# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 14:49:57 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 9-(4-carboxybutyl)-2-[(4-carboxybutyl)amino]-7-methyl-6-oxo-6,7-dihydro-1H-purin-9-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1c[n+](CCCCC(O)=O)c2N=C(NCCCCC(O)=O)NC(=O)c12
#
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
 29R  29R  9-(4-carboxybutyl)-2-[(4-carboxybutyl)amino]-7-methyl-6-oxo-6,7-dihydro-1H-purin-9-ium  ligand  48  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_29R
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
 29R  N1    N  NR16   0  -0.750   1.4359   3.2694  -0.5322
 29R  C2    C  CR6    0   0.778   0.5736   2.2589  -0.1898
 29R  N2    N  NH1    0  -0.676  -0.7249   2.5052  -0.3174
 29R  N3    N  N      0  -0.511   0.9863   1.0895   0.2524
 29R  C4    C  CR6    0   0.515   2.3097   0.9898   0.3256
 29R  C5    C  CR6    0   0.091   3.2448   1.9428  -0.0009
 29R  C6    C  CR6    0   0.553   2.8259   3.2219  -0.4766
 29R  O6    O  O      0  -0.445   3.5173   4.1667  -0.8014
 29R  N7    N  N      0  -0.470   4.4883   1.3981   0.2272
 29R  C8    C  C1     0   0.258   4.3113   0.1728   0.6723
 29R  N9    N  N      1  -0.502   3.0080  -0.1105   0.7502
 29R  C11   C  CH2    0  -0.307   2.4322  -1.3844   1.1698
 29R  C12   C  CH2    0  -0.437   1.8699  -2.1756  -0.0004
 29R  C13   C  CH2    0  -0.415   1.3518  -3.5343   0.4565
 29R  C14   C  CH2    0  -0.583   0.7450  -4.3280  -0.6889
 29R  C15   C  C      0   0.413   0.2162  -5.7272  -0.3263
 29R  O16   O  O      0  -0.608   0.2135  -6.0550   0.8764
 29R  O17   O  OC    -1  -0.632  -0.1800  -6.4249  -1.2837
 29R  C31   C  CH2    0  -0.236  -1.7534   1.5043  -0.0932
 29R  C32   C  CH2    0  -0.471  -3.1257   2.1543  -0.1515
 29R  C33   C  CH2    0  -0.409  -4.2530   1.1346  -0.0505
 29R  C34   C  CH2    0  -0.582  -5.6217   1.7944  -0.0936
 29R  C35   C  C      0   0.412  -6.8315   0.8467  -0.0164
 29R  O36   O  O      0  -0.608  -6.6105  -0.3709   0.1325
 29R  O37   O  OC    -1  -0.634  -7.9538   1.3888  -0.1054
 29R  CM7   C  CH3    0  -0.522   5.7708   2.0503   0.0231
 29R  HN1   H  HNR6   0   0.437   1.0451   4.1426  -0.8655
 29R  HN2   H  HNH1   0   0.416  -1.0110   3.3766  -0.7355
 29R  H8    H  H      0   0.367   5.1033  -0.5072   0.9402
 29R  H11   H  HCH2   0   0.281   3.2228  -1.9389   1.6739
 29R  H11A  H  HCH2   0   0.282   1.6595  -1.1704   1.9080
 29R  H12   H  HCH2   0   0.240   1.0631  -1.6073  -0.4704
 29R  H12A  H  HCH2   0   0.234   2.6502  -2.3070  -0.7551
 29R  H13   H  HCH2   0   0.214   2.1717  -4.0999   0.9083
 29R  H13A  H  HCH2   0   0.215   0.6076  -3.3946   1.2447
 29R  H14   H  HCH2   0   0.224  -0.0813  -3.7576  -1.1299
 29R  H14A  H  HCH2   0   0.219   1.4787  -4.4332  -1.4958
 29R  H31   H  HCH2   0   0.238  -1.6747   0.7139  -0.8461
 29R  H31A  H  HCH2   0   0.245  -1.5953   1.0376   0.8803
