# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 11:14:54 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-(7-benzyl-1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)piperazin-1-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C)c2nc(N3CC[NH2+]CC3)n(Cc4ccccc4)c2C1=O
#
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
 SC3  SC3  4-(7-benzyl-1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-8-yl)piperazin-1-ium  ligand  49  26  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SC3
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
 SC3  N1    N  NR6   0  -0.602   3.6098  -0.1688   0.3736
 SC3  C2    C  CR6   0   0.719   3.7565   0.8631  -0.5501
 SC3  N3    N  NR6   0  -0.593   2.6123   1.5262  -0.9234
 SC3  C4    C  CR56  0   0.468   1.4150   1.1559  -0.3916
 SC3  C5    C  CR56  0   0.130   1.2937   0.1338   0.5081
 SC3  C6    C  CR6   0   0.583   2.4224  -0.5807   0.9883
 SC3  N7    N  NR5   0  -0.525  -0.0516   0.0923   0.8293
 SC3  C8    C  CR5   0   0.720  -0.6256   1.0812   0.1119
 SC3  N9    N  N     0  -0.488   0.2348   1.7506  -0.6357
 SC3  N10   N  NT    0  -0.540  -1.9792   1.3269   0.1640
 SC3  C11   C  CH2   0  -0.322  -2.5357   1.9918  -1.0035
 SC3  C12   C  CH2   0  -0.332  -4.0408   1.8405  -0.9967
 SC3  N13   N  NT2   1  -0.644  -4.6008   2.3811   0.2715
 SC3  C14   C  CH2   0  -0.330  -3.9816   1.7598   1.4728
 SC3  C15   C  CH2   0  -0.348  -2.4796   1.9117   1.4063
 SC3  C16   C  CH2   0  -0.447  -0.7408  -1.0312   1.4585
 SC3  C17   C  CR6   0   0.135  -1.0916  -2.0920   0.4477
 SC3  C18   C  CR16  0  -0.287  -2.3326  -2.0786  -0.1828
 SC3  C19   C  CR16  0  -0.244  -2.6487  -3.0315  -1.1412
 SC3  C20   C  CR16  0  -0.261  -1.7234  -4.0104  -1.4792
 SC3  C21   C  CR16  0  -0.240  -0.4850  -4.0336  -0.8511
 SC3  C22   C  CR16  0  -0.297  -0.1718  -3.0808   0.1086
 SC3  O23   O  OC    0  -0.478   2.4294  -1.4623   1.8331
 SC3  C24   C  CH3   0  -0.530   4.8116  -0.8833   0.7933
 SC3  O25   O  OC    0  -0.488   4.8451   1.1649  -1.0010
 SC3  C26   C  CH3   0  -0.535   2.6537   2.6231  -1.8773
 SC3  H111  H  HCH2  0   0.260  -2.2649   3.0544  -1.0417
 SC3  H112  H  HCH2  0   0.299  -2.1580   1.5231  -1.9103
 SC3  H121  H  HCH2  0   0.319  -4.4921   2.3890  -1.8193
 SC3  H122  H  HCH2  0   0.300  -4.3389   0.7956  -1.0588
 SC3  H131  H  HNT2  0   0.470  -4.4689   3.3944   0.3022
 SC3  H132  H  HNT2  0   0.486  -5.6110   2.2408   0.2933
 SC3  H141  H  HCH2  0   0.321  -4.3882   2.2548   2.3507
 SC3  H142  H  HCH2  0   0.303  -4.2793   0.7128   1.4820
 SC3  H151  H  HCH2  0   0.301  -2.0490   1.4116   2.2718
 SC3  H152  H  HCH2  0   0.276  -2.2038   2.9722   1.4810
 SC3  H161  H  HCH2  0   0.303  -0.0883  -1.4227   2.2348
 SC3  H162  H  HCH2  0   0.290  -1.6362  -0.6636   1.9544
 SC3  H18   H  HCR6  0   0.244  -3.0583  -1.3198   0.0803
 SC3  H19   H  HCR6  0   0.258  -3.6188  -3.0114  -1.6207
 SC3  H20   H  HCR6  0   0.259  -1.9677  -4.7562  -2.2246
 SC3  H21   H  HCR6  0   0.259   0.2387  -4.7970  -1.1057
 SC3  H22   H  HCR6  0   0.260   0.7932  -3.1107   0.5997
 SC3  H241  H  HCH3  0   0.270   5.6549  -0.5447   0.2061
 SC3  H242  H  HCH3  0   0.254   5.0176  -0.6992   1.8462
 SC3  H243  H  HCH3  0   0.255   4.6835  -1.9527   0.6415
 SC3  H261  H  HCH3  0   0.273   3.6739   2.7741  -2.2075
