# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 18:31:55 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  50  26  .  2021-08-04  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.681   1.6140   3.7692  -0.0179
 29R  C2    C  CR6   0   0.756   0.6474   2.9041   0.4235
 29R  N2    N  NH1   0  -0.669  -0.5813   3.3781   0.6058
 29R  N3    N  N     0  -0.609   0.8975   1.6375   0.6794
 29R  C4    C  CR56  0   0.424   2.1566   1.2897   0.4597
 29R  C5    C  CR56  0   0.213   3.1932   2.0825   0.0344
 29R  C6    C  CR6   0   0.451   2.9554   3.4616  -0.2515
 29R  O6    O  O     0  -0.527   3.7503   4.3011  -0.6241
 29R  N7    N  NR5   0  -0.466   4.3104   1.2797  -0.0528
 29R  C8    C  CR15  0   0.198   3.9581   0.0598   0.2955
 29R  N9    N  NR5   1  -0.285   2.6624   0.0267   0.6179
 29R  C11   C  CH2   0  -0.327   1.8553  -1.1352   0.9701
 29R  C12   C  CH2   0  -0.437   1.0970  -1.6696  -0.2369
 29R  C13   C  CH2   0  -0.396   0.0161  -2.6611   0.1751
 29R  C14   C  CH2   0  -0.581  -0.6567  -3.2616  -1.0487
 29R  C15   C  C     0   0.520  -1.8286  -4.1478  -0.7277
 29R  O16   O  O     0  -0.358  -2.2647  -4.3480   0.3781
 29R  O17   O  OH1   0  -0.613  -2.3958  -4.6271  -1.8301
 29R  C31   C  CH2   0  -0.263  -1.6664   2.5259   1.0573
 29R  C32   C  CH2   0  -0.484  -2.2060   1.5909  -0.0180
 29R  C33   C  CH2   0  -0.407  -3.1750   0.5734   0.5711
 29R  C34   C  CH2   0  -0.569  -3.6368  -0.4230  -0.4782
 29R  C35   C  C     0   0.579  -4.5169  -1.5140   0.0662
 29R  O36   O  O     0  -0.536  -4.9073  -1.5897   1.2043
 29R  O37   O  OH1   0  -0.571  -4.8499  -2.3929  -0.8743
 29R  CM7   C  CH3   0  -0.491   5.6391   1.6907  -0.4752
 29R  HN1   H  HNR6  0   0.419   1.3547   4.7324  -0.1978
 29R  HN2   H  HNH1  0   0.420  -0.7969   4.3193   0.3207
 29R  H8    H  HCR5  0   0.347   4.6221  -0.7888   0.3238
 29R  H11   H  HCH2  0   0.287   2.5162  -1.8888   1.3949
 29R  H11A  H  HCH2  0   0.308   1.1703  -0.8170   1.7552
 29R  H12   H  HCH2  0   0.219   0.6314  -0.8386  -0.7735
 29R  H12A  H  HCH2  0   0.243   1.8027  -2.1382  -0.9276
 29R  H13   H  HCH2  0   0.248   0.4471  -3.4559   0.7883
 29R  H13A  H  HCH2  0   0.211  -0.7199  -2.1485   0.8007
 29R  H14   H  HCH2  0   0.294  -0.9972  -2.4752  -1.7309
 29R  H14A  H  HCH2  0   0.249   0.0637  -3.8479  -1.6267
 29R  H31   H  HCH2  0   0.237  -1.3112   1.9436   1.9090
 29R  H31A  H  HCH2  0   0.259  -2.4535   3.1823   1.4259
 29R  H32   H  HCH2  0   0.270  -2.6924   2.1739  -0.8049
 29R  H32A  H  HCH2  0   0.246  -1.3709   1.0618  -0.4841
 29R  H33   H  HCH2  0   0.260  -2.6798   0.0399   1.3872
 29R  H33A  H  HCH2  0   0.190  -4.0370   1.0822   1.0096
 29R  H34   H  HCH2  0   0.286  -4.1788   0.0850  -1.2822
 29R  H34A  H  HCH2  0   0.286  -2.7734  -0.8882  -0.9654
 29R  HM7   H  HCH3  0   0.292   5.9895   2.4999   0.1580
 29R  HM7A  H  HCH3  0   0.286   6.3102   0.8436  -0.3829