 29R  H32   H  HCH2   0   0.231  -3.2134   2.8884   0.6550
 29R  H32A  H  HCH2   0   0.226  -3.2234   2.7094  -1.0910
 29R  H33   H  HCH2   0   0.211  -4.1605   0.4141  -0.8678
 29R  H33A  H  HCH2   0   0.211  -4.1463   0.5600   0.8738
 29R  H34   H  HCH2   0   0.221  -5.7057   2.5169   0.7271
 29R  H34A  H  HCH2   0   0.218  -5.7120   2.3952  -1.0062
 29R  HM7   H  HCH3   0   0.284   5.8396   2.9285   0.6581
 29R  HM7A  H  HCH3   0   0.281   6.5589   1.3516   0.2837
 29R  HM7B  H  HCH3   0   0.284   5.8730   2.3390  -1.0185

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
 29R  N1   C2    single    1.372  0.020  1.372
 29R  N1   C6    single    1.392  0.020  1.392
 29R  C2   N2    single    1.328  0.020  1.328
 29R  C2   N3    double    1.317  0.020  1.317
 29R  N2   C31   single    1.453  0.020  1.453
 29R  N3   C4    single    1.329  0.020  1.329
 29R  C4   C5    aromatic  1.375  0.020  1.375
 29R  C4   N9    aromatic  1.371  0.020  1.371
 29R  C5   C6    single    1.427  0.020  1.427
 29R  C5   N7    aromatic  1.377  0.020  1.377
 29R  C6   O6    double    1.215  0.020  1.215
 29R  N7   C8    aromatic  1.316  0.020  1.316
 29R  N7   CM7   single    1.453  0.020  1.453
 29R  C8   N9    aromatic  1.336  0.020  1.336
 29R  N9   C11   single    1.460  0.020  1.460
 29R  C11  C12   single    1.520  0.020  1.520
 29R  C12  C13   single    1.524  0.020  1.524
 29R  C13  C14   single    1.520  0.020  1.520
 29R  C14  C15   single    1.539  0.020  1.539
 29R  C15  O16   deloc     1.247  0.020  1.247
 29R  C15  O17   deloc     1.249  0.020  1.249
 29R  C31  C32   single    1.519  0.020  1.519
 29R  C32  C33   single    1.523  0.020  1.523
 29R  C33  C34   single    1.520  0.020  1.520
 29R  C34  C35   single    1.539  0.020  1.539
 29R  C35  O36   deloc     1.246  0.020  1.246
 29R  C35  O37   deloc     1.250  0.020  1.250
 29R  N1   HN1   single    0.860  0.020  1.020
 29R  N2   HN2   single    0.860  0.020  1.020
 29R  C8   H8    single    0.930  0.020  1.080
 29R  C11  H11   single    0.970  0.020  1.090
 29R  C11  H11A  single    0.970  0.020  1.090
 29R  C12  H12   single    0.970  0.020  1.090
 29R  C12  H12A  single    0.970  0.020  1.090
 29R  C13  H13   single    0.970  0.020  1.090
 29R  C13  H13A  single    0.970  0.020  1.090
 29R  C14  H14   single    0.970  0.020  1.090
 29R  C14  H14A  single    0.970  0.020  1.090
 29R  C31  H31   single    0.970  0.020  1.090
 29R  C31  H31A  single    0.970  0.020  1.090
 29R  C32  H32   single    0.970  0.020  1.090
 29R  C32  H32A  single    0.970  0.020  1.090
 29R  C33  H33   single    0.970  0.020  1.090
 29R  C33  H33A  single    0.970  0.020  1.090
 29R  C34  H34   single    0.970  0.020  1.090
 29R  C34  H34A  single    0.970  0.020  1.090
 29R  CM7  HM7   single    0.970  0.020  1.090
 29R  CM7  HM7A  single    0.970  0.020  1.090