 SC3  H262  H  HCH3  0   0.259   2.0319   2.3905  -2.7395
 SC3  H263  H  HCH3  0   0.259   2.2901   3.5386  -1.4147

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
 SC3  N1   C2    aromatic  1.393  0.020  1.393
 SC3  N1   C6    aromatic  1.399  0.020  1.399
 SC3  N1   C24   single    1.460  0.020  1.460
 SC3  C2   N3    aromatic  1.374  0.020  1.374
 SC3  C2   O25   double    1.216  0.020  1.216
 SC3  N3   C4    aromatic  1.361  0.020  1.361
 SC3  N3   C26   single    1.454  0.020  1.454
 SC3  C4   C5    aromatic  1.367  0.020  1.367
 SC3  C4   N9    aromatic  1.344  0.020  1.344
 SC3  C5   C6    aromatic  1.419  0.020  1.419
 SC3  C5   N7    aromatic  1.384  0.020  1.384
 SC3  C6   O23   double    1.221  0.020  1.221
 SC3  N7   C8    aromatic  1.350  0.020  1.350
 SC3  N7   C16   single    1.461  0.020  1.461
 SC3  C8   N9    aromatic  1.322  0.020  1.322
 SC3  C8   N10   single    1.377  0.020  1.377
 SC3  N10  C11   single    1.454  0.020  1.454
 SC3  N10  C15   single    1.461  0.020  1.461
 SC3  C11  C12   single    1.513  0.020  1.513
 SC3  C11  H111  single    0.970  0.020  1.090
 SC3  C11  H112  single    0.970  0.020  1.090
 SC3  C12  N13   single    1.488  0.020  1.488
 SC3  C12  H121  single    0.970  0.020  1.090
 SC3  C12  H122  single    0.970  0.020  1.090
 SC3  N13  C14   single    1.488  0.020  1.488
 SC3  N13  H131  single    0.890  0.020  1.040
 SC3  N13  H132  single    0.890  0.020  1.040
 SC3  C14  C15   single    1.511  0.020  1.511
 SC3  C14  H141  single    0.970  0.020  1.090
 SC3  C14  H142  single    0.970  0.020  1.090
 SC3  C15  H151  single    0.970  0.020  1.090
 SC3  C15  H152  single    0.970  0.020  1.090
 SC3  C16  C17   single    1.507  0.020  1.507
 SC3  C16  H161  single    0.970  0.020  1.090
 SC3  C16  H162  single    0.970  0.020  1.090
 SC3  C17  C18   aromatic  1.392  0.020  1.392
 SC3  C17  C22   aromatic  1.392  0.020  1.392
 SC3  C18  C19   aromatic  1.388  0.020  1.388
 SC3  C18  H18   single    0.930  0.020  1.080
 SC3  C19  C20   aromatic  1.389  0.020  1.389
 SC3  C19  H19   single    0.930  0.020  1.080
 SC3  C20  C21   aromatic  1.389  0.020  1.389
 SC3  C20  H20   single    0.930  0.020  1.080
 SC3  C21  C22   aromatic  1.388  0.020  1.388
 SC3  C21  H21   single    0.930  0.020  1.080
 SC3  C22  H22   single    0.930  0.020  1.080
 SC3  C24  H241  single    0.970  0.020  1.090
 SC3  C24  H242  single    0.970  0.020  1.090
 SC3  C24  H243  single    0.970  0.020  1.090
 SC3  C26  H261  single    0.970  0.020  1.090
 SC3  C26  H262  single    0.970  0.020  1.090
 SC3  C26  H263  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
 SC3  C24   N1   C6    115.35  3.000
 SC3  C24   N1   C2    117.82  3.000
 SC3  C6    N1   C2    126.80  3.000
 SC3  O25   C2   N3    121.66  3.000
 SC3  O25   C2   N1    121.60  3.000
 SC3  N3    C2   N1    116.74  3.000
 SC3  C26   N3   C4    119.11  3.000
 SC3  C26   N3   C2    121.23  3.000
 SC3  C4    N3   C2    119.66  3.000
 SC3  N9    C4   C5    111.87  3.000
 SC3  N9    C4   N3    125.52  3.000
 SC3  C5    C4   N3    122.58  3.000
 SC3  N7    C5   C6    132.80  3.000
 SC3  N7    C5   C4    105.15  3.000
 SC3  C6    C5   C4    121.90  3.000
 SC3  O23   C6   C5    127.01  3.000
 SC3  O23   C6   N1    120.78  3.000
 SC3  C5    C6   N1    112.21  3.000
 SC3  C16   N7   C8    126.29  3.000