 29R  HM7B  H  HCH3  0   0.302   5.6082   2.0196  -1.5097
 29R  H17   H  HOH1  0   0.472  -3.1670  -5.1657  -1.5996
 29R  H37   H  HOH1  0   0.496  -5.4253  -3.0760  -0.4999

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    1.370  0.020  1.370
 29R  N1   C6    single    1.396  0.020  1.396
 29R  C2   N2    single    1.329  0.020  1.329
 29R  C2   N3    double    1.316  0.020  1.316
 29R  N2   C31   single    1.452  0.020  1.452
 29R  N3   C4    single    1.325  0.020  1.325
 29R  C4   C5    aromatic  1.373  0.020  1.373
 29R  C4   N9    aromatic  1.370  0.020  1.370
 29R  C5   C6    single    1.428  0.020  1.428
 29R  C5   N7    aromatic  1.378  0.020  1.378
 29R  C6   O6    double    1.215  0.020  1.215
 29R  N7   C8    aromatic  1.317  0.020  1.317
 29R  N7   CM7   single    1.454  0.020  1.454
 29R  C8   N9    aromatic  1.336  0.020  1.336
 29R  N9   C11   single    1.458  0.020  1.458
 29R  C11  C12   single    1.522  0.020  1.522
 29R  C12  C13   single    1.524  0.020  1.524
 29R  C13  C14   single    1.520  0.020  1.520
 29R  C14  C15   single    1.504  0.020  1.504
 29R  C15  O16   double    1.205  0.020  1.205
 29R  C15  O17   single    1.329  0.020  1.329
 29R  C31  C32   single    1.524  0.020  1.524
 29R  C32  C33   single    1.524  0.020  1.524
 29R  C33  C34   single    1.519  0.020  1.519
 29R  C34  C35   single    1.504  0.020  1.504
 29R  C35  O36   double    1.206  0.020  1.206
 29R  C35  O37   single    1.330  0.020  1.330
 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
 29R  O17  H17   single    0.850  0.020  0.980
 29R  O37  H37   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
 29R  HN1   N1   C6    115.19  3.000
 29R  HN1   N1   C2    118.47  3.000
 29R  C6    N1   C2    126.35  3.000
 29R  N3    C2   N2    119.47  3.000
 29R  N3    C2   N1    122.42  3.000
 29R  N2    C2   N1    118.10  3.000
 29R  HN2   N2   C31   118.47  3.000
 29R  HN2   N2   C2    119.50  3.000
 29R  C31   N2   C2    121.61  3.000
 29R  C4    N3   C2    113.65  3.000
 29R  N9    C4   C5    106.83  3.000
 29R  N9    C4   N3    125.03  3.000
 29R  C5    C4   N3    128.14  3.000
 29R  N7    C5   C6    133.20  3.000
 29R  N7    C5   C4    107.18  3.000
 29R  C6    C5   C4    119.60  3.000
 29R  O6    C6   C5    128.30  3.000
 29R  O6    C6   N1    121.86  3.000
 29R  C5    C6   N1    109.83  3.000
 29R  CM7   N7   C8    125.69  3.000
 29R  CM7   N7   C5    126.48  3.000
 29R  C8    N7   C5    107.82  3.000
 29R  H8    C8   N9    124.88  3.000
 29R  H8    C8   N7    124.86  3.000
 29R  N9    C8   N7    110.27  3.000
 29R  C11   N9   C8    127.96  3.000
 29R  C11   N9   C4    123.95  3.000
 29R  C8    N9   C4    107.91  3.000
 29R  H11A  C11  H11   107.62  3.000
 29R  H11A  C11  C12   111.14  3.000
 29R  H11   C11  C12   111.64  3.000
 29R  H11A  C11  N9    106.82  3.000
 29R  H11   C11  N9    108.05  3.000
 29R  C12   C11  N9    111.35  3.000
 29R  H12A  C12  H12   106.90  3.000