 29R  CM7  HM7B  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
 29R  HN1   N1   C6    115.33  3.000
 29R  HN1   N1   C2    118.32  3.000
 29R  C6    N1   C2    126.34  3.000
 29R  N3    C2   N2    120.24  3.000
 29R  N3    C2   N1    122.75  3.000
 29R  N2    C2   N1    117.01  3.000
 29R  HN2   N2   C31   117.30  3.000
 29R  HN2   N2   C2    118.54  3.000
 29R  C31   N2   C2    123.36  3.000
 29R  C4    N3   C2    113.41  3.000
 29R  N9    C4   C5    106.48  3.000
 29R  N9    C4   N3    125.77  3.000
 29R  C5    C4   N3    127.75  3.000
 29R  N7    C5   C6    132.44  3.000
 29R  N7    C5   C4    107.50  3.000
 29R  C6    C5   C4    120.05  3.000
 29R  O6    C6   C5    128.24  3.000
 29R  O6    C6   N1    122.07  3.000
 29R  C5    C6   N1    109.69  3.000
 29R  CM7   N7   C8    125.75  3.000
 29R  CM7   N7   C5    126.60  3.000
 29R  C8    N7   C5    107.64  3.000
 29R  H8    C8   N9    124.66  3.000
 29R  H8    C8   N7    124.95  3.000
 29R  N9    C8   N7    110.39  3.000
 29R  C11   N9   C8    125.92  3.000
 29R  C11   N9   C4    126.07  3.000
 29R  C8    N9   C4    107.98  3.000
 29R  H11A  C11  H11   107.52  3.000
 29R  H11A  C11  C12   111.17  3.000
 29R  H11   C11  C12   111.08  3.000
 29R  H11A  C11  N9    107.64  3.000
 29R  H11   C11  N9    106.92  3.000
 29R  C12   C11  N9    112.26  3.000
 29R  H12A  C12  H12   107.00  3.000
 29R  H12A  C12  C13   110.02  3.000
 29R  H12   C12  C13   109.97  3.000
 29R  H12A  C12  C11   109.26  3.000
 29R  H12   C12  C11   109.47  3.000
 29R  C13   C12  C11   111.04  3.000
 29R  H13A  C13  H13   106.18  3.000
 29R  H13A  C13  C14   109.78  3.000
 29R  H13   C13  C14   109.91  3.000
 29R  H13A  C13  C12   109.49  3.000
 29R  H13   C13  C12   109.27  3.000
 29R  C14   C13  C12   112.04  3.000
 29R  H14A  C14  H14   104.98  3.000
 29R  H14A  C14  C15   108.44  3.000
 29R  H14   C14  C15   107.98  3.000
 29R  H14A  C14  C13   109.74  3.000
 29R  H14   C14  C13   109.40  3.000
 29R  C15   C14  C13   115.74  3.000
 29R  O17   C15  O16   126.29  3.000
 29R  O17   C15  C14   115.86  3.000
 29R  O16   C15  C14   117.85  3.000
 29R  H31A  C31  H31   107.12  3.000
 29R  H31A  C31  C32   110.37  3.000
 29R  H31   C31  C32   110.33  3.000
 29R  H31A  C31  N2    109.26  3.000
 29R  H31   C31  N2    109.91  3.000
 29R  C32   C31  N2    109.80  3.000
 29R  H32A  C32  H32   106.56  3.000
 29R  H32A  C32  C33   109.27  3.000
 29R  H32   C32  C33   109.93  3.000
 29R  H32A  C32  C31   109.28  3.000
 29R  H32   C32  C31   109.34  3.000
 29R  C33   C32  C31   112.30  3.000
 29R  H33A  C33  H33   106.10  3.000
 29R  H33A  C33  C34   109.87  3.000
 29R  H33   C33  C34   109.93  3.000
 29R  H33A  C33  C32   109.60  3.000
 29R  H33   C33  C32   109.20  3.000
 29R  C34   C33  C32   111.96  3.000
 29R  H34A  C34  H34   104.80  3.000
 29R  H34A  C34  C35   108.33  3.000
 29R  H34   C34  C35   107.94  3.000
