2247  -0.2570
 7BH  C9   C  CR16  0  -0.379   3.3727   0.9148  -1.2630
 7BH  C10  C  CR16  0  -0.258   4.4306   1.7580  -0.9374
 7BH  C11  C  CR16  0  -0.274   4.8213   1.9146   0.3807
 7BH  C12  C  CR16  0  -0.289   4.1415   1.2217   1.3785
 7BH  C13  C  CR6   0  -0.009   3.0819   0.3751   1.0874
 7BH  C14  C  CR6   0   0.558  -1.6015  -0.1575  -0.4742
 7BH  C16  C  CR16  0   0.024  -2.2876   1.7855  -1.5136
 7BH  C19  C  CR56  0   0.151  -2.2607   0.3274   0.6733
 7BH  C21  C  CR15  0   0.114  -3.1529   0.8814   2.5867
 7BH  C4   C  CH2   0  -0.307  -1.0317  -2.3801   0.4491
 7BH  N5   N  NR5   0  -0.503  -0.9594  -1.3306  -0.5519
 7BH  C6   C  CH2   0  -0.212   1.1158  -0.7264  -1.7667
 7BH  O7   O  O2    0  -0.463   1.6760  -0.6157  -0.4757
 7BH  N15  N  N     0  -0.446  -2.9476   2.3159  -0.5071
 7BH  N17  N  N     0  -0.486  -1.6347   0.6261  -1.5558
 7BH  C18  C  CR56  0   0.272  -2.9121   1.5594   0.5979
 7BH  N20  N  NR15  0  -0.656  -2.4328  -0.0771   1.9748
 7BH  N22  N  N     0  -0.460  -3.4670   1.8796   1.8009
 7BH  C23  C  CH3   0  -0.709   2.3459  -0.3643   2.1653
 7BH  H1   H  HCR5  0   0.268  -0.6120  -1.6367  -2.6061
 7BH  H2   H  HCH2  0   0.259   0.4246  -3.7208  -2.2391
 7BH  H3   H  HCH2  0   0.246   1.3472  -3.1205  -0.8676
 7BH  H4   H  HCH2  0   0.244  -1.5692  -3.9845  -0.8772
 7BH  H5   H  HCH2  0   0.255  -0.3149  -4.4335   0.2800
 7BH  H6   H  HCR6  0   0.274   3.0864   0.8043  -2.3004
 7BH  H7   H  HCR6  0   0.255   4.9445   2.2909  -1.7270
 7BH  H8   H  HCR6  0   0.248   5.6455   2.5674   0.6363
 7BH  H9   H  HCR6  0   0.247   4.4412   1.3448   2.4127
 7BH  H10  H  HCR6  0   0.247  -2.2691   2.3586  -2.4353
 7BH  H11  H  HCR5  0   0.294  -3.4242   0.7969   3.6280
 7BH  H12  H  HCH2  0   0.255  -2.0321  -2.4482   0.8774
 7BH  H13  H  HCH2  0   0.245  -0.3087  -2.2183   1.2567
 7BH  H14  H  HCH2  0   0.241   1.8342  -1.1448  -2.4820
 7BH  H15  H  HCH2  0   0.246   0.7997   0.2525  -2.1365
 7BH  H16  H  HNR5  0   0.433  -2.0799  -0.9068   2.4233
 7BH  H18  H  HCH3  0   0.242   2.4494  -1.4457   2.0587
 7BH  H19  H  HCH3  0   0.242   2.7230  -0.0896   3.1492
 7BH  H20  H  HCH3  0   0.236   1.2761  -0.1484   2.1445

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
 7BH  C2   C1   single    1.536  0.020  1.536
 7BH  C2   C3   single    1.523  0.020  1.523
 7BH  N22  C21  aromatic  1.309  0.020  1.309
 7BH  N22  C18  aromatic  1.363  0.020  1.363
 7BH  C21  N20  aromatic  1.346  0.020  1.346
 7BH  N20  C19  aromatic  1.374  0.020  1.374
 7BH  C18  C19  aromatic  1.396  0.020  1.396