 29R  H12A  C12  C13   110.49  3.000
 29R  H12   C12  C13   108.98  3.000
 29R  H12A  C12  C11   109.26  3.000
 29R  H12   C12  C11   109.54  3.000
 29R  C13   C12  C11   111.56  3.000
 29R  H13A  C13  H13   106.58  3.000
 29R  H13A  C13  C14   110.36  3.000
 29R  H13   C13  C14   109.83  3.000
 29R  H13A  C13  C12   109.09  3.000
 29R  H13   C13  C12   110.20  3.000
 29R  C14   C13  C12   110.70  3.000
 29R  H14A  C14  H14   105.09  3.000
 29R  H14A  C14  C15   108.07  3.000
 29R  H14   C14  C15   108.29  3.000
 29R  H14A  C14  C13   110.22  3.000
 29R  H14   C14  C13   110.82  3.000
 29R  C15   C14  C13   113.94  3.000
 29R  O17   C15  O16   123.13  3.000
 29R  O17   C15  C14   111.59  3.000
 29R  O16   C15  C14   125.14  3.000
 29R  H17   O17  C15   110.06  3.000
 29R  H31A  C31  H31   107.03  3.000
 29R  H31A  C31  C32   110.66  3.000
 29R  H31   C31  C32   109.79  3.000
 29R  H31A  C31  N2    106.96  3.000
 29R  H31   C31  N2    108.22  3.000
 29R  C32   C31  N2    113.91  3.000
 29R  H32A  C32  H32   106.93  3.000
 29R  H32A  C32  C33   109.12  3.000
 29R  H32   C32  C33   110.57  3.000
 29R  H32A  C32  C31   109.12  3.000
 29R  H32   C32  C31   109.77  3.000
 29R  C33   C32  C31   111.23  3.000
 29R  H33A  C33  H33   106.55  3.000
 29R  H33A  C33  C34   110.05  3.000
 29R  H33   C33  C34   109.47  3.000
 29R  H33A  C33  C32   110.24  3.000
 29R  H33   C33  C32   109.04  3.000
 29R  C34   C33  C32   111.37  3.000
 29R  H34A  C34  H34   105.11  3.000
 29R  H34A  C34  C35   108.32  3.000
 29R  H34   C34  C35   108.23  3.000
 29R  H34A  C34  C33   110.26  3.000
 29R  H34   C34  C33   110.71  3.000
 29R  C35   C34  C33   113.81  3.000
 29R  O37   C35  O36   123.03  3.000
 29R  O37   C35  C34   111.72  3.000
 29R  O36   C35  C34   125.23  3.000
 29R  H37   O37  C35   109.97  3.000
 29R  HM7B  CM7  HM7A  109.59  3.000
 29R  HM7B  CM7  HM7   109.82  3.000
 29R  HM7A  CM7  HM7   109.44  3.000
 29R  HM7B  CM7  N7    109.66  3.000
 29R  HM7A  CM7  N7    108.67  3.000
 29R  HM7   CM7  N7    109.65  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  CONST_23  H17  O17  C15  C14   180.00   0.0  0
 29R  CONST_24  H37  O37  C35  C34   180.00   0.0  0
 29R  Var_01    C12  C11  N9   C4     78.42  30.0  2
 29R  Var_02    HM7  CM7  N7   C5     57.27  30.0  2
 29R  Var_03    C32  C31  N2   C2    -75.06  30.0  3
 29R  Var_04    C13  C12  C11  N9   -166.70  30.0  3
 29R  Var_05    C33  C32  C31  N2    170.68  30.0  3
 29R  Var_06    C14  C13  C12  C11  -175.68  30.0  3
 29R  Var_07    C15  C14  C13  C12  -174.22  30.0  3
 29R  Var_08    O16  C15  C14  C13     3.00  30.0  3
 29R  Var_09    C34  C33  C32  C31  -175.86  30.0  3
 29R  Var_10    C35  C34  C33  C32   175.75  30.0  3
 29R  Var_11    O36  C35  C34  C33     4.05  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-2  H17  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
 29R  plan-3  H37  0.020