 SC3  C16   N7   C5    125.58  3.000
 SC3  C8    N7   C5    105.55  3.000
 SC3  N10   C8   N9    124.82  3.000
 SC3  N10   C8   N7    121.92  3.000
 SC3  N9    C8   N7    113.25  3.000
 SC3  C8    N9   C4    104.17  3.000
 SC3  C15   N10  C11   111.62  3.000
 SC3  C15   N10  C8    116.12  3.000
 SC3  C11   N10  C8    115.30  3.000
 SC3  H112  C11  H111  107.60  3.000
 SC3  H112  C11  C12   107.81  3.000
 SC3  H111  C11  C12   110.04  3.000
 SC3  H112  C11  N10   109.83  3.000
 SC3  H111  C11  N10   112.10  3.000
 SC3  C12   C11  N10   109.35  3.000
 SC3  H122  C12  H121  109.12  3.000
 SC3  H122  C12  N13   107.12  3.000
 SC3  H121  C12  N13   107.78  3.000
 SC3  H122  C12  C11   111.61  3.000
 SC3  H121  C12  C11   111.05  3.000
 SC3  N13   C12  C11   109.99  3.000
 SC3  H132  N13  H131  105.27  3.000
 SC3  H132  N13  C14   109.72  3.000
 SC3  H131  N13  C14   109.64  3.000
 SC3  H132  N13  C12   109.93  3.000
 SC3  H131  N13  C12   109.71  3.000
 SC3  C14   N13  C12   112.33  3.000
 SC3  H142  C14  H141  109.21  3.000
 SC3  H142  C14  C15   111.65  3.000
 SC3  H141  C14  C15   111.20  3.000
 SC3  H142  C14  N13   107.14  3.000
 SC3  H141  C14  N13   107.84  3.000
 SC3  C15   C14  N13   109.64  3.000
 SC3  H152  C15  H151  106.87  3.000
 SC3  H152  C15  C14   110.10  3.000
 SC3  H151  C15  C14   108.17  3.000
 SC3  H152  C15  N10   111.00  3.000
 SC3  H151  C15  N10   110.90  3.000
 SC3  C14   C15  N10   109.73  3.000
 SC3  H162  C16  H161  106.87  3.000
 SC3  H162  C16  C17   110.62  3.000
 SC3  H161  C16  C17   111.43  3.000
 SC3  H162  C16  N7    108.96  3.000
 SC3  H161  C16  N7    107.54  3.000
 SC3  C17   C16  N7    111.25  3.000
 SC3  C22   C17  C18   119.04  3.000
 SC3  C22   C17  C16   120.64  3.000
 SC3  C18   C17  C16   120.31  3.000
 SC3  H18   C18  C19   119.76  3.000
 SC3  H18   C18  C17   119.63  3.000
 SC3  C19   C18  C17   120.61  3.000
 SC3  H19   C19  C20   120.16  3.000
 SC3  H19   C19  C18   119.83  3.000
 SC3  C20   C19  C18   120.01  3.000
 SC3  H20   C20  C21   120.08  3.000
 SC3  H20   C20  C19   120.19  3.000
 SC3  C21   C20  C19   119.73  3.000
 SC3  H21   C21  C22   119.73  3.000
 SC3  H21   C21  C20   120.11  3.000
 SC3  C22   C21  C20   120.16  3.000
 SC3  H22   C22  C21   119.70  3.000
 SC3  H22   C22  C17   119.85  3.000
 SC3  C21   C22  C17   120.45  3.000
 SC3  H243  C24  H242  108.88  3.000
 SC3  H243  C24  H241  108.89  3.000
 SC3  H242  C24  H241  108.93  3.000
 SC3  H243  C24  N1    110.13  3.000
 SC3  H242  C24  N1    110.55  3.000
 SC3  H241  C24  N1    109.41  3.000
 SC3  H263  C26  H262  109.00  3.000
 SC3  H263  C26  H261  109.10  3.000
 SC3  H262  C26  H261  109.06  3.000
 SC3  H263  C26  N3    110.26  3.000
 SC3  H262  C26  N3    110.01  3.000
 SC3  H261  C26  N3    109.40  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
 SC3  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 SC3  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 SC3  CONST_03  N7    C5   C6   N1    180.00   0.0  0
 SC3  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 SC3  CONST_05  C5    C4   N3   C2      0.00   0.0  0
 SC3  CONST_06  N9    C4   N3   C2    180.00   0.0  0
 SC3  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 SC3  CONST_08  C6    C5   C4   N3      0.00   0.0  0