 29R  H34A  C34  C33   109.61  3.000
 29R  H34   C34  C33   109.49  3.000
 29R  C35   C34  C33   116.06  3.000
 29R  O37   C35  O36   126.27  3.000
 29R  O37   C35  C34   115.81  3.000
 29R  O36   C35  C34   117.92  3.000
 29R  HM7B  CM7  HM7A  109.47  3.000
 29R  HM7B  CM7  HM7   109.88  3.000
 29R  HM7A  CM7  HM7   109.53  3.000
 29R  HM7B  CM7  N7    109.70  3.000
 29R  HM7A  CM7  N7    108.55  3.000
 29R  HM7   CM7  N7    109.68  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
 29R  CONST_01  C8   N7   C5   C4     0.00   0.0  0
 29R  CONST_02  N7   C8   N9   C4     0.00   0.0  0
 29R  CONST_03  C8   N9   C4   C5     0.00   0.0  0
 29R  CONST_04  N9   C8   N7   C5     0.00   0.0  0
 29R  CONST_05  N9   C4   C5   N7     0.00   0.0  0
 29R  CONST_06  C4   N3   C2   N1     0.00   0.0  0
 29R  CONST_07  C5   C6   N1   C2     0.00   0.0  0
 29R  CONST_08  C6   N1   C2   N3     0.00   0.0  0
 29R  CONST_09  C11  N9   C4   N3     0.00   0.0  0
 29R  CONST_10  CM7  N7   C5   C4   180.00   0.0  0
 29R  CONST_11  C11  N9   C4   C5   180.00   0.0  0
 29R  CONST_12  CM7  N7   C5   C6     0.00   0.0  0
 29R  CONST_13  C11  N9   C8   N7   180.00   0.0  0
 29R  CONST_14  CM7  N7   C8   N9   180.00   0.0  0
 29R  CONST_15  O6   C6   N1   C2   180.00   0.0  0
 29R  CONST_16  C6   N1   C2   N2   180.00   0.0  0
 29R  CONST_17  C4   N3   C2   N2   180.00   0.0  0
 29R  CONST_18  H8   C8   N9   C4   180.00   0.0  0
 29R  CONST_19  HN1  N1   C2   N3   180.00   0.0  0
 29R  CONST_20  C31  N2   C2   N1   180.00   0.0  0
 29R  CONST_21  C31  N2   C2   N3     0.00   0.0  0
 29R  CONST_22  HN2  N2   C2   N1     0.00   0.0  0
 29R  Var_01    C12  C11  N9   C4    71.93  30.0  2
 29R  Var_02    HM7  CM7  N7   C5    60.97  30.0  2
 29R  Var_03    C32  C31  N2   C2   172.93  30.0  3
 29R  Var_04    C13  C12  C11  N9   176.61  30.0  3
 29R  Var_05    C33  C32  C31  N2   174.77  30.0  3
 29R  Var_06    C14  C13  C12  C11  178.24  30.0  3
 29R  Var_07    C15  C14  C13  C12  178.97  30.0  3
 29R  Var_08    O16  C15  C14  C13    6.20  30.0  3
 29R  Var_09    C34  C33  C32  C31  179.35  30.0  3
 29R  Var_10    C35  C34  C33  C32  179.24  30.0  3
 29R  Var_11    O36  C35  C34  C33    3.02  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
 29R  plan-1  N1   0.020
 29R  plan-1  C2   0.020
 29R  plan-1  N2   0.020
 29R  plan-1  N3   0.020
 29R  plan-1  C4   0.020
 29R  plan-1  C5   0.020
 29R  plan-1  C6   0.020
 29R  plan-1  O6   0.020
 29R  plan-1  N7   0.020
 29R  plan-1  C8   0.020
 29R  plan-1  N9   0.020
 29R  plan-1  C11  0.020
 29R  plan-1  C31  0.020
 29R  plan-1  CM7  0.020
 29R  plan-1  HN1  0.020
 29R  plan-1  HN2  0.020
 29R  plan-1  H8   0.020
 29R  plan-2  C14  0.020
 29R  plan-2  C15  0.020
 29R  plan-2  O16  0.020
 29R  plan-2  O17  0.020
 29R  plan-3  C34  0.020
 29R  plan-3  C35  0.020
 29R  plan-3  O36  0.020
 29R  plan-3  O37  0.020