 7BH  C18  N15  aromatic  1.340  0.020  1.340
 7BH  C19  C14  aromatic  1.409  0.020  1.409
 7BH  C23  C13  single    1.500  0.020  1.500
 7BH  C14  N5   single    1.340  0.020  1.340
 7BH  C14  N17  aromatic  1.336  0.020  1.336
 7BH  N15  C16  aromatic  1.315  0.020  1.315
 7BH  C1   N5   single    1.462  0.020  1.462
 7BH  C1   C6   single    1.522  0.020  1.522
 7BH  N5   C4   single    1.452  0.020  1.452
 7BH  N17  C16  aromatic  1.331  0.020  1.331
 7BH  C4   C3   single    1.521  0.020  1.521
 7BH  O7   C6   single    1.412  0.020  1.412
 7BH  O7   C8   single    1.346  0.020  1.346
 7BH  C13  C8   aromatic  1.404  0.020  1.404
 7BH  C13  C12  aromatic  1.387  0.020  1.387
 7BH  C8   C9   aromatic  1.391  0.020  1.391
 7BH  C12  C11  aromatic  1.392  0.020  1.392
 7BH  C9   C10  aromatic  1.391  0.020  1.391
 7BH  C11  C10  aromatic  1.384  0.020  1.384
 7BH  C1   H1   single    0.970  0.020  1.090
 7BH  C2   H2   single    0.970  0.020  1.090
 7BH  C2   H3   single    0.970  0.020  1.090
 7BH  C3   H4   single    0.970  0.020  1.090
 7BH  C3   H5   single    0.970  0.020  1.090
 7BH  C9   H6   single    0.930  0.020  1.080
 7BH  C10  H7   single    0.930  0.020  1.080
 7BH  C11  H8   single    0.930  0.020  1.080
 7BH  C12  H9   single    0.930  0.020  1.080
 7BH  C16  H10  single    0.930  0.020  1.080
 7BH  C21  H11  single    0.930  0.020  1.080
 7BH  C4   H12  single    0.970  0.020  1.090
 7BH  C4   H13  single    0.970  0.020  1.090
 7BH  C6   H14  single    0.970  0.020  1.090
 7BH  C6   H15  single    0.970  0.020  1.090
 7BH  N20  H16  single    0.860  0.020  1.020
 7BH  C23  H18  single    0.970  0.020  1.090
 7BH  C23  H19  single    0.970  0.020  1.090
 7BH  C23  H20  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
 7BH  H1   C1   C6   107.61  3.000
 7BH  H1   C1   N5   110.12  3.000
 7BH  C6   C1   N5   112.37  3.000
 7BH  H1   C1   C2   110.79  3.000
 7BH  C6   C1   C2   112.49  3.000
 7BH  N5   C1   C2   103.48  3.000
 7BH  H3   C2   H2   107.54  3.000
 7BH  H3   C2   C3   109.90  3.000
 7BH  H2   C2   C3   112.94  3.000
 7BH  H3   C2   C1   110.28  3.000
 7BH  H2   C2   C1   111.26  3.000
 7BH  C3   C2   C1   104.94  3.000
 7BH  H5   C3   H4   108.06  3.000
 7BH  H5   C3   C4   112.31  3.000
 7BH  H4   C3   C4   109.64  3.000
 7BH  H5   C3   C2   113.05  3.000
 7BH  H4   C3   C2   110.82  3.000
 7BH  C4   C3   C2   102.89  3.000
 7BH  O7   C8   C13  115.33  3.000
 7BH  C13  C8   C9   120.66  3.000
 7BH  O7   C8   C9   124.01  3.000
 7BH  H6   C9   C10  119.18  3.000