 SC3  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 SC3  CONST_10  C8    N9   C4   N3    180.00   0.0  0
 SC3  CONST_11  C8    N7   C5   C4      0.00   0.0  0
 SC3  CONST_12  N7    C8   N9   C4      0.00   0.0  0
 SC3  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 SC3  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 SC3  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 SC3  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 SC3  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 SC3  CONST_18  C20   C19  C18  C17     0.00   0.0  0
 SC3  CONST_19  C20   C21  C22  C17     0.00   0.0  0
 SC3  CONST_20  C21   C22  C17  C18     0.00   0.0  0
 SC3  CONST_21  C21   C20  C19  C18     0.00   0.0  0
 SC3  CONST_22  C22   C17  C18  C19     0.00   0.0  0
 SC3  CONST_23  C22   C21  C20  C19     0.00   0.0  0
 SC3  CONST_24  N10   C8   N9   C4    180.00   0.0  0
 SC3  CONST_25  N10   C8   N7   C5    180.00   0.0  0
 SC3  CONST_26  C26   N3   C2   N1    180.00   0.0  0
 SC3  CONST_27  O23   C6   N1   C2    180.00   0.0  0
 SC3  CONST_28  C24   N1   C2   N3    180.00   0.0  0
 SC3  CONST_29  O25   C2   N3   C4    180.00   0.0  0
 SC3  CONST_30  O23   C6   C5   C4    180.00   0.0  0
 SC3  CONST_32  C26   N3   C4   C5    180.00   0.0  0
 SC3  CONST_33  C24   N1   C6   C5    180.00   0.0  0
 SC3  CONST_34  O25   C2   N1   C6    180.00   0.0  0
 SC3  CONST_36  O23   C6   C5   N7      0.00   0.0  0
 SC3  CONST_37  C26   N3   C4   N9      0.00   0.0  0
 SC3  CONST_40  C19   C18  C17  C16   180.00   0.0  0
 SC3  CONST_41  C21   C22  C17  C16   180.00   0.0  0
 SC3  CONST_42  H19   C19  C18  C17   180.00   0.0  0
 SC3  CONST_43  H21   C21  C22  C17   180.00   0.0  0
 SC3  CONST_44  H22   C22  C17  C18   180.00   0.0  0
 SC3  CONST_45  H20   C20  C19  C18   180.00   0.0  0
 SC3  CONST_46  H18   C18  C19  C20   180.00   0.0  0
 SC3  CONST_47  C24   N1   C6   O23     0.00   0.0  0
 SC3  CONST_48  O25   C2   N1   C24     0.00   0.0  0
 SC3  CONST_49  C26   N3   C2   O25     0.00   0.0  0
 SC3  Var_01    C11   N10  C8   N7   -155.52  30.0  2
 SC3  Var_02    C12   C11  N10  C8    163.76  30.0  1
 SC3  Var_03    C14   C15  N10  C8   -163.99  30.0  1
 SC3  Var_04    N13   C12  C11  N10    56.65  30.0  1
 SC3  Var_05    N13   C14  C15  N10   -56.42  30.0  1
 SC3  Var_06    C14   N13  C12  C11   -55.00  30.0  1
 SC3  Var_07    C15   C14  N13  C12    54.76  30.0  1
 SC3  Var_08    C17   C16  N7   C5    -80.96  30.0  2
 SC3  Var_09    C18   C17  C16  N7    -92.51  30.0  2
 SC3  Var_10    H241  C24  N1   C2     -6.31  30.0  2
 SC3  Var_11    H261  C26  N3   C2      0.95  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
 SC3  plan-1  C16  0.020
 SC3  plan-1  C17  0.020
 SC3  plan-1  C18  0.020
 SC3  plan-1  C19  0.020
 SC3  plan-1  C20  0.020
 SC3  plan-1  C21  0.020
 SC3  plan-1  C22  0.020
 SC3  plan-1  H18  0.020
 SC3  plan-1  H19  0.020
 SC3  plan-1  H20  0.020
 SC3  plan-1  H21  0.020
 SC3  plan-1  H22  0.020
 SC3  plan-2  N1   0.020
 SC3  plan-2  C2   0.020
 SC3  plan-2  N3   0.020
 SC3  plan-2  C4   0.020
 SC3  plan-2  C5   0.020
 SC3  plan-2  C6   0.020
 SC3  plan-2  N7   0.020
 SC3  plan-2  C8   0.020
 SC3  plan-2  N9   0.020
 SC3  plan-2  N10  0.020
 SC3  plan-2  C16  0.020
 SC3  plan-2  O23  0.020
 SC3  plan-2  C24  0.020
 SC3  plan-2  O25  0.020
 SC3  plan-2  C26  0.020