 7BH  H6   C9   C8   121.04  3.000
 7BH  C10  C9   C8   119.78  3.000
 7BH  H7   C10  C11  120.34  3.000
 7BH  H7   C10  C9   119.25  3.000
 7BH  C11  C10  C9   120.41  3.000
 7BH  H8   C11  C12  120.20  3.000
 7BH  H8   C11  C10  120.55  3.000
 7BH  C12  C11  C10  119.25  3.000
 7BH  H9   C12  C13  118.74  3.000
 7BH  H9   C12  C11  119.50  3.000
 7BH  C13  C12  C11  121.76  3.000
 7BH  C23  C13  C12  121.66  3.000
 7BH  C12  C13  C8   118.13  3.000
 7BH  C23  C13  C8   120.21  3.000
 7BH  N17  C14  N5   118.59  3.000
 7BH  N17  C14  C19  116.47  3.000
 7BH  N5   C14  C19  124.94  3.000
 7BH  H10  C16  N17  115.12  3.000
 7BH  H10  C16  N15  116.45  3.000
 7BH  N17  C16  N15  128.43  3.000
 7BH  N20  C19  C18  104.64  3.000
 7BH  C18  C19  C14  118.55  3.000
 7BH  N20  C19  C14  136.77  3.000
 7BH  H11  C21  N22  125.36  3.000
 7BH  H11  C21  N20  121.15  3.000
 7BH  N22  C21  N20  113.49  3.000
 7BH  H13  C4   H12  108.97  3.000
 7BH  H13  C4   N5   111.62  3.000
 7BH  H12  C4   N5   111.19  3.000
 7BH  H13  C4   C3   110.94  3.000
 7BH  H12  C4   C3   111.47  3.000
 7BH  N5   C4   C3   102.57  3.000
 7BH  C4   N5   C14  124.69  3.000
 7BH  C4   N5   C1   112.40  3.000
 7BH  C14  N5   C1   122.90  3.000
 7BH  H15  C6   H14  108.09  3.000
 7BH  H15  C6   O7   110.73  3.000
 7BH  H14  C6   O7   111.49  3.000
 7BH  H15  C6   C1   110.99  3.000
 7BH  H14  C6   C1   108.53  3.000
 7BH  O7   C6   C1   107.01  3.000
 7BH  C6   O7   C8   120.05  3.000
 7BH  C18  N15  C16  112.96  3.000
 7BH  C16  N17  C14  119.82  3.000
 7BH  N22  C18  N15  125.77  3.000
 7BH  N15  C18  C19  123.74  3.000
 7BH  N22  C18  C19  110.47  3.000
 7BH  H16  N20  C21  124.87  3.000
 7BH  H16  N20  C19  128.36  3.000
 7BH  C21  N20  C19  106.74  3.000
 7BH  C18  N22  C21  104.66  3.000
 7BH  H20  C23  H19  107.86  3.000
 7BH  H20  C23  H18  106.68  3.000
 7BH  H19  C23  H18  107.78  3.000
 7BH  H20  C23  C13  111.70  3.000
 7BH  H19  C23  C13  110.79  3.000
 7BH  H18  C23  C13  111.81  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
 7BH  CONST_01  C11  C12  C13  C8      0.00   0.0  0
 7BH  CONST_02  C11  C10  C9   C8      0.00   0.0  0
 7BH  CONST_03  C12  C13  C8   C9      0.00   0.0  0
 7BH  CONST_04  C12  C11  C10  C9      0.00   0.0  0
 7BH  CONST_05  C13  C8   C9   C10     0.00   0.0  0
 7BH  CONST_06  C13  C12  C11  C10     0.00   0.0  0
 7BH  CONST_07  C21  N20  C19  C14   180.00   0.0  0
 7BH  CONST_08  N22  C18  C19  C14   180.00   0.0  0
 7BH  CONST_09  N15  C18  C19  C14     0.00   0.0  0
 7BH  CONST_10  N15  C16  N17  C14     0.00   0.0  0
 7BH  CONST_11  N22  C18  N15  C16   180.00   0.0  0
 7BH  CONST_12  C19  C18  N15  C16     0.00   0.0  0
 7BH  CONST_13  C19  C14  N17  C16     0.00   0.0  0
 7BH  CONST_14  N22  C21  N20  C19     0.00   0.0  0
 7BH  CONST_15  C21  N22  C18  C19     0.00   0.0  0
 7BH  CONST_16  N15  C18  N22  C21   180.00   0.0  0
 7BH  CONST_17  C18  C19  N20  C21     0.00   0.0  0
 7BH  CONST_18  N20  C19  C18  N15   180.00   0.0  0
 7BH  CONST_19  N20  C19  C14  N17   180.00   0.0  0
 7BH  CONST_20  C18  C19  C14  N17     0.00   0.0  0
 7BH  CONST_21  C18  N15  C16  N17     0.00   0.0  0
 7BH  CONST_22  N20  C21  N22  C18     0.00   0.0  0
 7BH  CONST_23  N22  C18  C19  N20     0.00   0.0  0
 7BH  CONST_24  N5   C14  N17  C16   180.00   0.0  0
 7BH  CONST_25  N20  C19  C14  N5      0.00   0.0  0
 7BH  CONST_26  C18  C19  C14  N5    180.00   0.0  0
 7BH  CONST_27  C23  C13  C8   C9    180.00   0.0  0
 7BH  CONST_28  O7   C8   C9   C10   180.00   0.0  0
 7BH  CONST_29  C23  C13  C12  C11   180.00   0.0  0
 7BH  CONST_30  O7   C8   C13  C12   180.00   0.0  0
 7BH  CONST_31  H9   C12  C13  C8    180.00   0.0  0
 7BH  CONST_32  H7   C10  C9   C8    180.00   0.0  0
 7BH  CONST_33  H8   C11  C10  C9    180.00   0.0  0
 7BH  CONST_34  H6   C9   C10  C11   180.00   0.0  0
 7BH  CONST_35  H16  N20  C19  C14     0.00   0.0  0
 7BH  CONST_36  H10  C16  N17  C14   180.00   0.0  0
 7BH  CONST_37  H11  C21  N20  C19   180.00   0.0  0
 7BH  Var_01    C4   C3   C2   C1    -34.26  30.0  1
 7BH  Var_02    C19  C14  N5   C1   -167.29  30.0  3
 7BH  Var_03    C3   C4   N5   C1    -25.50  30.0  1
 7BH  Var_04    N5   C4   C3   C2     35.94  30.0  1
 7BH  Var_05    H18  C23  C13  C8     63.26  30.0  2
 7BH  Var_06    H14  C6   O7   C8     65.05  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
 7BH  chir_01  C1  C2  N5  C6  negativ

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
 7BH  plan-1  C8   0.020
 7BH  plan-1  C9   0.020
 7BH  plan-1  C10  0.020
 7BH  plan-1  C11  0.020
 7BH  plan-1  C12  0.020
 7BH  plan-1  C13  0.020
 7BH  plan-1  O7   0.020
 7BH  plan-1  C23  0.020
 7BH  plan-1  H6   0.020
 7BH  plan-1  H7   0.020
 7BH  plan-1  H8   0.020
 7BH  plan-1  H9   0.020
 7BH  plan-2  C14  0.020
 7BH  plan-2  C16  0.020
 7BH  plan-2  C19  0.020
 7BH  plan-2  C21  0.020
 7BH  plan-2  N5   0.020
 7BH  plan-2  N15  0.020
 7BH  plan-2  N17  0.020
 7BH  plan-2  C18  0.020
 7BH  plan-2  N20  0.020
 7BH  plan-2  N22  0.020
 7BH  plan-2  H10  0.020
 7BH  plan-2  H11  0.020
 7BH  plan-2  H16  0.020

